Fig. 5. DNA sequence recognition by RXR and RAR. (A) A view along the DNA-recognition helix (α1) of RAR showing residues Tyr13, Arg26, Lys22, Glu19 and Arg27 and their direct and water-mediated base contacts. Hydrogen-bonds and water molecules are shown as dotted blue lines and red spheres, respectively. The DNA sequence is numbered as in Figure 1B. (B) The corresponding view of the RXR interface. (C) Summary of the protein–DNA contacts of RAR. Bridging water molecules are shown as black circles. The base pairs in blue form the consensus AGGTCA recognition element. The gray circles indicate the DNA phosphates. (D) Summary of RXR–DNA interactions. The base pairs in orange form the consensus element.