Characteristics of protein residue-residue contacts and their application in contact prediction.

ABSTRACT: Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categorized by CATH and SCOP databases. The proteins represented alpha, beta, and alpha+beta classes. Contact maps of protein structures were obtained for a selected set of physical distances in the main backbone and separations in protein sequences. For each set a dependency between contact degree and distance parameters was quantified. We indicated residues forming contact sites most frequently and unique amino acid pairs which created contact sites most often within each structu

SUBMITTER: Wozniak PP 

PROVIDER: S-EPMC4221654 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature