The linked φψ chain plot for visual comparison of the backbone conformation of peptides and proteins

Abstract

A new graphic method is described for presenting in two dimensions the φ and ψ dihedral angles that describe the backbone conformation of a peptide or protein chain. For each residue in sequence, φ and ψ are plotted as dots on the y‐axis above the next two points on the x‐axis representing the residue number. Each dot is linked to the next dot by a slanting line segment (link) and each cis‐peptide bond (ω∼0°) between residues X and Y is indicated by marking dots ψx and φy with a diamond. This linked φ and ψ chain plot is more useful than an unlinked φ and ψ chain plot for visually recognizing helices, sheets and turns and for graphically comparing several protein structures. Overlaying the linked φ and ψ chain plots for 15 β‐hairpins classified as type‐I' β‐turns revealed that three were significantly different from the rest. The dihedral angles (mean f standard deviation) of the loop residues (L1, L2) for a cluster of 12 β‐hairpins with an inverse‐common, type‐I′β‐turn (φL1= 52±7°, ψL1=40±8°, φL2=80±9°, ψL2= ‐1±13°) are similar to the standard dihedral angles for the type‐1′ turn (60, 30, 90 and 0°, respectively).