Biology Reference
In-Depth Information
180
Atom i denotes atoms on one side of the single bond in consideration, and
atom j those on the other side of the single bond. For there is no
steric hindrance. For it does not necessarily indicate disallowed
configurations, since the minimum allowed van der Waal radii may be
smaller than those listed in Table 7-1, by as much as 0.3 A.
The rotation around the glycosidic bond is denoted by
in Fig. 7-1, but was
by
as illustrated in Fig. 7-2 (Wu, 1968).
Figure 7-2.
Definition of
rotation around the glycosidic bond.
The ring structure of the pyrimidine or purine base lies in the x,z-plane and
below the x,y-plane. It is held stationary. The glycosidic bond lies along
the negative z-axis, with C
1
' of the ribose ring at the origin. At all of
the solid bonds shown in Fig. 7-2 are in the x,z-plane. The angle is
defined as the angle between the x,z-plane and the plane formed by the
glycosidic bond and the C
2
'-C
1
' bond of the ribose ring. The right-hand rule
is used to define the positive direction of for rotation around the z-axis.
The torsion angle defined by Donohue and Trueblood (1960) is roughly
equal to Only those atoms shown in Fig. 7-2 are considered for
steric hindrance calculations.
