Protein contact map

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A protein contact map represents the distance between every two residues of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues i and j, the ij element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise.

Such matrices provide a more reduced representation of a protein structure than its full 3D atomic coordinates. It has also been shown that under certain circumstances it is possible to reconstruct the 3D coordinates of a protein using its contact map.

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