Figure 2.

Predicted DNA-contacting residues shown on the protein–DNA complexes. Predictions are shown in three different colors: actual DNA-contacting residues are in blue, their nearest neighbors are in cyan and incorrect predictions are in green. The rest of the protein surface is in yellow; the bound DNA is shown as red lines. (A) 1brn. (B) 1gd2. (C) 1s40. (D) 1u1q. In the last panel, there are two protein chains related by a 2-fold rotation, one on the left and one on the right. Within the left chain, the C and N-terminal RNA recognition motifs are at the top and bottom, respectively. The pictures here and those in Figures 4 and 6 are generated with PyMOL (http://www.pymol.org).