Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction
Figure 8
Optimal arrangement of Arg and Asp side chains simulated from the derived 4-D histograms.
In the preferred orientation the carboxyl group of Asp is closer to NH2 of Arg than to NH1. To generate the depicted orientation, two residues in arbitrary conformation were placed randomly relative to each other, multiple times. The top scoring orientation, according to Equation 2, was identified and drawn in the figure. This simulation was repeated several times resulting in similar asymmetric placement of Arg and Asp side chains.