Design of Multi-Specificity in Protein Interfaces
Figure 2
Dataset of Promiscuous Proteins
PDB codes and descriptions of 20 promiscuous proteins and their 65 crystallized interaction partners. For each binding partner, the total number of residues it contacts (within 4 Å) on its promiscuous binding protein as well as the number of these residues which are also utilized by at least one other characterized binding partner are given in the “Total” and “Shared” columns. Fold classes are as assigned using SCOP [20]. Protein–protein interaction maps of sequence homologs to the promiscuous proteins in our dataset (see Methods) are as taken directly from the Database of Interacting Proteins [21], http://dip.doe-mbi.ucla.edu/, see Table S21). Root nodes are colored red and the number of first (orange) and second (yellow) shell nodes for each map is given on the far left. Edges are color-coded based on the reliability of data used to infer interactions, with green lines indicating data verified by one or more computational methods and red lines depicting unverified high-throughput screens. The width of lines in interaction graphs reflects the number of independent experiments verifying each predicted interaction.