Tutorial: Detect Hydrophobic Patches
example, we will design a 3D motif from the active site of 1dmt, a
neutral endopeptidase and search for structures containing a similar
arrangement of residues.
Available from version 4.1
Step by Step
- First of all, open the pdb file 1hbg (using the File:Import menu)
- Using the Control Panel, Select the HEM148 and CMO201 groups (at the bottom of the list).
- Make sure that "ignore selected residues" of the Surface Preferences (Prefs menu) is checked.
and that the surface quality is smooth, let's say 4.
- Use the "Detect hydrophobic patches" (in the Tool Surface submenu)
At this stage, you should be in this situation.
- Note that the window "Surface and Cavities" (accessible from the Wind menu) will be opened
and list the patches identified sorted by their respective area.
Note that the patch at the top of the list is the hydrophilic surface of the protein, and it is hidden by default.
It is possible to quickly select and center the view on residues that form an hydrophobic patch by shift-control-clicking on a given line. Click on the question mark at the top left of the "Surface and Cavities" window to access the user guide.