Figure 2.

A protein-ligand interaction network. This example shows the protein-ligand interaction network transformed from the 3D coordinates of the complex of carboxypeptidase A and l-benzylsuccinate (PDB entry 1cbx). Each ligand atom in this network is represented by a combination of a red circle, its 3-code atom type, and its atom name from the PDB file in the parenthesis. Likewise, each protein atom is represented by a combination of a blue circle, its 3-code atom type and, in parentheses, its residue name, residue number, and atom name from the PDB file. Each black line connects a ligand atom and a protein atom for which connectivity (interaction) has been established based on distance thresholds.