Figure 5

Triplet buriedness classes 1 and 5. Instances of triplet buriedness class 1 (left) and 5 (right), shown in red. The tube represents the backbone, and Delaunay triangles are shown in blue. The class 1 triplet is formed by the residues 7LYS, 8PRO, and 10GLN in the protein 1VQB. The class 5 triplet is formed by residues 6LEU, 53GLY, and 86ILE in the protein 2ACY. Images generated using the package VMD [43]. It is best to visualize these as well as other triplet types in 3 D. Scripts to draw all the triangles for the above two proteins in VMD are made available on the web page for the paper [37]. The reader is encouraged to load the PDB file, run the script, and then rotate the molecule appropriately in 3 D in order to visualize the same.