[Chimera-users] How to show hydrophobic interactions

[Kenji MATSUI]

Dear   Elaine

Thank you for your time and kind response.

I apologize if this is outside of our business hours due to the time
difference.

Thank you also for your comments regarding hydrogen bonding.

I am afraid that I have not studied enough myself, but I would like to
confirm one point.

I have seen 3.5Å and 3.7Å as the distance of hydrogen bonding in many
papers, but am I correct in understanding that the distance between two
atoms is 4Å or less as a reasonable distance for hydrogen bonding to be
formed?

Thank you for attaching the diagram regarding the hydrophobic interaction.

I will check it out by actually operating the system myself.
---------------------------------------------------------------------------
松井 健治
 東京農工大学大学院 工学府産業技術専攻 修士 2年
〒184-8588 東京都小金井市中町2-24-16
 Mail: s214903z at st.go.tuat.ac.jp

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


2022年6月18日(土) 1:06 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji,
> "Examine residues" just  means to look at the residues in the Chimera
> graphics window, and put the mouse cursor over them to see a pop-up label
> of residue number, etc.
>
> However, these menu actions that you mentioned:
>   (1) Select... Residue... Amino acid category... hydrophobic
>   (2) Actions... Atoms/Bonds... Show
> ... do not specifically identify hydrophobic interactions with your
> ligand.  Instead they would show ALL of the hydrophobic amino acids in your
> whole structure, no matter where they are.
>
> There is no tool to identify only hydrophobic interactions.  Instead you
> have to look at the residues near the ligand yourself and see which parts
> of the pocket are hydrophobic.  There are tools that might help do part of
> this, however:
>
> (A) Find Contacts tool.  You can use this to find ALL contacts with
> ligand, but it does not tell you which contacts are polar or which are
> hydrophobic.  This tutorial gives an example of using Find Contacts to
> identify contacts with ligand named FPS
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
> >
>
> (B) You can show the surface of the protein and color it by hydrophobicity
> (e.g. menu: Presets... interactive 3, there is an example below) ... the
> orange parts are the hydrophobic amino acids.  However, this does not mean
> it is a hydrophobic interaction with your ligand, you still have to see
> whether the ligand has hydrophobic atoms and where they are in the pocket,
> whether or not they are near the orange surfaces.
>
> Your session is very confusing because it has a target (#0) and many
> docked ligands (#1) plus three different combination models (#2-4 but only
> #2 is shown).  If you are trying to analyze #2, probably better to close
> all that other stuff first (close #0,1,3,4) as long as you already have
> them saved as a session file.  You can make a new session with only the
> part that you are trying to analyze.
>
> Example commands to show receptor atoms within 5 Angstroms of ligand
> residues named LIG, except hiding the hydrogens on cartons (atom type HC):
> close #0,1,3,4
> ~ribbon
> ~select
> repr stick
> show :LIG z<5
> color byhet
> ~disp HC
>
> See image.  I can see you have two lines drawn to show H-bonds, I guess,
> but they do not look like good H-bonds.  In fact, if you put the mouse over
> the one on the right (in Chimera, not the image), you can see that it is
> 4.9 Angstroms long, which is way too long for a reasonable H-bond.
>
>
> Also your combination model seems to be messed up somehow because it
> thinks the ligands are part of the protein and get put inside the surface
> unless I use some extra commands when trying to show receptor surface
> hydrophobicity.
>
> command: surfcat rec protein
> menu: Presets... interactive 3 (hydrophobicity surface)
> command: surf rec
> command: ~surf :lig
>
> See image.  The pocket on the left is mostly hydrophobic (orange) but the
> one on the right is not.  Also it does not look like the ligands fit the
> pocket shapes very well.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> On Jun 16, 2022, at 11:27 PM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Dear Chimera
>
> Thank you for taking the time to answer my question the other day.
>
> I also apologize for contacting you outside of business hours due to the
> time difference.
>
> I'm Kenji Matsui, a second-year master's student at a national university
> in Japan.
>
> I have shown hydrophobic interactions between ligands and amino acid
> residues, how should I display them?
>
> I refer to these methods.
>
> But, I did not know where to find Examine residues.
>
> Therefore, could you please tell me the location of Examine residues?
>
> If possible, we would appreciate it if you could attach a diagram after
> the operation so that we can confirm the operating procedure.
>
> A:Find hydrophobic interactions
> Select >> Residue(s) (either in entire structure or within a selected set
> (see above $ or %)) >>
> Amino acid category >> hydrophobic >> Action >> Atoms/Bonds >> Show >>
> Examine residues >> Mouse over atoms or Left click on them to identify them
> ---------------------------------------------------------------------------
> 松井 健治
>  東京農工大学大学院 工学府産業技術専攻 修士 2年
> 〒184-8588 東京都小金井市中町2-24-16
>
> 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
> <LXRα_24,25_epoxy_hydrogen_1.85_1.135.py>
>
>
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