Base-Phosphate Catalog

Locations of known base-phosphate interactions for each base

Nomenclature for base-phosphate (BPh) interactions and superpositions of idealized BPh interactions observed in RNA 3D crystal structures for each base. Hydrogen bonds are indicated with dashed lines. BPh categories are numbered 0 to 9, starting at the H6 (pyrimidine) or H8 (purine) base positions. BPh interactions that involve equivalent functional groups on different bases are grouped together, i.e. 0BPh (A,C,G,U) 5BPh (G,U), 6BPh (A,C), 7BPh (A,C) and 9BPh (C,U).

No. Interacting Edge Symbol Link to Optimal Geometries
1 Sugar Edge
2 Sugar Edge or Watson-Crick
3 Watson-Crick
4 Watson-Crick
5 Watson-Crick
6 Watson-Crick
7 Hoogsteen
8 Hoogsteen
9 Hoogsteen
10 Hoogsteen