What is the glycine sidechain?

Andrew Dalke dalke at ks.uiuc.edu
Tue Mar 5 18:25:40 EST 1996


  It is a simple question, does glycine have a sidechain?  If you say an amino
acid base has an group "R" off the CA which is called a sidechain, then the
answer is, "yes, and the sidechain is a hydrogen".
  I can accept that.  However, as I think I've mentioned here before, I'm
working on a visualization and analysis program (ObPlug:
http://www.ks.uiuc.edu/Research/vmd).  I want to add an atom selection term
called "sidechain" which picks the sidechain atoms.  It works for every case
except glycine, where I have to determine which of the two hydrogens (in an all
atom model, such as charmm-22) is the sidechain.

  Currently I choose the one with the alphabetically smallest name, so for a
charmm-22 model, HC1 is the sidechain and HC2 is not.  One of the researchers
pointed out that I could find the hydrogen which is closest in position to where
a C-beta would be.  The problem is when we compute the molecular dynamics of the
protein I don't know if the closest hydrogen will always be the same one.  I
consider it bad if the sidechain alternates between two atoms.
  Of course, in a reduced atom model, glycine doesn't even have hydrogen off the
CA.

  So, does glycine really have a side chain?  If so, what is the "right"
(IUPAC?) way of finding it?

						Andrew
						dalke at ks.uiuc.edu



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