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Novel 3-D Ramachandran Plot

IP.com Disclosure Number: IPCOM000101378D
Original Publication Date: 1990-Aug-01
Included in the Prior Art Database: 2005-Mar-16
Document File: 2 page(s) / 53K

Publishing Venue

IBM

Related People

Jackman, T: AUTHOR [+2]

Abstract

Disclosed is a novel 3-D Ramachandran plot for biochemists. The standard Ramachandran plot for polypeptides indicates (Image Omitted) stable conformations as a function of d and c on a 2-D plot. d corresponds to the angle of rotation of the Ca - N bond, and c to the angle of rotation of the Ca - C bond. In addition, sometimes contours of n are shown as a function of c and d, where n is the number of units per turn of a helical molecule.

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Novel 3-D Ramachandran Plot

       Disclosed is a novel 3-D Ramachandran plot for
biochemists. The standard Ramachandran plot for polypeptides
indicates

                            (Image Omitted)

 stable conformations as a
function of d and c on a 2-D plot. d corresponds to the angle of
rotation of the Ca - N bond, and c to the angle of rotation of
the Ca - C bond.  In addition, sometimes contours of n are shown as a
function of c and d, where n is the number of units per turn of
a helical molecule.

      This 25-year-old plot can be updated with modern computer
graphics, and a complement to this plot is presented here which may
be of use to students, researchers, and introductory biochemistry
textbook publishers.  The plot contains the usual d, c angles as its
x and y axis. However, we present additional information.  d, the
distance traversed parallel to the helix axis per unit, is
represented as height in a 3-D plot, a function of d and c. Small
values of d are at the bottom left of the figure.  In addition, we
present contours of n mapped to the surface of the d=f(c, d) plot.
In this way, d, d, c and n values are all shown in one plot.
A student or researcher wishing to understand how deviations in phi
and psi effect n and d simply moves his eye along the surface of the
plot. Previously, researchers resorted to several plots, and often
had to plot n and d as two separate lines for a constant phi value.

      In order to he...