[Chimera-users] Question: How to find the area of hydrophobic interaction?

[Kenji MATSUI]

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 at 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#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 at 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 at st.go.tuat.ac.jp
> > _______________________________________________
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>
>
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