Examples of cis and trans T-shaped interactions. PDB code, crystallographic resolution, interaction code (horizontal base [chain id]—vertical base [chain id]) and complete nomenclature (i.e., vertical base [interacting atom]—horizontal base [interacting ring], edge of the vertical base, face of the horizontal base, and the relative glycosidic orientation) are provided for each interaction. Dotted line indicates the T-shaped interaction between the C-H group of the vertical base involving the Hoogsteen edge and the ring of the vertical base. The distance between the carbon atom of the C-H group of the vertical base and the center of the interacting ring of the horizontal base is provided. Although one atom belonging to the interacting edge may visually appear closer than the other atom of the same edge, the interacting atom is that which is closest to the centroid of the receiving base. This was identified using the unbiased quantitative method according to the algorithm described in the Materials and Methods section. Note that including the information on the ring identity of the horizontal base and the interacting atom/group of the vertical base is optional and can be removed in ambiguous cases.
