[chimerax-users] How to discover hydrophobic between two chains

[Elaine Meng]

Hi Phil,
No rationale at all for 4.5 specifically.  It was merely to illustrate that you can put in whatever angstrom distance you want and that it can be a floating-point value.

Note that "alphafold contacts" doesn't predict contacs per se, it just draws pseudobonds between the alpha-carbons of residues in the model with *any atom* within the distance specified in in the command, and colors the pseudobonds by the Predicted Aligned Error.  This is a pairwise, order-dependent measure.  It is different than the pLDDT which is per individual residue.  See 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#pae>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 2, 2022, at 4:35 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine-
> 
> As always thank you for your very useful advice.  I selected just the regions of interest where two proteins interacted in the pocket in chain C.  I then used the 
> 
> alphafold contacts 
> 
> command and limited the interaction to just those hydrophobic residues in the targeted portions of the two proteins that were less than 4.5 A apart.  This displayed not only the contacts, but also the AF2 confidence score (pLDDT) for each residue pair.  In this way we are able to demonstrate that not only are the contacts at a specific distance but that the contacts are between hydrophobic residues whose positions are highly supported.
> 
> Side bar question: what rationale did you use for the 4.5 distance you mentioned.
> 
> Phil
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, November 1, 2022 1:10 PM
> To: McClean, Phillip <phillip.mcclean at ndsu.edu>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] How to discover hydrophobic between two chains
>  
> Hi Phil,
> If you hover the cursor over the surface it will show in a pop-up label the residue name at that location, or Ctrl-click to select and then use menu Actions... Label... [etc.] or command "label sel."  The label command has other options like color, height, etc.  Or you can hide the surface or make it partly transparent to show displayed atoms inside.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html>
> 
> Or if you mean you want a list of pairwise atomic interactions in the interface, see the atomic Contacts tool (although it will not automatically separate hydrophobic from polar interactions, you would have to do that yourself based on atom and residue types either by limiting the scope of input or by filtering the results).  It's in the menu under Tools.. Structure Analysis,  or you can use the equivalent "contacts" command.  Results can be written to Log or file.
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
> 
> There is also an Interfaces command to identify interface residues, although it doesn't say which residues are interacting with which
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>
> 
> Or if you can think of a simple rule you can often express that as a selection in the command line, e.g.
> 
> name bphob /B:phe,trp,tyr,leu,ile,ala,val & sidechain
> name cphob /C:phe,trp,tyr,leu,ile,ala,val & sidechain
> sel bphob & cphob :<4.5
> show sel
> label sel height 2 color red
> sel cphob & bphob :<4.5
> show sel
> label sel height 2 color red
> 
> ...meaning find in each chain those atoms I defined as "phob" (you could certainly use a different definition) that are within 4.5 A of "phob" atoms in the other chain. The above would just  label them all, however, not list pairwise interactions, although you could probably identify them easily by visual inspection.   To automatically write out a list of pairwise interactions you would need to use Contacts, however.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Nov 1, 2022, at 10:26 AM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hi Everyone,
> > 
> > I ran AF2 multimer and have a two-chain complex.  I ran the mlp command on the two chains separately and together.  The two chains seem to interact via hydrophobic residues where chain B fits into a pocket on chain C.  Here are the chain residues:
> > 
> > /b:72-124
> > /c:1-190
> > 
> > Is there any way to determine which residues (hydrophobic) in each of these two regions are interacting via hydrophobic interactions.
> > 
> > Thanks for any help you can provide.
> > 
> > Phil McClean
> 
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