TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Božidarka
AU  - Zarić, Snežana
PY  - 2009
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6531
AB  - This study aims to characterize the interface hot spot
residues of subunits in Sm proteins. We performed an analysis of the X ray structure of 15 Sm
motif containing proteins from the Protein Data Bank (PDB) and summarize physicochemical
properties in an effort to understand the origin of their stabilizing contributions to protein–
protein associations.Our results show that low relCompASA is critical for a residue to be a hot spot. Though
many of the hot spot residues have similar relCompASA values with nonhot spot residues,
they have different mean values (hot spots: 5.1%, non-hot spots: 29.1%). The P-value for
relCompASA is less than 0.05, which indicate that hot spots located near the center of the
interface are a general property of the interfaces, and largely protected from bulk solvent
(corresponding to low relCompASA). RelDASA indicates the change in the solvent
accessibility of a residue, and correlate significantly with relCompASA. Additionally,
knowledge-based pair potentials of residues is statistically significant to discriminate hot
spots and non-hot spots (P-value = 5.7×10−6). These results indicate that hot spots are mostly
buried, tightly packed and form a network of favorable interactions with other residues.
Structurally conserved residues and hot spots correlate significantly, and demonstrate
that hot spots play an important role in the stability of oligomers.
PB  - Belgrade, Serbia : Faculty of Chemistry, University of Belgrade
PB  - Germany : Alexander von Humboldt Foundation
C3  - Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia
T1  - Identification of Hot spots in Sm protein interfaces
SP  - 75
EP  - 75
UR  - https://hdl.handle.net/21.15107/rcub_cer_6531
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Božidarka and Zarić, Snežana",
year = "2009",
abstract = "This study aims to characterize the interface hot spot
residues of subunits in Sm proteins. We performed an analysis of the X ray structure of 15 Sm
motif containing proteins from the Protein Data Bank (PDB) and summarize physicochemical
properties in an effort to understand the origin of their stabilizing contributions to protein–
protein associations.Our results show that low relCompASA is critical for a residue to be a hot spot. Though
many of the hot spot residues have similar relCompASA values with nonhot spot residues,
they have different mean values (hot spots: 5.1%, non-hot spots: 29.1%). The P-value for
relCompASA is less than 0.05, which indicate that hot spots located near the center of the
interface are a general property of the interfaces, and largely protected from bulk solvent
(corresponding to low relCompASA). RelDASA indicates the change in the solvent
accessibility of a residue, and correlate significantly with relCompASA. Additionally,
knowledge-based pair potentials of residues is statistically significant to discriminate hot
spots and non-hot spots (P-value = 5.7×10−6). These results indicate that hot spots are mostly
buried, tightly packed and form a network of favorable interactions with other residues.
Structurally conserved residues and hot spots correlate significantly, and demonstrate
that hot spots play an important role in the stability of oligomers.",
publisher = "Belgrade, Serbia : Faculty of Chemistry, University of Belgrade, Germany : Alexander von Humboldt Foundation",
journal = "Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia",
title = "Identification of Hot spots in Sm protein interfaces",
pages = "75-75",
url = "https://hdl.handle.net/21.15107/rcub_cer_6531"
}

Stojanović, S., Zarić, B.,& Zarić, S.. (2009). Identification of Hot spots in Sm protein interfaces. in Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia
Belgrade, Serbia : Faculty of Chemistry, University of Belgrade., 75-75.
https://hdl.handle.net/21.15107/rcub_cer_6531

Stojanović S, Zarić B, Zarić S. Identification of Hot spots in Sm protein interfaces. in Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia. 2009;:75-75.
https://hdl.handle.net/21.15107/rcub_cer_6531 .

Stojanović, Srđan, Zarić, Božidarka, Zarić, Snežana, "Identification of Hot spots in Sm protein interfaces" in Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia (2009):75-75,
https://hdl.handle.net/21.15107/rcub_cer_6531 .

