The nature of the turn in omega loops of proteins

Abstract

An analysis of Ω loops in a nonredundant set of protein stuctures from the Protein Data Bank has been carried out to determine the nature of the “turn elements” present. Because Ω loops essentially reverse their direction in three‐dimensional space, this analysis was made with respect to four turn elements identified as (1) Gly; (2) Pro; (3) a residue with α‐helical ϕ,ψ angles, termed a helical residue; and (4) a cis peptide. A set of 1079 Ω loops from a set of 680 proteins were used for the analysis. Apart from other criteria that define Ω loops, the selection of an Ω loop from a cluster of loops is based on an exposure index. In this study, analyses have been made with two sets of data: (1) Ω loops arising from a minimum exposure index indicative of a less exposed loop (xmin set) and (2) Ω loops with a maximum exposure index indicative of a relatively exposed loop (xmax set). Overall residue preferences and positional preferences have been examined. Positions of the turn elements for Ω loops of varying length have also been studied. Specific positional preferences are observed for particular turn elements with regard to the length of Ω loops. Analysis in terms of the turn elements can provide guidelines for modeling of loops in proteins. Apart from Pro, which has the natural tendency to form cis peptide bonds, a higher occurrence of non‐Pro cis peptide bonds is observed. Torsion angles in Ω loops also indicate the occurrence of a large number of residues with helical ϕ,ψ angles, necessary for the turn in the loop structures.