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PROCHECK sample plots
Plot 6. Residue properties
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: Optional properties
The first three graphs at the top of the page, can be selected from
14 possibles by the user. The three default graphs, which are
plotted when you first run PROCHECK, are the first three of:-
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
4. Absolute deviation from mean of H-bond energy
5. Gamma atom B-value
6. Average B-value of main-chain atoms
7. Average B-value of side-chain atoms
8. G-factor for phi-psi distribution
9. G-factor for chi1-chi2 distribution
10. Residue-by-residue G-factor
11. Approx. accessibility (estimated by Ooi numbers)
12. Percentage residue main-chain accessibility
13. Standard deviation of main-chain B-values
14. Standard deviation of side-chain B-values
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.
Options
The main options for the plot are:-
- Which 3 of 14 plots to be printed in the 3 main graphs at the top of
the page.
- Number of standard deviations for highlighting outliers (default is
2.0).
- The plot can be in colour or black-and-white.
These options can be altered by editing the parameter file,
procheck.prm, as described here.
PROCHECK sample plots
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