TY  - JOUR
AU  - Malkov, Saga N.
AU  - Zivkovic, Miodrag V.
AU  - Beljanski, Milos V.
AU  - Stojanović, Srđan
AU  - Zarić, Snežana D.
PY  - 2009
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/550
AB  - Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between -9 and 10. The results show that the substituents on C beta or C gamma atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on alpha-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements.
PB  - Springer, New York
T2  - Protein Journal
T1  - A Reexamination of Correlations of Amino Acids with Particular Secondary Structures
VL  - 28
IS  - 2
SP  - 74
EP  - 86
DO  - 10.1007/s10930-009-9166-3
ER  - 

@article{
author = "Malkov, Saga N. and Zivkovic, Miodrag V. and Beljanski, Milos V. and Stojanović, Srđan and Zarić, Snežana D.",
year = "2009",
abstract = "Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between -9 and 10. The results show that the substituents on C beta or C gamma atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on alpha-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements.",
publisher = "Springer, New York",
journal = "Protein Journal",
title = "A Reexamination of Correlations of Amino Acids with Particular Secondary Structures",
volume = "28",
number = "2",
pages = "74-86",
doi = "10.1007/s10930-009-9166-3"
}

Malkov, S. N., Zivkovic, M. V., Beljanski, M. V., Stojanović, S.,& Zarić, S. D.. (2009). A Reexamination of Correlations of Amino Acids with Particular Secondary Structures. in Protein Journal
Springer, New York., 28(2), 74-86.
https://doi.org/10.1007/s10930-009-9166-3

Malkov SN, Zivkovic MV, Beljanski MV, Stojanović S, Zarić SD. A Reexamination of Correlations of Amino Acids with Particular Secondary Structures. in Protein Journal. 2009;28(2):74-86.
doi:10.1007/s10930-009-9166-3 .

