Ca virtual torsion angles

Sherry Mowbray mowbray at xray.bmc.uu.se
Tue Jul 1 03:35:57 EST 1997


>Hi,
>
>I've been playing with using the "virtual torsion angle"
>defined by the positions of four consecutive residues'
>alpha carbons to define pieces of structure.
>
>I've heard of other people doing this before.

You might want to look at our paper on this subject.

Ca-based torsion angles: a simple tool to analyze protein conformational
changes. M.M. Flocco and S. L. Mowbray, Protein Science, 4, 2118-2122
(1995)

The approach was by no means new at that point, but we considered it well
worth a revival. This an excellent way of seeing conformational
differences, whether crystallographic or "real". Of course, it is used in
DSSP, to define structure.


>Does anyone know if there's a standard name for this
>angle (ala calling the N..Ca..C..N angle "psi")?

We were lazy and called it "alpha", following DSSP.

>--
>                                   _____________
>                                   |        ___/_
>                                   |        |/  /
>                                   --  /\  //  /--
>                                   ||  ||  /  /||
>                                   ||  || /  / ||
>                                   ||  ||/  /  ||
>John Kuszewski                     ||  |/  /|  ||
>johnk at spasm.niddk.nih.gov          ||  /  /||  ||
>                                   \/ /  / ||  \/
>that's MISTER protein G to you!     |/__/|      |
>                                      /_________|
>
>My parents went to Zaire and all I got
>was this lousy retrovirus.

Sherry Mowbray
Swedish Agricultural University
Department of Molecular Biology
Box 590, Biomedical Center
S-751 24 Uppsala, Sweden

e-mail: mowbray at xray.bmc.uu.se
tele: 46-18-174990 (after 28 June, 1997: 46-18-4714990)
FAX:  46-18-536971





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