The metric plotted is the 'Relative Entropy' at an amino acid position in the sequence. The reliability of this measure of sequence variability depends on the number and degree of similarity of the sequences used in the alignment. Not all entries in either database have HSSP sequence alignments with high information content, these entries were usually assigned a variability of -99.999. and have no images of sequence variability displayed on the surface. Many of the alignments, when their conservation is mapped to the surface are hard to interpret due to a low overall information content. We are in the process of attempting to screen out undesirable sequence alignments from this database.
Ideal angles are from Stickle, et.
Only one contact is reported per residue pair. Cavities were created in Grasp. Due to idiosyncrasies in Grasp, all pdb files with numerical chain ids were converted to lower case letters. However, the heuristic we used to select the display angle does fail occasionally and we did not verify all pictures by hand. For any given interface, simply click on the link in the frame at the bottom of the page.