CoeViz 2: Protein Graphs Derived from Amino Acid Covariance.

Proteins by and large carry out their molecular functions in a folded state when residues, distant in sequence, assemble together in 3D space to bind a ligand, catalyze a reaction, form a channel, or exert another concerted macromolecular interaction. It has been long recognized that covariance of amino acids between distant positions within a protein sequence allows for the inference of long range contacts to facilitate 3D structure modeling. In this work, we investigated whether covariance analysis may reveal residues involved in the same molecular function.