Figure 8

Contact map of a protein-nucleic acid complex. A double-stranded RNA binding domain of S. cerevisiae RNAse III in complex with an AAGU tetraloop hairpin (PDB code: 2LBS, only the first model is shown, the same as in a traditional rendering in Figure 7). In a contact map picture, protein contacts are displayed in yellow, RNA contacts are blue, and the protein-RNA interface contacts are displayed in orange. Metrics preset: all-atoms for RNA and protein molecules, 3.5 Å contact threshold. However, the atom type and the distance threshold can be set independently for RNA-RNA, protein-protein, and protein-RNA contacts. In the protein part of the map, red and green bars indicate secondary structures (alpha helices and beta strands, respectively), read directly from the PDB file. In the RNA part of the map, purple and violet bars indicate RNA secondary structure computed using the RNAView program.