The Protein Journal

, Volume 28, Issue 2, pp 74–86 | Cite as

A Reexamination of Correlations of Amino Acids with Particular Secondary Structures

  • Saša N. Malkov
  • Miodrag V. Živković
  • Miloš V. Beljanski
  • Srđan Đ. Stojanović
  • Snežana D. Zarić
Article

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.

Keywords

Protein Amino acid Protein secondary structure Statistical correlation 

Abbreviations

DSSP

Define secondary structure of proteins the standard method for assigning secondary structure to the amino acids of a protein with determined atomic-resolution coordinates of the protein

PDB

Protein data bank a repository for 3-D structural data of proteins and nucleic acids

PDBSELECT

PDB selection of a representative set of PDB chains

Notes

Acknowledgments

This work was supported under projects No 144030 and No 142037 by the Ministry of Science of Republic of Serbia.

Supplementary material

10930_2009_9166_MOESM1_ESM.pdf (1.1 mb)
For each amino acid a diagram contains eight graphs of correlations of the amino acid and each secondary structure type (PDF 1078 kb)
10930_2009_9166_MOESM2_ESM.pdf (922 kb)
For each secondary structure type a diagram contains 20 graphs of correlations of the type and each amino acid (PDF 922 kb)
10930_2009_9166_MOESM3_ESM.pdf (1.1 mb)
For each amino acid group and secondary structure type a diagram contains graphs presenting correlations of amino acid belonging to the group and the secondary structure type (PDF 1115 kb)

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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Saša N. Malkov
    • 1
  • Miodrag V. Živković
    • 1
  • Miloš V. Beljanski
    • 2
  • Srđan Đ. Stojanović
    • 3
  • Snežana D. Zarić
    • 4
  1. 1.Department of MathematicsUniversity of BelgradeBelgradeSerbia
  2. 2.Institute of General and Physical ChemistryBelgradeSerbia
  3. 3.IHTM—Department of ChemistryUniversity of BelgradeBelgradeSerbia
  4. 4.Department of ChemistryUniversity of BelgradeBelgradeSerbia

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