Check it

http://www.clcbio.com/products/clc-drug-discovery-workbench/

You are asking for in vitro studies or in silico studies?

If in vitro studies, use a 2D NMR experiment (1H,13C- or 1H,15N-HSQC) of the proteins with and without the ligand. Large perturbations should be observed in the sidechains and/or amide protons of the amino acids involved in binding.

Visualization software like Chimera from UCSC could help in this case.

You could use the Find Clashes/Contacts tool command to find all kinds of contacts, both polar and non-polar (hydrophobic). If you specify to take in account for  hydrophobic atoms only to check for contacts, your results would only include hydrophobic contacts.

Hi Tomek

This is a very easy to use tool called COCOMAPS

https://www.molnac.unisa.it/BioTools/cocomaps/

You will get a map of the contacts of your protein complex in a very easy way. 

Hope it helps. Best

Paco

Hello,

For in silico, and if you have the x-ray structures of the four protein-ligand complexes, we have two algorithms available: Gemini and SpectralPro. Gemini will give you  the minimum amino acid-ligand pairs of interactions while spectralpro will give you the most likely amino acid-ligand pairs of interactions. The two software are based on measuring the closest neighbors and not on cut off distances and as such the selections of the interactions are naturally based on the geometry of the ligand-protein surface. Moreover, the algorithms are based on graph theory and consider the ligand-protein contacts as a network of interactions. This allows to address question relative to dynamics of contacts.There is no user friendly version of our alogrithms, but if you tell us the PDB we can send you the result as graphs or text files. It takes about 2sec to produce the result, so do not hesitate if you think that can help.

if you want some publications let me know

best

claire

Hi Tomek!

Using your favourite molecular viewer, select all atoms within e.g. 3.0 A of ligand belonging to the protein. Inspect results and go from there, further varying / tuning your selection criteria focus on different residue types (charged, polar, neutral).

For MD trajectories, in VMD within X of ligand and protein will do (just make sure to activate the update selection option). For GroMACS you could simply use g_mindist which does pretty much what its name suggests.

Hope that helps a bit.

Cheerz,

Christian

Aaa thanks for all the replies, reluctantly I'm doing in silico studies, and unfortunatelly on GPCRs so crystallography isn't a possiblity even if I had the money ;-) I have a crystal structure, and I can see the polar and polar hydrogen interractions on my own well enough, but it's the hydrophobic interractions and aromatic interractions that are really troublesome (they can be even as long as 6 A from the ligand, so the binding pocket is always very large), I of course used algorithms from my viewers, but they can't get out all the contact chains, and I've been strongly disencouraged to do it that way, so what I'm looking for is a kind of rule of thumb, or a general workflow do determine sidechains in contact with my ligand

Tomek, 

in this case I'd use for example pyhton scripting - easy & flexible way of customized contacts analysis. If you need any help - contact me, I got a lot of own scirpts so I could suit somethig for you.

Good luck :)

You can easily use iCn3D (https://github.com/ncbi/icn3d) to find contacting residues with your defined distance. The option is available in the menu "Select > by Distance" in the viewer, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1gpk.