Help for a rookie? (peptide sequences)

Rob Miller rmiller at
Thu Sep 14 07:23:35 EST 1995

Mark Haythorn (MHAYTHOR at wrote:

: I've been given a 5-amino acid sequence and need to make a
: 3-dimensional picture of it.  Suppose I had Phe-Ala-Glu-Val-Tyr; what
: would it look like in 3-D?  What if I added a hydroxly group or a
: Fluorine to one of the amino acids?  What would it do?

 It's one thing to know how the individual atoms are connected
up, but quite another to really know what the 3D structure of 
the peptide would be -- if such a short piece really has any.
It sounds like you probably don't want to do a quick synthesis 
and pop it into a 2D NMR for a few months (?) project.  I 
would suggest inding some proteins which (a) have the sequence
you're interested in and (b) have a known structure.  You can 
then get the PDB (Brookhaven Protein Data Bank, structs available
by ftp but don't know the site offhand) file, clip out the 
piece you want (edit the file), then use Raswin to to view it.
You'll still be vulnerable to arguments that the larger protein
microenvironment is affecting the structure, but oh well -- if 
you have multiple examples from *different* proteins that 
would help.  Fluorine or hydroxyl group on the end ?  Well,
maybe you could do a molecular dynamics simulation starting 
from the structure(s) you hacked up above, with the added atoms
and a few hydrogens to keep everybdy happy, but don't expect
me to believe your results :-)


Rob Miller, Ph.D.  

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

Tel: +44 171419 3896           Fax: +44 171380 7193

Internet: rmiller at

More information about the Proteins mailing list