Question: How to find the area of hydrophobic interaction?
Dear Chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. We are investigating hydrophobic interactions between protein and ligand. ,but how can I display the following? distance between faces:show how many Å2 are within Å of each other. I found a hydrophobic contact, but does it work well in my case? https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html Please confirm. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z@st.go.tuat.ac.jp
Dear Kenji, (1) The "findclash" command or "Find Clashes/Contacts" tool described in that link finds short atom-atom distances. Like the "hbonds" command, it just gives you a list of atom-atom pairs and can draw a line between each pair of atoms. It does not use surface area (Å**2). <https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html> (2) If you want to instead get buried surface area (Å**2), see command "measure buriedArea" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea> Both methods (1 and 2 above) include all kinds of interactions, not just hydrophobic. You would need to use additional steps to figure out only the hydrophobic part. For method (1), you could specify only atoms that may be hydrophobic in the command, for example, something like the following would find only contacts between atoms of element carbon and list the results in the Reply Log: open 2gbp findclash ligand&C test protein&C overlap -0.4 hb 0.0 reveal true log true I don't know if "ligand" and "protein" would work with your specific data, you may need to use model number and/or residue name(s)/number(s) instead. Also you may decide to use some other criteria (not just element C) to specify what you think is hydrophobic. For method (2), you would measure the whole buried area between ligand and protein, but then use the resulting "buriedSESArea" or "buriedSASArea" attribute to see how much of that area is from atoms that may be hydrophobic. For example open 2gbp measure buriedArea ligand protein preset apply interactive 2 hide solvent select protein&C ... then use menu: Tools... Structure Analysis...Attribute Calculator, <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html> ...and in that tool calculate attribute [any name] for "molecules". Turn on the option "Restrict formula domain to current selection, if any" and use Formula: sum(atom.buriedSESArea) ...to get total buried area of protein carbon atoms (or you can use buriedSASArea if you want SAS instead of SES). See the image here for the difference between Solvent Excluded Surface and Solvent Accessible Surface: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces> select ligand&C ... then use Attribute Calculator again to get total buried area of ligand carbon atoms. Just like I mentioned for method 1, in the method 2 "select" commands, if "ligand" or "protein" does not work for your specific data, you may need to use model number and/or residue name(s)/number(s) instead, and you may decide to use some other criteria (not just element C) to specify what you think is hydrophobic. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 5, 2022, at 11:51 PM, Kenji MATSUI via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day.
We are investigating hydrophobic interactions between protein and ligand. ,but how can I display the following?
distance between faces:show how many Å2 are within Å of each other.
I found a hydrophobic contact, but does it work well in my case?
https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html
Please confirm.
--------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z@st.go.tuat.ac.jp _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Dear Chimera Thank you for taking the time to respond. I will try the method you have taught me. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2022年12月7日(水) 4:41 Elaine Meng <meng@cgl.ucsf.edu>:
Dear Kenji, (1) The "findclash" command or "Find Clashes/Contacts" tool described in that link finds short atom-atom distances. Like the "hbonds" command, it just gives you a list of atom-atom pairs and can draw a line between each pair of atoms. It does not use surface area (Å**2). < https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html
(2) If you want to instead get buried surface area (Å**2), see command "measure buriedArea" < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedA...
Both methods (1 and 2 above) include all kinds of interactions, not just hydrophobic. You would need to use additional steps to figure out only the hydrophobic part.
For method (1), you could specify only atoms that may be hydrophobic in the command, for example, something like the following would find only contacts between atoms of element carbon and list the results in the Reply Log:
open 2gbp findclash ligand&C test protein&C overlap -0.4 hb 0.0 reveal true log true
I don't know if "ligand" and "protein" would work with your specific data, you may need to use model number and/or residue name(s)/number(s) instead. Also you may decide to use some other criteria (not just element C) to specify what you think is hydrophobic.
For method (2), you would measure the whole buried area between ligand and protein, but then use the resulting "buriedSESArea" or "buriedSASArea" attribute to see how much of that area is from atoms that may be hydrophobic. For example
open 2gbp measure buriedArea ligand protein preset apply interactive 2 hide solvent select protein&C
... then use menu: Tools... Structure Analysis...Attribute Calculator, < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcul...
...and in that tool calculate attribute [any name] for "molecules". Turn on the option "Restrict formula domain to current selection, if any" and use Formula:
sum(atom.buriedSESArea)
...to get total buried area of protein carbon atoms (or you can use buriedSASArea if you want SAS instead of SES). See the image here for the difference between Solvent Excluded Surface and Solvent Accessible Surface: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfac...
select ligand&C
... then use Attribute Calculator again to get total buried area of ligand carbon atoms. Just like I mentioned for method 1, in the method 2 "select" commands, if "ligand" or "protein" does not work for your specific data, you may need to use model number and/or residue name(s)/number(s) instead, and you may decide to use some other criteria (not just element C) to specify what you think is hydrophobic.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 5, 2022, at 11:51 PM, Kenji MATSUI via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day.
We are investigating hydrophobic interactions between protein and ligand. ,but how can I display the following?
distance between faces:show how many Å2 are within Å of each other.
I found a hydrophobic contact, but does it work well in my case?
https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html
Please confirm.
---------------------------------------------------------------------------
Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z@st.go.tuat.ac.jp _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Kenji MATSUI