A Reexamination of Correlations of Amino Acids with Particular Secondary Structures
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2009
Authors
Malkov, Saga N.Živković, Miodrag V.
Beljanski, Milos V.
Stojanović, Srđan Đ.
Zarić, Snežana D.
Article (Published version)
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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.
Keywords:
Protein / Amino acid / Protein secondary structure / Statistical correlationSource:
Protein Journal, 2009, 28, 2, 74-86Publisher:
- Springer, New York
Funding / projects:
- Automatsko rezonovanje i napredne obrade velikih količina podataka i teksta (RS-MESTD-MPN2006-2010-144030)
- Proučavanje odnosa reaktivnosti, nekovalentnih interakcija i strukture molekula i modelovanje hemijskih sistema (RS-MESTD-MPN2006-2010-142037)
DOI: 10.1007/s10930-009-9166-3
ISSN: 1572-3887
PubMed: 19280326
WoS: 000266563000003
Scopus: 2-s2.0-63449106826
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Institution/Community
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Malkov, Saga N. AU - Živković, Miodrag V. AU - Beljanski, Milos V. AU - Stojanović, Srđan Đ. AU - Zarić, Snežana D. PY - 2009 UR - https://cherry.chem.bg.ac.rs/handle/123456789/991 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 Živković, Miodrag V. and Beljanski, Milos V. and Stojanović, Srđan Đ. 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., Živković, M. V., Beljanski, M. V., Stojanović, S. Đ.,& 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, Živković MV, Beljanski MV, Stojanović SĐ, 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., Živković, Miodrag V., Beljanski, Milos V., Stojanović, Srđan Đ., 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 . .