Comparison of rates of evolution to structures of protein-DNA complexes implies a model for the variation in the rate of evolution across binding motifs. The DNA backbone appears as a red helix; proteins appear as linked coloured cylinders. We propose that the formation of the protein-DNA complex is the functional constraint that leads to purifying selection, and therefore fewer substitutions at certain positions in the binding motif. Images of protein-DNA complex structures are from the Protein Data Bank . Rate of evolution is in substitutions per site (estimated by maximum parsimony) and error bars represent exact 95 % confidence intervals for a Poisson distribution.