Basepairing follows the paper Leontis, Stombaugh, Westhof Nucleic Acids Research 30 No. 16, August 15, 2002. See the FR3D Basepair catalog. Basepairs are either cis or trans, denoted c and t below. Each base can use one of three edges, the Waston-Crick edge (W), the Hoogsteen edge (H) or the Sugar edge (S). Basepairs listed below indicate which base is using which edge. For example, a line reading A108 G130 tSH would mean that A108 is using its Sugar Edge and G130 is using its Hoogsteen edge. In the case that both bases use the same edge, a capital letter indicates which base uses the edge in the dominant way. For perfectly symmetric basepairs such as AU cWW, the capital and lowercase letters are irrelevant. Bifurcated basepairs are indicated by the text bif. It does not indicate which base uses which edge.
Base stacking is divided into three subcategories, according to the faces used by each base. The faces are named this way: Imagine a base making a Watson-Crick basepair in a helical context. The side of the base that faces toward the 3' end of the strand is called the 3 face, while the side that faces the 5' end is called the 5 face. The stacking one finds in a helix is thus refered to as s35, meaning that the first base uses the 3 face and the second uses the 5 face. Two other types of stacking (s33 and s55) occur in other contexts.
Each pair is listed twice. For instance, if A108 G130 tSH is listed, then so is G130 A108 tHS. The order in which the edges are listed still corresponds to the base which is using that edge. Similarly with stacking. The chain is indicated in parentheses.
Starting from hairpin loops, cWW interactions are classified as being nested if they do not cross any previously established nested cWW pairs. The last column indicates, for all interactions, the number of nested cWW pairs crossed by the interaction (which may be visualized on the circular diagram of pairwise interactions).
Classification of basepairs and base stacking is done using the program FR3D developed by the Bowling Green State University RNA group, including Neocles Leontis, Craig L. Zirbel, Jesse Stombaugh, Ali Mokdad, Michael Sarver, and Anton Petrov.
Base-phosphate interactions are described in this paper by the BGSU RNA group. See the catalog of FR3D Base-phosphate interactions. Base-ribose interactions are annotated using the same method. Backbone connectivity relations are denoted c35 or c53. c35 indicates that the first nucleotide uses its O3' atom to connect to the phosphorus of the second nucleotide and then to the O5' atom of the second nucleotide. c53 is used when the order of the nucleotides is reversed.
Backbone conformations are two-character codes which apply to the portion of the backbone shared by the two listed nucleotides. They are only listed once, with the nucleotides in increasing order. Nucleotides missing a base in the PDB file are omitted by FR3D. Conformations are calculated by Dangle and Suitename from the Richardson lab at Duke University.
Please write to Craig L. Zirbel at with questions or comments.
1 G 1(A) - G 1(A) - !! - 0