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  - 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 .