A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence

doi:10.1371/journal.pcbi.1000488

A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence

Figure 13

PDZ domains.

A: Matrix of relative coevolution scores for the PDZ domain family. The 4 identified networks have been manually selected on the matrix. Signals for detection are noisy and errors in clustering positions are likely; due to red scores, the last position of the matrix, for instance, seem misplaced and better clustered with positions appeared before in the matrix. BCD: Coevolved residues networks on the third PDZ domain of PSD-95 1BE9 (chain A). The binding site is illustrated on the front (left) and on the side (right) bound to a peptide indicated in green. Residues in the networks are indicated using the Van der Walls representation. B: network associated to highly conserved structural positions (red, first in A); C: network associated to peptide specificity (blue, second in A.); D: third (orange, third in A) and fourth (violet, fourth in A) networks surrounding the network associated to ligand specificity. E: Global overview of the four networks.

doi: https://doi.org/10.1371/journal.pcbi.1000488.g013