Tutorial: Contact Surface

In this example, we will visualize how the heme is bound to the hemoglobin

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).
  • Use the 'Inverse Selection' item of the Select menu, and then the 'Remove Selected Residues' from the Build menu to keep only the heme with its bound oxygen.
  • Compute the molecular surface using the Surface:Compute item of the Tools menu.
  • open a second copy of the pdb file 1hbg (it will be in the list of the recent files at the bottom of the File menu)
  • Use the pop up menu located at the top of the Control Panel to activate it.
  • 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.
  • Compute the molecular surface using the Surface:Compute item of the Tools menu.
  • Detect the Contact Surface between the two layers using the appropriate item of the Tools Surface submenu.
  • Note that the window "Surface and Cavities" (accessible from the Wind menu) will be opened and list two surface patches. The blue one corresponds to tight contact with the molecular surface of the entity in the other layer.
  • Make the first one invisible (click on the checkmark in front of the first line)

At this stage, you should be in this situation.

contact1

  • Make the first patch visible again (click on the checkmark in front of the first line)
  • Center the view on the Heme Oxygen (option+click on the CMO201 group in the Control Panel)
  • Enable the slab mode using thew Display Menu
  • Repeatedly use the Control+Tab key to switch the view between the two layers.

contact2

View of the heme (layer 1)

contact3

View of the protein cavity with the heme in position (layer 2)