Figure 13.

Local frustration patterns in globular proteins. Examples of frustratograms of natural proteins. The structural coordinates from protein models were taken the protein data bank (pdb)(Berman et al. 2000. The chain backbone is shown as a continuous trace and interactions between residues are represented by thin lines. Minimally frustrated contacts are green, highly frustrated contacts are red, and water-mediated interactions are shown with dotted lines. Two complementary ways of localized frustration are shown for each protein. At right the patterns are calculated with the mutational frustration definition: how favorable is a native interaction relative to the interactions other residues would form in those locations? At left the patterns are calculated with the configurational frustration definition: how favorable is the native interaction relative to the interactions these residues would form in other compact structures? A statistical survey was performed with a non-redundant sample of the pdb (Ferreiro et al. 2007a). The pair distribution functions between the centers of mass of the contacts are shown below for the minimally frustrated (green), neutral (gray), or highly frustrated (red) groups. Neutral interactions follow the distribution of all contacts (black); highly frustrated interactions cluster at short distances; and minimally frustrated interactions form a tight network that percolates the structure.