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What is the glycine sidechain?

Rob Miller rmiller at bsm.bioc.ucl.ac.uk
Wed Mar 6 11:25:18 EST 1996


Andrew Dalke (dalke at ks.uiuc.edu) wrote:
:   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".

<snip>

:   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.


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



Normally occurring amino acids have L-chirality, so I'd base it on that.
Jane Richardson's `Anatomy and Taxonomy of Protein Structure' (think that's
the name) paper gives a `corn crib' model for correct L-amino acid chirality; 
looking along the H-Calpha bond for an amino acid with an R group, you
would see:

  

        C=O   R
         \   /
           H               ( the C-alpha is behind the H; read `corn' clockwise )
           |
           N



This is also how we build `virtual' Glycine C-betas for various modelling
and analysis tasks here.



						rob.

--
-----------------------------------------------------
Rob Miller, Ph.D.  

"...life too closely scrutinized 
                    will lead to madness or suicide."

                              Mihaly Csikszentmihalyi

Biomolecular Structure and Modelling Unit (BSM),
Department of Biochemistry and Molecular Biology,
University College / Gower Street / London WC1E 6BT.
United Kingdom.

Tel: +44 171419 3890           Fax: +44 171380 7193

Internet: rmiller at bsm.bioc.ucl.ac.uk 
http://www.biochem.ucl.ac.uk/~rmiller

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