Figure 6

Relative entropy analysis of canonical positions in 2,751 PDZ domains. (a) Positions in the graph are shown in the order found in Pfam and with the same numbering. Only positions with greater than 50% occupancy were calculated. The eight variable binding positions are marked with arrows, and the corresponding residue number in PSD95-3 is listed. (b) The structure of PSD95-3 with its cognate ligand peptide, KQTSV [44]. Note that atoms are missing from the ligand lysine sidechain due to lack of electron density in the X-ray data. The structurally-determined binding residues (see text) are colored, and the eight predicted specificity-determining positions are labeled with residue numbers as in (a). Rendered with PyMOL from PDB entry 1BE9.