[Chimera-users] Surface exposed residue in a protein assembly

[Elaine Meng]

Hi Alessandro,
If the assembly is opened from a single file, by default Chimera puts a molecular surface around all of the subunits together as one "blob" (does not make an individual surface for each subunit) so it should be the same as what you do for monomers.  I.e. buried residues including the ones in the interfaces should have zero or small surface area.

The hydrophobicity assigned by Chimera is a simple lookup table based only on the residue type.  See "kdHydrophobicity" in this table.
<https://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>

I'm not completely sure what outputs you need, but maybe something like the following steps, which might be the same as you are doing already for monomers:

(1) show the molecular surface so that surface area values are calculated (residue attribute areaSAS for solvent-accessible, or areaSES for solvent-excluded).  See diagram explaining these types of surfaces:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

(2) select residues with area greater than some cutoff value, whatever you think is enough to make the residue a "surface" residue.  E.g. command

select :/areaSAS>50

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>

... or for GUI approach showing the histogram of values in the structure, menu: Select... by Attribute Value.., set to Attributes of "residues", name "areaSAS" or "areaSES" as you prefer, then use the vertical bars to set value range of selection.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select>

(3) write list of selected residues only, and their surface areas, and their hydrophobicity values. Menu:  Tools... Depiction... Render by Attribute, and then in the menu of that tool, File... Save Attribute.  You could save residue areaSAS or areaSES, and then another file with residue kdHydrophobicity.  In the saving dialog, turn on the option "Restrict save to current selection, if any"
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 30, 2021, at 7:06 AM, Alessandro Strofaldi via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Dear Chimera developers, 
> I’m working on a protein complex and I’d like to analyse the SASA and hydrophobicity on the surface.
> I have worked with Chimera before so I know how to do those basic tasks for a monomeric protein; however, since I have five monomers interacting together I was wondering how to calculate the SASA (and later showing the hydrophobic residues of the surface) excluding the monomer-monomer interfacial regions.
> I would also need those values tabulated to show hydrophobicity vs primary sequence but still excluding the monomer-monomer interfaces!
> It seems like there is no basic tool to do that (or am I missing something?); is there any procedure I could apply?
> Unfortunately I can’t code in Python so I’m looking for a solution that involves using the GUI.
> Thank you,
> Best regards,
> Alessandro Strofaldi, PhD
> University of Bristol