A reexamination of correlations of amino acids with particular secondary structures.
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 Cbeta or Cgamma 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.
Malkov
Sasa N
SN
Department of Mathematics, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia. smalkov@matf.bg.ac.rs
Zivković
Miodrag V
MV
Beljanski
Milos V
MV
Stojanović
Srdan D
SD
Zarić
Snezana D
SD
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D008956:Models, Chemical; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins