Figure 2.

(a) Schematic diagram showing the contacts made between λ-repressor and DNA on the consensus half of the complex (6). The half-site shown, numbering from top to bottom, consists of bps 1–9 of O_L1. When referring to a given base in the text the (+) or (−) strand prefix is added. Also, when referring to the nonconsensus half of the operator a prime is used. For positions that are equivalent in both halves, just the bp number is used. Bases and phosphates contacted by the protein are darkened. Hydrogen bonds are indicated by solid lines, van der Waals contacts by dashed lines, and nonhydrogen bond electrostatic interactions by dotted lines. Residues that make direct contact with bases are enclosed in solid boxes, those that contact the backbone are enclosed in broken boxes. Residues are grouped if they belong to the HTH or N-terminal arm. Residues in λ-repressor, which do not make direct contact with bases, but are analogous to those in Cro which do, are shown in parentheses. (b) Schematic diagram showing the contacts made between λ-repressor and DNA within the nonconsensus half of operator O_L1 (6). (c) Schematic diagram showing the contacts between Cro and its operator DNA (unpublished results).