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RNA Base Pair Families

No.

Bond Orientation

Interacting Edges

Symbol

Strand Orientation

Abbreviated notation

1

Cis

Watson-Crick/Watson-Crick

Anti-Parallel

cWW

2

Trans

Watson-Crick/Watson-Crick

Parallel

tWW

3

Cis

Watson-Crick/Hoogsteen

Parallel

cWH

4

Trans

Watson-Crick/Hoogsteen

Anti-Parallel

tWH

5

Cis

Watson-Crick/Sugar Edge

Anti-Parallel

cWS

6

Trans

Watson-Crick/Sugar Edge

Parallel

tWS

7

Cis

Hoogsteen/Hoogsteen

Anti-Parallel

cHH

8

Trans

Hoogsteen/Hoogsteen

Parallel

tHH

9

Cis

Hoogsteen/Sugar Edge

Parallel

cHS

10

Trans

Hoogsteen/Sugar Edge

Anti-Parallel

tHS

11

Cis

Sugar Edge/Sugar Edge

Anti-Parallel

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 Base-pair geometric isomerism. (Upper left) An adenosine showing the three base edges (Watson-Crick, Hoogsteen and Sugar-edge) available for hydrogen-bonding 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 base-pairing geometries, illustrated for two bases interacting with Watson-Crick edges. (Leontis & Westhof, 2001).


Figure B: Basepairs geometric families and their annotation. Upper panel: Twelve geometric basepair families resulting from all combinations of edge-to-edge interactions of two bases with cis or trans orientation of the glycosidic bonds. Circles represent Watson-Crick 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).


  1. Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512.
  2. Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30:3497-3531




RNA Base-Phosphate Families

No.

Interacting Edge

Symbol

Notation

1

Sugar Edge

1BPh

2

Sugar Edge or

Watson-Crick

2BPh

3

Watson-Crick

3BPh

4

Watson-Crick

4BPh

5

Watson-Crick

5BPh

6

Watson-Crick

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. H-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).

Zirbel C L et al. Nucl. Acids Res. 2009;37:4898-4918




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




Non Redundant list:

Nonredundant (NR) datasets of 3D structures for RNA is a list of best resolved and modeled representatives of each structure class available for analysis. Redundant files in the RNA 3D structure database are identified and clustered into equivalence classes and a representative structure is listed for each class.




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:10.1007/978-3-642-25740-7_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 Watson-Crick/Watson-Crick (cWW) interaction among them. Then the relative Frequency of cWW in the structure is 25/50= 0.5