Identifying type of interaction
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
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/findhbo...> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla...> <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@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
Thank you for your help! On Fri, Jan 8, 2021 at 3:33 PM Elaine Meng <meng@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/findhbo...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla...
<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@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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Elaine Meng -
nitya yerabandi