Malkov, Saga N., Zivkovic, Miodrag V., Beljanski, Milos V., Stojanović, Srđan, Zarić, Snežana D., "A Reexamination of Correlations of Amino Acids with Particular Secondary Structures" in Protein Journal, 28, no. 2 (2009):74-86,
https://doi.org/10.1007/s10930-009-9166-3 . .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6575
AB  - This study aims to systematically characterize all hydrogen bonds of porphyrins in porphyrin
containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB)
Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in
order to find out hydrogen bonds of porphyrins in proteins. The study has revealed that hydrogen
bonds are commonly found in porphyrin containing proteins and are widely present in different
regions of the protein chain, such as the backbone, or side chain, and in different secondary
structural regions such as helices, strands and turns. The results revealed that the significant
number of hydrogen bonds with acetyl and propionate groups of porphyrins exists. The most
frequently observed donors are charged amino acid residues from porphyrin surrounding. Sidechains
hydrogen bonds are more frequent than those with peptide donors; they involve water
molecules sometimes that are classified as bridged hydrogen bonds. The average conservation
score for the amino acids making hydrogen bonds with the porphyrin is statistically significantly
higher than for the amino acids that do not make hydrogen bonds. The significance of hydrogen
bonds as stabilizers of porphyrin rings in proteins has been illustrated on several examples.
AB  - Cilj ovih istraživanja je sistematska karakterizacija svih vodoničnih veza porfirina u proteinima 
koji sadrže porfirin. Za ispitivanje pojave vodoničnih veza smo koristili proteinsku bazu podataka 
(PDB Select, januar 2007), ne-redundantna lista (verzija 25%). Istraživanja pokazuju da su 
vodonične veze u proteinima koji sadrže porfirin prisutne u različitim regionima proteinskog lanca, 
kao što su polipeptidna kičma ili bočni ostaci, i u različitim sekundarnim strukturnim regionima 
(heliks, nabrana pločica i zavijutak). Rezultati pokazuju značajan broj vodoničnih veza sa acetil i 
propionat grupama porfirina. Najučestaliji donori su naelektrisane aminokiseline iz okruženja 
porfirinskog prstena. Vodonične veze aminokiselinskih ostataka su učestalije od vodoničnih veza 
peptidnih donora; one ponekad uključuju molekul vode pri čemu se klasifikuju kao premošćene 
vodonične veze. Konzervacioni skor aminokiselina koje grade vodonične veze sa porfirinima je 
statistički značajno veći u odnosu na aminokiseline koje ne grade vodonične veze. Značaj 
vodoničnih veza kao stabilizatora strukture porfirinskog prstena u proteinima je prikazana na 
nekoliko primera.
PB  - Belgrade : Serbian Chemical Society
C3  - Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia
T1  - Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin
T1  - Hydrogen bonds of porphyrins in porphyrin containing proteins
SP  - 88
EP  - 88
UR  - https://hdl.handle.net/21.15107/rcub_cer_6575
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2008",
abstract = "This study aims to systematically characterize all hydrogen bonds of porphyrins in porphyrin
containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB)
Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in
order to find out hydrogen bonds of porphyrins in proteins. The study has revealed that hydrogen
bonds are commonly found in porphyrin containing proteins and are widely present in different
regions of the protein chain, such as the backbone, or side chain, and in different secondary
structural regions such as helices, strands and turns. The results revealed that the significant
number of hydrogen bonds with acetyl and propionate groups of porphyrins exists. The most
frequently observed donors are charged amino acid residues from porphyrin surrounding. Sidechains
hydrogen bonds are more frequent than those with peptide donors; they involve water
molecules sometimes that are classified as bridged hydrogen bonds. The average conservation
score for the amino acids making hydrogen bonds with the porphyrin is statistically significantly
higher than for the amino acids that do not make hydrogen bonds. The significance of hydrogen
bonds as stabilizers of porphyrin rings in proteins has been illustrated on several examples., Cilj ovih istraživanja je sistematska karakterizacija svih vodoničnih veza porfirina u proteinima 
koji sadrže porfirin. Za ispitivanje pojave vodoničnih veza smo koristili proteinsku bazu podataka 
(PDB Select, januar 2007), ne-redundantna lista (verzija 25%). Istraživanja pokazuju da su 
vodonične veze u proteinima koji sadrže porfirin prisutne u različitim regionima proteinskog lanca, 
kao što su polipeptidna kičma ili bočni ostaci, i u različitim sekundarnim strukturnim regionima 
(heliks, nabrana pločica i zavijutak). Rezultati pokazuju značajan broj vodoničnih veza sa acetil i 
propionat grupama porfirina. Najučestaliji donori su naelektrisane aminokiseline iz okruženja 
porfirinskog prstena. Vodonične veze aminokiselinskih ostataka su učestalije od vodoničnih veza 
peptidnih donora; one ponekad uključuju molekul vode pri čemu se klasifikuju kao premošćene 
vodonične veze. Konzervacioni skor aminokiselina koje grade vodonične veze sa porfirinima je 
statistički značajno veći u odnosu na aminokiseline koje ne grade vodonične veze. Značaj 
vodoničnih veza kao stabilizatora strukture porfirinskog prstena u proteinima je prikazana na 
nekoliko primera.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia",
title = "Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin, Hydrogen bonds of porphyrins in porphyrin containing proteins",
pages = "88-88",
url = "https://hdl.handle.net/21.15107/rcub_cer_6575"
}

Stojanović, S.,& Zarić, S.. (2008). Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin. in Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia
Belgrade : Serbian Chemical Society., 88-88.
https://hdl.handle.net/21.15107/rcub_cer_6575

Stojanović S, Zarić S. Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin. in Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia. 2008;:88-88.
https://hdl.handle.net/21.15107/rcub_cer_6575 .

