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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".


:   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 )

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


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 


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