Figure 4.

For some protein–DNA complexes, the pattern of minor groove width variation in part of the binding site is similar to that of the same sequence as naked DNA, and in part of the binding site the pattern is different when protein is bound. Patterns were quantitatively compared by computing the Spearman's rank correlation coefficient ρ and the P-value for the similarity. The y-axis scale for expORChID2 values differs slightly between plots to facilitate comparison of individual patterns. This does not affect the calculation of the Spearman's rank correlation coefficient (see Materials and Methods). Red filled circles, expORChID2 values; blue filled triangles, minor groove width measured from the protein–DNA complex. Arrows, locations of arginine residues bound to the minor groove in the protein–DNA complex, for reference. (A) Tc3; (B) PhoB; (C) MATα2-MCM1; (D) Oct-1 (PORE). Dashed green lines in (D) demarcate segments of the binding site that interact with the POU-homeodomains (left and right sides) and the POU-specific domains (center) of the Oct-1 (PORE) binding site (see Supplementary Figure S6 for more details).