The repressors of the λ-like phages possess recognition helices that fit sideways into the major groove of the operator DNA. Specific amino acids on the DNA-facing side of the recognition helix establish precise contacts with bases in the operator, and these interactions determine the specificity of the protein-DNA binding. Altering these amino acids can modify the specificity of the repressor. Both the λ repressor and the Cro protein exhibit affinity for the same operators, but their microspecificities for OR1 or OR3 are defined by interactions between distinct amino acids in the recognition helices of the two proteins and the base pairs in the respective operators.

The cocrystal structure of a λ repressor fragment bound to an operator fragment provides detailed insight into the protein-DNA interactions. The most critical contacts occur in the major groove, where amino acids on the recognition helix, along with other amino acids, form hydrogen bonds with the edges of DNA bases and the DNA backbone. Some of these hydrogen bonds are reinforced by hydrogen bond networks involving two amino acids and multiple sites on the DNA. The structural data derived from the cocrystal closely align with prior biochemical and genetic findings.

X-ray crystallography of a phage 434 repressor fragment/operator-fragment complex reveals probable hydrogen bonding between amino acid residues in the recognition helix and base pairs in the repressor. It also indicates a potential van der Waals interaction between an amino acid in the recognition helix and a base in the operator. The DNA in the deviates significantly from its typical regular shape, bending slightly to facilitate the necessary base/amino acid contacts. Additionally, the central region of the helix, the two half-sites, is wound more tightly, while the outer regions are wound more loosely than usual. These structural deviations are supported by the base sequence of the operator.