Fig. 8
From: An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system
Pairwise alignments based on canonical matching regions. The two rows of DNA structures in this figure represent two HTH-DNA complexes, for which there are 50 possible pairwise alignments. Each complex has five canonical matching regions (depicted schematically to the right of every complex), which can be matched with any of the five canonical matching regions of the other HTH-DNA complex, yielding 25 possible pairings (represented by dashed lines). Since each pairing can yield two distinct alignments (Fig. 6), there are 50 possible alignments