Protein contact map

A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues

i

{\displaystyle i}

and

j

{\displaystyle j}

, the

i

j

{\displaystyle ij}

element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been proposed: The distance between the Cα-Cα atom with threshold 6-12 Å; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine); and distance between the side-chain centers of mass.

Overview

Contact maps provide a more reduced representation of a protein structure than its full 3D atomic coordinates. The advantage is that contact maps are invariant to rotations and translations. They are more easily predicted by machine learning methods. It has also been shown that under certain circumstances (e.g. low content of erroneously predicted contacts) it is possible to reconstruct the 3D coordinates of a protein using its contact map.

Contact maps are also used for protein superimposition and to describe similarity between protein structures. They are either predicted from protein sequence or calculated from a given structure.