Overview and biochemical contacts
The first step in building a full model of AraC was to position each DBD onto a half-site using known residue-base interactions determined biochemically and geometric analysis of how much the DNA half-site needed to be bent in order to achieve satisfactory binding to the DBD. We refer to the two AraC DBDs as DBD-A and DBD-B. To approximately position the DBDs on the I1-I2 half-sites, we used the HDOCK webserver17 to initially place DBD-A onto I1and DBD-B onto I2 . HDOCK uses a rigid-body docking approach and can incorporate biochemical contacts to constrain the number of putative binding modes. S209 and H213 in the first HTH of the DBD were specified as these residues are known to contact the major groove of DNA at bases -69 and -48 (modern residue numbering).8, 10 Q258 also makes a weak contact. The top 100 models can be downloaded.