[Chimera-users] Relevant interacting amino acids between molecules

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 15 15:28:01 PDT 2014


Dear Abisola,
You can use the "Find Clashes/Contacts" tool or just a simple distance cutoff to find all the amino acid residues in one protein that are close to another molecule, which could be a small ligand, or another protein, DNA, etc.

There is an example of using "FindHBond" and "Find Clashes/Contacts" to identify amino acids interacting with a ligand molecule in the "Structure Analysis and Comparison" tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

It would be very similar to find the H-bonds and contacts between amino acids and some other kind of molecule (such as another protein), you would just need to select that other molecule instead of the ligand molecule.  I think it will be clearer if you try that tutorial.

Or, for simple cutoff you can first select one molecule and then use menu: Select... Zone to also select the nearby residues.  Once they are selected, you can do other stuff with the Actions menu like labeling them, or getting a list of them as in the tutorial mentioned above. How to select:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

There is a more advanced example of using findclash (the command version of Find Clashes/Contacts) to color the atoms involved in a protein-protein interaction in the "Opened Interface" image tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>

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

On Apr 15, 2014, at 2:34 PM, Ogunniyan, Abisola wrote:

> Hi,
> My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class.
> I have been having difficulty in trying to determine the relevant interacting amino acids between molecules.
> Please, I will really appreciate it if this is made clearer to me.
> Thank You.
> Best Regards,
> Abisola Abisoye-Ogunniyan.




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