Stojanović, Srđan, Zarić, Snežana, "Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin" in Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia (2008):88-88,
https://hdl.handle.net/21.15107/rcub_cer_6575 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6569
AB  - This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain. Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side­ chains hydrophobic interactions are more frequent than those with backbone. The average conservation score for the amino acids making hydrophobic interactions with the porphyrin is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions with porphyrin.
PB  - Srpsko kristalografsko društvo
C3  - Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac
T1  - Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin
T1  - Hydrophobic interactions of porphyrins in porphyrin containing proteins
SP  - 44
EP  - 44
UR  - https://hdl.handle.net/21.15107/rcub_cer_6569
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2008",
abstract = "This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain. Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side­ chains hydrophobic interactions are more frequent than those with backbone. The average conservation score for the amino acids making hydrophobic interactions with the porphyrin is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions with porphyrin.",
publisher = "Srpsko kristalografsko društvo",
journal = "Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac",
title = "Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin, Hydrophobic interactions of porphyrins in porphyrin containing proteins",
pages = "44-44",
url = "https://hdl.handle.net/21.15107/rcub_cer_6569"
}

Stojanović, S.,& Zarić, S.. (2008). Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin. in Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac
Srpsko kristalografsko društvo., 44-44.
https://hdl.handle.net/21.15107/rcub_cer_6569

Stojanović S, Zarić S. Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin. in Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac. 2008;:44-44.
https://hdl.handle.net/21.15107/rcub_cer_6569 .

Stojanović, Srđan, Zarić, Snežana, "Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin" in Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac (2008):44-44,
https://hdl.handle.net/21.15107/rcub_cer_6569 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6529
AB  - This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic in­teractions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain.
Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic inte­ractions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score.
PB  - Society of Physical Chemists of Serbia
C3  - Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia
T1  - Hydrophobic interactions in the stability of porphyrin-containing proteins
VL  - II
SP  - 707
EP  - 709
UR  - https://hdl.handle.net/21.15107/rcub_cer_6529
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2008",
abstract = "This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic in­teractions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain.
Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic inte­ractions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score.",
publisher = "Society of Physical Chemists of Serbia",
journal = "Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia",
title = "Hydrophobic interactions in the stability of porphyrin-containing proteins",
volume = "II",
pages = "707-709",
url = "https://hdl.handle.net/21.15107/rcub_cer_6529"
}

Stojanović, S.,& Zarić, S.. (2008). Hydrophobic interactions in the stability of porphyrin-containing proteins. in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia
Society of Physical Chemists of Serbia., II, 707-709.
https://hdl.handle.net/21.15107/rcub_cer_6529

Stojanović S, Zarić S. Hydrophobic interactions in the stability of porphyrin-containing proteins. in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia. 2008;II:707-709.
https://hdl.handle.net/21.15107/rcub_cer_6529 .

Stojanović, Srđan, Zarić, Snežana, "Hydrophobic interactions in the stability of porphyrin-containing proteins" in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia, II (2008):707-709,
https://hdl.handle.net/21.15107/rcub_cer_6529 .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
AU  - Beljanski, Miloš
AU  - Zarić, Snežana
PY  - 2007
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6507
AB  - Searching structures of porphyrin-containing
proteins from the Protein Data Bank revealed that the
p system of every porphyrin ring is involved in XH/p
interactions, with most of the porphyrins having several
interactions. Both five-membered pyrrole rings and sixmembered
chelate rings are involved in XH/p interactions;
the number of interactions with five-membered rings is
larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as
hydrogen-atom donors; however, the number of CH/p
interactions is much larger than the number of NH/p
interactions. The amino acids involved in the interactions
show a high conservation score. Our results that every
porphyrin is involved in XH/p interactions and that amino
acids involved in these interactions are highly conserved 
demonstrate that XH/p interactions play an important role
in porphyrin–protein stability.
PB  - Springer
T2  - Journal of Biological Inorganic Chemistry
T1  - XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins
VL  - 12
SP  - 1063
EP  - 1071
DO  - 10.1007/s00775-007-0276-0
ER  - 

