Visualizing Protein Protein residue interaction in Pymol

Question

[Omar Santiago]

Hello! I have knowledge of the residues that are interacting between proteins (say Protein A and Protein B, and I know that, for example, residue 5 from protein A is interacting with residue 11 from protein B, etc.) and I was wondering: Is there a Pymol function that would allow me to input these residue interacting pairs and for Pymol to show me how the structure of the protein complex looks like (maybe by orienting the proteins appropriately so the predicted contact regions are close and/or by showing me lines connecting the interacting residues)?

As a second question, if I have Protein A and I know that the residues X, Y, ... are interacting with residues from Protein B with some strengths S_X, S_Y, ..., (so that S_X is associated to residue X, etc.), is there a way for Pymol to allow me to color these residues in a gradient based on the values of the strength (maybe like the larger the strength, the darker it is)?

Thank you!

Answer 1

[jgreener]

Is there a Pymol function that would allow me to input these residue interacting pairs and for Pymol to show me how the structure of the protein complex looks like

PyMOL is mainly concerned with visualisation; this problem of docking with constraints is a non-trivial task in itself and can be achieved with tools like HADDOCK.

showing me lines connecting the interacting residues

PyMOL can show lines connecting residues, see here, though that is only useful once the proteins have been docked.

is there a way for Pymol to allow me to color these residues in a gradient based on the values of the strength

Yes, you could put the strength values in the temperature factor column of the PDB file and colour by that. Or you could use the PyMOL scripting interface and loop over residues, colouring them by the desired values.

[Omar Santiago]

This is very helpful, thank you very much!