A Reexamination of Correlations of Amino Acids with Particular Secondary Structures Sas ˇa N. Malkov Æ Miodrag V. Z ˇ ivkovic ´ Æ Milos ˇ V. Beljanski Æ Srd ¯an Ð. Stojanovic ´ Æ Snez ˇana D. Zaric ´ Published online: 12 March 2009 Ó Springer Science+Business Media, LLC 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 Cb or Cc 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 a-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 1 Introduction Understanding relation of primary and secondary structure of proteins is very important. There are many methods that consider protein folding and many of them use some information about the protein secondary structure [6, 8, 17–19, 30, 34, 35, 37, 38, 47, 56, 60, 61, 66]. Conformational preferences of amino acids, usually called propensities, are used to predict secondary and tertiary structures of pro- teins. Propensities of amino acids were introduced long time ago and it is known that amino acids have various propensities for the adoption of helical, strand, and random Electronic supplementary material The online version of this article (doi:10.1007/s10930-009-9166-3) contains supplementary material, which is available to authorized users. S. N. Malkov  M. V. Z ˇ ivkovic ´ Department of Mathematics, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia S. N. Malkov e-mail: smalkov@matf.bg.ac.rs M. V. Z ˇ ivkovic ´ e-mail: ezivkovm@matf.bg.ac.rs M. V. Beljanski Institute of General and Physical Chemistry, Studentski Trg 16, 11000 Belgrade, Serbia e-mail: mbel@matf.bg.ac.rs S. Ð. Stojanovic ´ IHTM—Department of Chemistry, University of Belgrade, Njegos ˇeva 12, 11001 Belgrade, Serbia e-mail: srdjanst@chem.bg.ac.rs S. D. Zaric ´(&) Department of Chemistry, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia e-mail: szaric@chem.bg.ac.rs 123 Protein J (2009) 28:74–86 DOI 10.1007/s10930-009-9166-3