@article{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran and Beljanski, Miloš and Zarić, Snežana",
year = "2007",
abstract = "Searching structures of porphyrin-containing
proteins from the Protein Data Bank revealed that the
p system of every porphyrin ring is involved in XH/p
interactions, with most of the porphyrins having several
interactions. Both five-membered pyrrole rings and sixmembered
chelate rings are involved in XH/p interactions;
the number of interactions with five-membered rings is
larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as
hydrogen-atom donors; however, the number of CH/p
interactions is much larger than the number of NH/p
interactions. The amino acids involved in the interactions
show a high conservation score. Our results that every
porphyrin is involved in XH/p interactions and that amino
acids involved in these interactions are highly conserved 
demonstrate that XH/p interactions play an important role
in porphyrin–protein stability.",
publisher = "Springer",
journal = "Journal of Biological Inorganic Chemistry",
title = "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins",
volume = "12",
pages = "1063-1071",
doi = "10.1007/s00775-007-0276-0"
}

Stojanović, S., Medaković, V., Predović, G., Beljanski, M.,& Zarić, S.. (2007). XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry
Springer., 12, 1063-1071.
https://doi.org/10.1007/s00775-007-0276-0

Stojanović S, Medaković V, Predović G, Beljanski M, Zarić S. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry. 2007;12:1063-1071.
doi:10.1007/s00775-007-0276-0 .

Stojanović, Srđan, Medaković, Vesna, Predović, Goran, Beljanski, Miloš, Zarić, Snežana, "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins" in Journal of Biological Inorganic Chemistry, 12 (2007):1063-1071,
https://doi.org/10.1007/s00775-007-0276-0 . .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2007
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6530
AB  - Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrogen bonds and XH/pi interactions of porphyrins in proteins.Side-chains hydrogen bonds are more frequent than those with peptide donors; they involve water molecules sometimes that are classified as bridged hydrogen bonds. Besides, pi-system of every porphyrin ring is involved in XH/pi interactions, most of the porphyrins are making several interactions. The average conservation score for the amino acids making noncovalent interactions with the porphyrin is statistically significantly higher than for the amino acids that do not make interactions.
PB  - Belgrade, Serbia : Faculty of Chemistry, University of Belgrade
PB  - Germany : Alexander von Humboldt Foundation
C3  - Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia
T1  - Hydrogen bonds and XH/pi interactions of porphyrins in proteins
SP  - 39
EP  - 39
UR  - https://hdl.handle.net/21.15107/rcub_cer_6530
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2007",
abstract = "Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrogen bonds and XH/pi interactions of porphyrins in proteins.Side-chains hydrogen bonds are more frequent than those with peptide donors; they involve water molecules sometimes that are classified as bridged hydrogen bonds. Besides, pi-system of every porphyrin ring is involved in XH/pi interactions, most of the porphyrins are making several interactions. The average conservation score for the amino acids making noncovalent interactions with the porphyrin is statistically significantly higher than for the amino acids that do not make interactions.",
publisher = "Belgrade, Serbia : Faculty of Chemistry, University of Belgrade, Germany : Alexander von Humboldt Foundation",
journal = "Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia",
title = "Hydrogen bonds and XH/pi interactions of porphyrins in proteins",
pages = "39-39",
url = "https://hdl.handle.net/21.15107/rcub_cer_6530"
}

Stojanović, S.,& Zarić, S.. (2007). Hydrogen bonds and XH/pi interactions of porphyrins in proteins. in Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia
Belgrade, Serbia : Faculty of Chemistry, University of Belgrade., 39-39.
https://hdl.handle.net/21.15107/rcub_cer_6530

Stojanović S, Zarić S. Hydrogen bonds and XH/pi interactions of porphyrins in proteins. in Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia. 2007;:39-39.
https://hdl.handle.net/21.15107/rcub_cer_6530 .

