Figure 3.

Hydrogen bond donor to oxygen distance and angle parameters for instances of BPh interactions extracted from 3D structures in the reduced-redundancy list having resolution 2.5 Å or better. Upper left, intra-nucleotide (self) interactions involving C6 and C8 H-bond donors. Upper right, interactions with base carbon atom H-bond donors, excluding self-interactions between a base and its own phosphate group. Lower-left, interactions with imino Nitrogen, lower-right, interactions with exocyclic amino Nitrogen. Red dots correspond to H-bonds to anionic O1P or O2P acceptor atoms, green dots, H-bonds to O5′ acceptor atoms and dark blue dots, H-bonds to O3′ acceptor atoms. Black vertical and horizontal lines indicate implemented thresholds for distances and bond angles for classification as BPh (upper-left lines) and near-BPh interactions (lower right lines). Self-interactions with C6/C8 are too numerous to display all instances, so 4000 were chosen at random for display.