[Chimera-users] nonpolar and polar surface area

[Elaine Meng]

Hi Bailey,
As I said before, this is a research judgment call that you should decide for yourself, as different scientists have different opinions, and there is no single universally agreed-upon answer.  You also have to consider what you you want to use these values for.  In the previous replies I mentioned you could already use the words “polar” and “nonpolar” but they are based on one publication and not everybody agrees with which amino acids it puts in those groups, and there was a link to a table listing what they are, as well as the citation of that publication.  Another possibility in Chimera (also described in the previous replies with link to table and literature references) is to use a cutoff in kdHydrophobicity value.

It is beyond the scope of this helpdesk to provide general research consulting. I have semi-informed opinions, but I’m not the oracle.

If you just want to put in your protein and get results for its polar and apolar solvent-accessible surface areas without having to decide what you want to put in each category, take a look at the GetArea web server mentioned in the second link.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 17, 2019, at 8:31 AM, Bailey Onken <onken031 at umn.edu> wrote:
> 
> Thank you for the feedback.
> 
> Could you go into more description as to how to decide and choose which residues are polar and nonpolar. 
> 
> Thank you,
> Bailey 
> 
> On Mon, Sep 16, 2019, 3:52 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Bailey,
> You will have to decide for yourself which residues you want to consider as polar and nonpolar.  Then after you show the surface of the protein, you can select any subset of the residues (or atoms) and then sum the surface area from that subset using the Attribute Calculator tool.
> 
> This is described in more detail in this recent post.  Skip down to the fourth paragraph, starting "However, you can get the total surface area given some range of hydrophobicity values…”
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html>
> 
> Alternatively, you could take a look at the GetArea web server mentioned in this follow-up:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html>
> 
> (I changed the subject line of the message to something more descriptive to help others find it later.)
> 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 16, 2019, at 12:23 PM, Bailey Onken <onken031 at umn.edu> wrote:
> > 
> > Hello,
> > I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. 
> > Thank you very much, 
> > Bailey 
> 
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