FIGURE 2.

(A–G) The configurations for seven base triples selected from the BWYV (Su et al. 1999), ScYLV (Cornish et al. 2005), and hTR pseudoknots (Theimer et al. 2005). (H) A simplified configuration for the base triple U•(A–U). Nucleotide 3 (U) forms a base triple interaction with base pair 2 (A)–1 (U), and we use three atoms (P, C_4′, and N₁ or N₉) to represent a nucleotide. D_N12 or D_N13 denotes the N_{1 or 9}–N_{1 or 9} distance between two nucleotides. γ is the torsion angle C_4′–N_{1 or 9}–C_4′–N_{1 or 9}. α is the bond angle for C_4′–N_{1 or 9}–C_4′.