DBD-A/I1 and DBD-B/I2 complexes
After applying the DNA segment method, we placed high priority on the known biochemical contacts and made sure that the first HTH of I1docked satisfactorily onto DBD-A. This resulted in a large gap between the second HTH and DNA (Figure 2A). Since I1 contains an A-tract with a length of 5 bp, we knew that a bend had to occur in the neighborhood of 11-28°.25 Large-scale bending of DNA was then performed starting within the A-tract, and a more successful dock resulted (Figure 2B). For the DBD-B/I2 complex (Figure 2C), less bending was needed than for DBD-A/I1 . Values for roll adjustments to achieve bending are given in Table 1.