Figure 6.

Functional motif-pair inter-relationships. Proteins must often be positioned in a particular orientation with respect to the DNA molecule to induce potential interactions (3,62,63). Interactions between protein A and protein B occur when the latter is positioned at B1. The same interaction frequently occurs one turn of the double-helix away from B1 (i.e. at B2), since the orientation of protein B is consistent relative to the turn of the DNA molecule. However, the interaction cannot occur when protein B is at B3 due to its inconsistent orientation. The distance between factors A and B is determined by the size of the proteins and is unique between different TF-pairs. In contrast, phasing intervals (i.e. the distance between B1 and B2) remains relatively consistent, as they correspond approximately to the number of nucleotides in a turn of the DNA double-helix.