RNA Base Pair Families
No. 
Bond Orientation 
Interacting Edges 
Symbol 
Strand Orientation 
Abbreviated notation 
1 
Cis 
WatsonCrick/WatsonCrick 
AntiParallel 
cWW 

2 
Trans 
WatsonCrick/WatsonCrick 
Parallel 
tWW 

3 
Cis 
WatsonCrick/Hoogsteen 
Parallel 
cWH 

4 
Trans 
WatsonCrick/Hoogsteen 
AntiParallel 
tWH 

5 
Cis 
WatsonCrick/Sugar Edge 
AntiParallel 
cWS 

6 
Trans 
WatsonCrick/Sugar Edge 
Parallel 
tWS 

7 
Cis 
Hoogsteen/Hoogsteen 
AntiParallel 
cHH 

8 
Trans 
Hoogsteen/Hoogsteen 
Parallel 
tHH 

9 
Cis 
Hoogsteen/Sugar Edge 
Parallel 
cHS 

10 
Trans 
Hoogsteen/Sugar Edge 
AntiParallel 
tHS 

11 
Cis 
Sugar Edge/Sugar Edge 
AntiParallel 
cSS 

12 
Trans 
Sugar Edge/Sugar Edge 
Parallel 
tSS 
When the notation is preceded by n, it indicates that the interaction is “near” or close to a particular interaction, but do not meet the strict criteria for membership.
Figure A: Base edges and Basepair geometric isomerism. (Upper left) An adenosine showing the three base edges (WatsonCrick, Hoogsteen and Sugaredge) available for hydrogenbonding interactions. (Lower left) Representation of RNA base as a triangle. The position of the ribose is indicated with a circle in the corner defined by the Hoogsteen and Sugar edge. (Right) Cis and Trans basepairing geometries, illustrated for two bases interacting with WatsonCrick edges. (Leontis & Westhof, 2001).
Figure B: Basepairs geometric families and their annotation. Upper panel: Twelve geometric basepair families resulting from all combinations of edgetoedge interactions of two bases with cis or trans orientation of the glycosidic bonds. Circles represent WatsonCrick edges, squares Hoogsteen edges, and triangles Sugar edges. Basepair symbols are composed by combining edge symbols, with solid symbols indicating cis basepairs and open symbol, trans basepairs. Lower Left: Symbols for other pairwise interactions (Leontis et al., 2002).
 Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7:499512.
 Leontis NB, Stombaugh J, Westhof E. 2002. The nonWatsonCrick base pairs and their associated isostericity matrices. Nucleic Acids Res 30:34973531
RNA BasePhosphate Families
No. 
Interacting Edge 
Symbol 
Notation 
1 
Sugar Edge 
1BPh 

2 
Sugar Edge or WatsonCrick 
2BPh  
3 
WatsonCrick 
3BPh 

4 
WatsonCrick 
4BPh 

5 
WatsonCrick 
5BPh 

6 
WatsonCrick 
6BPh 

7 
Hoogsteen 
7BPh 

8 
Hoogsteen 
8BPh  
9 
Hoogsteen 
9BPh  
10 
Hoogsteen 
0BPh 
Proposed nomenclature for BPh interactions and superpositions of idealized BPh interactions observed
in RNA 3D crystal structures for each base. Hbonds 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).
Zirbel C L et al. Nucl. Acids Res. 2009;37:48984918
Base Stacking Interactions
s35 is a stacking interaction in which the first base uses its 3 face, and the second base uses its 5 face. Similarly, in s53, s33, s55, s stands for stacking and the two number stand for the face used by the first base and second base in the interaction respectively.
When the notation is preceded by n, it indicates that the interaction is “near” or close to a particular interaction, but do not meet the strict criteria for membership
Information from : WebFR3D Help Page
Representative RNA 3D Structure Sets:
RNA equivalence classes cluster RNAcontaining 3D structures based on similarity of RNA sequence and geometry. Representative structure sets are created by selecting the highest quality structure from each equivalence class. Selection is based on a composite score that evaluates Xray resolution, Rfree, realspace R factor, realspace correlation coefficient, percent of atoms with clashes, and fraction unobserved.
Equivalence classes:
Structures that are provisionally redundant based on sequence similarity and also geometrical similarity are grouped into one Equivalence class.
Leontis, N. B., & Zirbel, C. L. (2012). Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking. In N. Leontis & E. Westhof (Eds.), (Vol. 27, pp. 281–298). Springer Berlin Heidelberg. doi:10.1007/9783642257407_13
RNA 3D Motifs:
RNA 3D motif is a well defined geometric arrangement of interacting nucleotides.
These motifs are identified from a nonredundant set of RNA containing PDB files. These structures were compared, the loops were clustered and distinct motif groups were identified, including all hairpin and internal loop motifs previously described in the literature.
For more information please go to RNA 3D Motif Atlas
The RNA 3D motif data is available only for those structures in NDB that make up the non redundant list.
Relative Frequency:
Relative Frequency is the number of observations of a given interaction type divided by the total number of observations of all the interactions.
Eg: If a structure had a total number of 50 Base pair interactions and a total of 25 Cis WatsonCrick/WatsonCrick (cWW) interaction among them. Then the relative Frequency of cWW in the structure is 25/50= 0.5
Ligand IDs:
NDB uses 3character alphanumeric identifier codes for ligand IDs from the PDB Chemical Component Dictionary. Larger polymeric ligands (e.g. antibiotics) are an exception: they are listed according to their common name (e.g., actinomycin, echinomycin).