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Fig. 4 | BMC Bioinformatics

Fig. 4

From: An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Fig. 4

Criteria for comparing two recognition helices. a Schematic depiction of a recognition helix, with each residue position represented by a numbered square whose number refers to the residue position. The central residue is the 0th position. A 41-residue window centered on the central residue is used as the basis for comparing two HTH domains. An 11-residue window flanking the central residue defines the minimum region of overlap for a recognition helix. b Examples illustrating allowable (top) and unallowable (bottom) shifts between two helices. Only allowable shifts are used when computing the distance between two helices

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