Figure 1

Examples of the four categories of normalized distributions of protein-ligand interatomic distances. The four represent strong interactions, weak interactions, non-specific interactions, and rare interactions (see text). Each is represented by a specific example, namely: a) a hydrogen bonding contact in the interaction of NRD with OLC; b) a van der Waals contact in the interaction of C2N with CRN; c) a non-specific contact in the interaction of C3N with C2P; and d) a rarely seen contact in the interaction of NLC with S3N. The red arrows mark the upper and lower distance cutoffs used to connect atoms in constructing the protein-ligand interaction networks: those separated by a distance within the upper and the lower threshold would be connected, while no connection was made for the non-specific interactions in the third category.