Figure 8. Patterns of electrostatic similarity in the S1 specificity pockets of trypsins and chymotrypsins, relative to P1 binding preferences.

The color coding, which is independent of tree topology, indicates the types of P1 residue preferred by each protein. Trypsins (blue) prefer basic amino acids and chymotrypsins (red) prefer large hydrophobic amino acids. The topology of the tree reflects patterns of similarity measured with the Jaccard distance. Proteins on adjacent branches have greater similarity than proteins on different subtrees. The topological separation of the chymotrypsins from the trypsins indicates that similarities and differences in the electrostatic character of S1 subsites, which create the differences in their binding preferences, were detected and correctly classified by VASP-E, using the Jaccard distance.