Stojanović, Srđan, Zarić, Snežana, "Hydrogen bonds and XH/pi interactions of porphyrins in proteins" in Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia (2007):39-39,
https://hdl.handle.net/21.15107/rcub_cer_6530 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
PY  - 2006
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6528
AB  - The significant number of XH/TI interactions with Ti-system of five-membered pyrrole rings and six-membered chelate rings from porphyrin was found in crystal structures of proteins. There is a larger number of the interactions with five-membered than with six-membered rings. Hydrogen-atom donors can be C-H and N-H groups. The num­ ber of CH/TI interactions is much larger than number of NH/TI interactions. The list of amino acids involved in CH/TI interactions contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Besides, amino acids involving in these interactions shows significant conservation score.
PB  - Society of Physical Chemists of Serbia
C3  - Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia
T1  - Non-conventional interactions in proteins containing porphyrine
VL  - I
SP  - 368
EP  - 370
UR  - https://hdl.handle.net/21.15107/rcub_cer_6528
ER  - 

@conference{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran",
year = "2006",
abstract = "The significant number of XH/TI interactions with Ti-system of five-membered pyrrole rings and six-membered chelate rings from porphyrin was found in crystal structures of proteins. There is a larger number of the interactions with five-membered than with six-membered rings. Hydrogen-atom donors can be C-H and N-H groups. The num­ ber of CH/TI interactions is much larger than number of NH/TI interactions. The list of amino acids involved in CH/TI interactions contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Besides, amino acids involving in these interactions shows significant conservation score.",
publisher = "Society of Physical Chemists of Serbia",
journal = "Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia",
title = "Non-conventional interactions in proteins containing porphyrine",
volume = "I",
pages = "368-370",
url = "https://hdl.handle.net/21.15107/rcub_cer_6528"
}

Stojanović, S., Medaković, V.,& Predović, G.. (2006). Non-conventional interactions in proteins containing porphyrine. in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia
Society of Physical Chemists of Serbia., I, 368-370.
https://hdl.handle.net/21.15107/rcub_cer_6528

Stojanović S, Medaković V, Predović G. Non-conventional interactions in proteins containing porphyrine. in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia. 2006;I:368-370.
https://hdl.handle.net/21.15107/rcub_cer_6528 .

Stojanović, Srđan, Medaković, Vesna, Predović, Goran, "Non-conventional interactions in proteins containing porphyrine" in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia, I (2006):368-370,
https://hdl.handle.net/21.15107/rcub_cer_6528 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
AU  - Zarić, Snežana
PY  - 2006
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6577
AB  - For this study, the Protein Data Bank (PDB) Select October 2004 list of non-redundant protein chains (25% threshold version, 2485 protein chains and 388067 amino acid residues) was used to examine systematically the occurrence and the role of X-H⋅⋅⋅π-interactions in heme-protein structures. The following criteria were employed to assemble the set: (1) no theoretical model structures and no NMR structures were accepted, (2) only crystal structures with a resolution of 3.0 Å or better and a crystallographic R-factor of 25.0% or lower were accepted, (3) crystal structures containing porphyrin were accepted.
The significant number of interactions with π system of five-membered pyrrole rings and with π system of six-membered chelate rings were founded to satisfy selection criteria. H-atom donors can be Cα-H, Cali-H, Caro-H and N-H. The number of C-H⋅⋅⋅π-interactions is much larger than the number of N-H⋅⋅⋅π-interactions. The list of Cali-H with five-membered rings contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Analysis of average distances for Cali and Caro of C-H⋅⋅⋅π interactions indicate that Cali makes interactions with shorter distances. Another interesting observation is the possibility of C-H(porphyrin) donor groups to exhibit an interaction between five-membered rings from another porphyrine group in proteins and its own side-chain groups (involving hydrogen atoms from methyl and propionyl groups). Amino acids involving in X-H⋅⋅⋅π-interactions shows significant conservation score. The number of these interactions as well as conservation of amino acids indicates importance of X-H⋅⋅⋅π-interactions in heme-protein stability.
AB  - Za ispitivanje pojave i uloge X-H⋅⋅⋅π-interakcija u hem-proteinskim strukturama korišćena 
je proteinska baza podataka (PDB Select) iz oktobra 2004. godine, ne-redundantna lista
(verzija 25%) koja sadrži 2485 proteinskih lanaca i 388067 aminokiselinskih ostataka.
Primenjeni su sledeći kriterijumi za sastavljanje skupa: (1) nisu prihvaćeni teorijski modeli 
i NMR strukture, (2) samo su prihvaćene kristalne strukture sa rezolucijom 3.0 Å ili boljom
i kristalografskim R-faktorom 25.0% ili nižim, (3) obuhvaćene su kristalne strukture koje 
sadrže porfirinski prsten.
PB  - Belgrade : Serbian Crystallographic Society
C3  - XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia
T1  - Nekonvencionalne interakcije u proteinima koji sadrže hem
T1  - Non-conventional interactions in proteins with the heme group
SP  - 38
EP  - 39
UR  - https://hdl.handle.net/21.15107/rcub_cer_6577
ER  - 

