[Chimera-users] Identifying type of interaction

[nitya yerabandi]

Thank you for your help!

On Fri, Jan 8, 2021 at 3:33 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Nitya,
> This is not really a Chimera question. In general you would use your own
> knowledge of chemistry and atom types (elements), or maybe you can find the
> information in textbooks or on the web. It's beyond the scope of this
> mailing list to provide all details, but I will try to give some brief
> hints.
>
> In general, the H-bonds between proteins are the polar interactions, and
> the nonpolar interactions are the ones between nonopolar groups (C-H).
>
> Besides just measuring a lot of distances, you can use the FindHBond tool
> to find H-bonds and Find Clashes/Contacts to find contacts of all kinds.
> See the manual pages for these tools, and a tutorial that gives examples of
> using them:
>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html
> >
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
> >
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
> >
>
> You can also color protein surfaces by ESP or hydrophobicity to evaluate
> their complementarity. This tutorial covers coloring surfaces to show these
> properties:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jan 8, 2021, at 2:54 PM, nitya yerabandi <nityayerabandi at gmail.com>
> wrote:
> >
> > Hi,
> >
> > I'm using UCSF Chimera right now to analyze the contact residues between
> two proteins, Hsp70 and BAG3. I have created a distance monitor table on
> chimera that shows residues, atoms, and the distances between them. I am
> now trying to identify the type of interaction between each pair of atoms,
> like polar, nonpolar, hydrogen,etc. However, I am having difficulty doing
> this. I was wondering if you could assist me with this.
> >
> > Thank you,
> > Nitya Yerabandi
>
>
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