Figure 7

Divergent pattern of the set 1 in a model for a representative C . elegans DBD, as viewed at two different angles at a complex with a hypothetical 5'-NNTTCA-3' half site. It can be noted the over-packing of the R160 residue between the thimidine at the third dinucleotide and the F147, in an analogous way that the VDR-DBD at a similar half site (Figure 6-C). The DBD modeled was NHR28. The half-site used was from the 3' side of the HNF4:(MODY related promoter) complex (PDB 3CBB). Residues from the set 1 of the correlation network are depicted with the carbons colored in purple (and labeled at this same color) while the two more conserved basic positions R160 and R161 (that do not appear at the correlation set) are depicted with carbons in white and labeled in black. For clarity, in the picture at the right residue A156 is identified with a dashed red circle.