Figure 4.

Network diagrams illustrating how ligand binding fits the small world network paradigm. Gray nodes denote protein binding site groups. The black node represents the ligand, and an edge represents a noncovalent favorable or covalent interaction. (a) Schematic representation of an unliganded binding site and (b) an occupied binding site. The network diagrams show how the addition of just one new node and a few extra edges leads to shorter path lengths between many pairs of nodes in the network. The presence of individual nodes with connections that lead to short paths between many pairs of nodes is a key feature of small world networks.