A protein with PDB ID 4RI1 was used (same as in the Task 1). The CLUD service was run with Distance Threshold=5 and Show Clusters Not Smaller Than=20.
Figure 1. The protein's structure.
Figure 2. The found clusters.
As can be seen on Fig. 1, the structure consists of three chains. Each one of them can be assumed to be a single domain as they are tightly packed in almost a spherical form. However, the service merged the clusters of two left chains into one. This probably happend because they are linked via beta-sheet and the link is quite tight and thick.
To further investigate why the service merged cores of two domains, hydrophobic clusters on the interfaced were found. The CLUD service was run with Distance Threshold=5 and Show Clusters Not Smaller Than=10; also it was set to find clusters between chains B and C.
Figure 3. The found clusters on the interface.
The service found 3 clusters (77, 14 and 14 atoms). The biggest one streches across the whole interface (Fig. 3). This explains why CLUD couldn't distinguish two clusters in these chains -- they are connected with a "hydrophobic bridge".
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