I'm looking at a protein in a 3D visualization program (PyMol). I have the full amino acid sequence list.
How do I determine *where* there are hydrophobic interactions that are stabilizing the tertiary structure? I know what hydrophobic interactions are in general, and I can look up the hydropathy indices for all the residues, but how can I visually detect or calculate which specific residues are exhibiting hydrophobic interactions that are stabilizing the overall tertiary structure?
Same question for hydrogen bonding and ionic interactions.
Please, I'm really stumped on this. Any help is greatly appreciated.