Biology Reference
In-Depth Information
134
Figure 5-13.
Restriction of
φ
to about -60
0
for proline residue.
The calculations for the allowed regions are very sensitive to the value of
the or the angle. This angle is usually assumed to be 110
0
, but
may indeed vary by about 5
0
(Ramakrishnan and Ramachandran, 1965).
In general, for every three-dimensional structure of protein determined by
X-ray diffraction studies, the angles should be calculated from the
atomic coordinates of non-hydrogen atoms, as discussed above, in order to
investigate how the three-dimensional structure can be refined. However,
these angles are usually not listed in the protein data bank,
http://www.rcsb.org/pdb/. In a recent study of the structure of 30S
ribosomal subunits, Wimberly
et al.
(2000) mentioned:
“For the proteins, 95.7% of the residues were in the core or allowed regions
of the Ramachandran plot, 2.4% in the generously allowed region and 1.9%
in the disallowed region.”
The configurations of the 1.9% of disallowed amino acid residues may have
their
angles adjusted to be included in the allowed regions after
refinement.
