A Reexamination of Correlations of Amino Acids with Particular Secondary Structures |
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Authors: | Sa?a N Malkov Miodrag V ?ivkovi? Milo? V Beljanski Sr?an ? Stojanovi? Sne?ana D Zari? |
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Institution: | (1) Department of Mathematics, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia;(2) Institute of General and Physical Chemistry, Studentski Trg 16, 11000 Belgrade, Serbia;(3) IHTM—Department of Chemistry, University of Belgrade, Njegoševa 12, 11001 Belgrade, Serbia;(4) Department of Chemistry, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia |
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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 Cβ or Cγ 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 α-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.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Protein Amino acid Protein secondary structure Statistical correlation |
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