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Fig. 2 | BMC Bioinformatics

Fig. 2

From: CoeViz: a web-based tool for coevolution analysis of protein residues

Fig. 2

Amino acid coevolution profile reveals residues constituting the active site of the Cys-Gly metallodipeptidase (SwissProt: DUG1_YEAST). a A fragment of the heat map displaying amino acid coevolution computed using χ2 weighted by sequence dissimilarity derived from sequence alignments to the protein sequence defined in PDB ID 4G1P against NR database with 90 % identity reduction. b A fragment of the cluster tree derived from the chi-square data converted to a distance matrix. c The zoomed in cluster of amino acids that contains known Zn binding residues (H102, D137, E172, H450) and a catalytic site (E171). d From the heat map, one can retrieve a circular diagram representing the closest relationships to a given residue; here is to the one of catalytic residues (E171) after applying a ≥0.3 cutoff to χ2-based cumulative probabilities. e From the circular diagram, one can map the clustered residues to the submitted protein 3D structure; here is to DUG1 (PDB:4G1P). Residues highlighted red (H102, D137, E172, D200, H450) are amino acids binding Zn (grey spheres); magenta – catalytic residues (D104, E171); blue is a residue involved in substrate recognition (R348). The substrate (Cys-Gly) is rendered as sticks colored by an atom type

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