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6. Residue properties plot
Description
The various graphs and diagrams on this plot show how the protein's
geometrical properties vary along its sequence. This gives a visualization
of which regions appear to have consistently poor or unusual geometry
(perhaps because they are poorly defined) and which have more normal
geometry.
The properties plotted are:-
- Graphs a-c: Stereochemical properties
The first three graphs at the top of the page show:
1. Absolute deviation from mean Chi-1 value (excl. Pro)
2. Absolute deviation from mean of omega torsion
3. C-alpha chirality: abs. deviation of zeta torsion
For each graph, unusual values (usually those more than 2.0
standard deviations away from the "ideal" mean value) are shown
highlighted.
- Graph d: Secondary structure & average estimated accessibility
The secondary structure plot shows a schematic representation
of the Kabsch & Sander (1983)
secondary structure assignments. The key just below the picture shows which
structure is which. Beta strands are taken to include all residues with a
Kabsch & Sander assignment of E, helices corresponds to both
H and G assignments, while everything else is taken to be
random coil.
The shading behind the schematic picture gives an approximation
to the residue accessibilities. The approximation is a fairly
crude one, being based on each residue's Ooi number (Nishikawa
& Ooi, 1986). An Ooi number is a count of the number of
other Calpha atoms within a radius of, in this case,
14Å of the given residue's own
Calpha. Although crude, this does give a good impression of
which parts of the structure are buried and which are exposed on the
surface. Future versions of PROCHECK will include an accurate
calculation of residue accessibility.
- Graph e: Sequence & Ramachandran regions
The next section shows the sequence of the structure (using the
20 standard one-letter amino-acid codes) and a set of markers that
identify the region of the Ramachandran
plot in which each residue is located. There are four
marker types, one for each of the four different types of region:
core (ie most favoured), allowed,
generous and
disallowed.
- Graph f: Max. deviation
The small histogram of asterisks and plus-signs shows each
residue's maximum deviation from one of the ideal values given on
the residue-by-residue listing in the
.out file. Refer to the final column of the .out file to see
which is the parameter that deviates by the amount shown here.
- Graph g: G-factors
The shaded squares give a schematic representation of each residue's
G-factor
values. (Note that the chi-1 G-factors are shown only
for those residues that do not have a chi-2, and hence no
chi1-chi2 G-factor).
Regions with many dark squares correspond to regions where the properties
are "unusual", as defined by a low (or negative)
G-factor. These may correspond to highly mobile or poorly
defined regions such as loops, or may need further investigation.
Reference
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Nishikawa K and Ooi T (1986). Radial locations of
amino-acid residues in a globular protein - correlation with the
sequence. J. Biochem., 100, 1043-1047.
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Sep 1995
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