Figure 1. Parameterization of residues.
For arginine (A) and histidine (B), spherical coordinates for an interacting oxygen are defined by three geometric parameters (ρ, ψ, θ). ψ measures the angle around the guanidinium (A) or imidazole (B) plane, while θ measures the degree out of that plane (with 0 degrees being in plane). ρ is the distance from the central point, Cε for Arg and the midpoint between Nδ and Nε for His, to the oxygens. For lysine (C), the relevant parameters are (1) the angle of the oxygen with the ζ nitrogen and ε carbon and (2) the dihedral angle of the oxygen relative to the final three heavy atoms of lysine. For the acidic residues asparatate and glutamate (D), the lone pair used to form salt bridges is categorized as syn or anti.