@conference{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran and Zarić, Snežana",
year = "2006",
abstract = "For this study, the Protein Data Bank (PDB) Select October 2004 list of non-redundant protein chains (25% threshold version, 2485 protein chains and 388067 amino acid residues) was used to examine systematically the occurrence and the role of X-H⋅⋅⋅π-interactions in heme-protein structures. The following criteria were employed to assemble the set: (1) no theoretical model structures and no NMR structures were accepted, (2) only crystal structures with a resolution of 3.0 Å or better and a crystallographic R-factor of 25.0% or lower were accepted, (3) crystal structures containing porphyrin were accepted.
The significant number of interactions with π system of five-membered pyrrole rings and with π system of six-membered chelate rings were founded to satisfy selection criteria. H-atom donors can be Cα-H, Cali-H, Caro-H and N-H. The number of C-H⋅⋅⋅π-interactions is much larger than the number of N-H⋅⋅⋅π-interactions. The list of Cali-H with five-membered rings contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Analysis of average distances for Cali and Caro of C-H⋅⋅⋅π interactions indicate that Cali makes interactions with shorter distances. Another interesting observation is the possibility of C-H(porphyrin) donor groups to exhibit an interaction between five-membered rings from another porphyrine group in proteins and its own side-chain groups (involving hydrogen atoms from methyl and propionyl groups). Amino acids involving in X-H⋅⋅⋅π-interactions shows significant conservation score. The number of these interactions as well as conservation of amino acids indicates importance of X-H⋅⋅⋅π-interactions in heme-protein stability., Za ispitivanje pojave i uloge X-H⋅⋅⋅π-interakcija u hem-proteinskim strukturama korišćena 
je proteinska baza podataka (PDB Select) iz oktobra 2004. godine, ne-redundantna lista
(verzija 25%) koja sadrži 2485 proteinskih lanaca i 388067 aminokiselinskih ostataka.
Primenjeni su sledeći kriterijumi za sastavljanje skupa: (1) nisu prihvaćeni teorijski modeli 
i NMR strukture, (2) samo su prihvaćene kristalne strukture sa rezolucijom 3.0 Å ili boljom
i kristalografskim R-faktorom 25.0% ili nižim, (3) obuhvaćene su kristalne strukture koje 
sadrže porfirinski prsten.",
publisher = "Belgrade : Serbian Crystallographic Society",
journal = "XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia",
title = "Nekonvencionalne interakcije u proteinima koji sadrže hem, Non-conventional interactions in proteins with the heme group",
pages = "38-39",
url = "https://hdl.handle.net/21.15107/rcub_cer_6577"
}

Stojanović, S., Medaković, V., Predović, G.,& Zarić, S.. (2006). Nekonvencionalne interakcije u proteinima koji sadrže hem. in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia
Belgrade : Serbian Crystallographic Society., 38-39.
https://hdl.handle.net/21.15107/rcub_cer_6577

Stojanović S, Medaković V, Predović G, Zarić S. Nekonvencionalne interakcije u proteinima koji sadrže hem. in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia. 2006;:38-39.
https://hdl.handle.net/21.15107/rcub_cer_6577 .

Stojanović, Srđan, Medaković, Vesna, Predović, Goran, Zarić, Snežana, "Nekonvencionalne interakcije u proteinima koji sadrže hem" in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia (2006):38-39,
https://hdl.handle.net/21.15107/rcub_cer_6577 .