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Tutorial: Detect Hydrophobic Patches

In this 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.

hpatch1

hpatch2

  • 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.

hpatch3