What do the colors represent in the binding pocket surface?

[Andrew Orry]

Q. What do the colors represent in the binding pocket?

A. White=aromatic lipophilic, Green=non-aromatic other (mostly aliphatic) lipophilic surface, Red=hydrogen bonding acceptor potential, Blue=hydrogen bond donor potential.

To display the Receptor Pocket Surface:

• As an example we will use the PDB structure 1STP. Type 1STP in the pdb search tab and press return.
• Convert the protein to an ICM object. If you do not convert a generic surface will be displayed that is not colored by binding property.
• Right click on the ligand "abtn" and select Pocket/Receptor Pocket.
• Select whether you would like to display side-chain hydrogen bonds and label.
• The receptor pocket will be displayed colored by binding property - White=aromatic lipophilic, Green=non-aromatic other (mostly aliphatic) lipophilic surface, Red=hydrogen bonding acceptor potential, Blue=hydrogen bond donor potential.
• The surface can be toggled on and off by selecting in the ICM Workspace in the meshes section.