title: The linked phi psi 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 phi and psi dihedral angles that describe the backbone conformation of a peptide or protein chain. For each residue in sequence, phi and psi 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 (omega approximately 0 degrees) between residues X and Y is indicated by marking dots psi X and phi Y with a diamond. This linked phi psi chain plot is more useful than an unlinked phi psi chain plot for visually recognizing helices, sheets and turns and for graphically comparing several protein structures. Overlaying the linked phi psi chain plots for 15 beta-hairpins classified as type-I' beta-turns revealed that three were significantly different from the rest. The dihedral angles (mean +/- standard deviation) of the loop residues (L1, L2) for a cluster of 12 beta-hairpins with an inverse-common, type-I' beta-turn (phi L1 = 52 +/- 7 degrees, psi L1 = 40 +/- 8 degrees, phi L2 = 80 +/- 9 degrees, psi L2 = -1 +/- 13 degrees) are similar to the standard dihedral angles for the type-1' turn (60, 30, 90 and 0 degrees, respectively).
authors.affiliation: Department of Chemistry, University of North Carolina at Chapel Hill, USA.
authors.forename: R D
authors.initials: RD
authors.lastname: McClain
authors.forename: B W
authors.initials: BW
authors.lastname: Erickson
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation
chemical_list: D010455:Peptides