Secondary structure of ubiquitin with locations of modules and major clusters. The location of the major clusters associated with the four major modules is shown, for clarity, on two identical secondary structure ribbons, taken from model 1UBQ. An example of smaller clusters nested within larger clusters can be seen in the clusters associated with Module 2. The attribute (site) clusters associated with Modules 1 and 2 were found to be compact, with only a small region of interlacing involving sites 26, 28, and 31. Of particular interest are the two clusters associated with Module 4 that contain some sites that are quite distant in the primary structure. The key sites in these very extended clusters are sites 30, 43, and 69 which, although widely separated in the primary sequence, are actually in Van der Waals contact, as shown in Figure 3.