PROCHECK Operating Manual
Appendix D - Residue-by-residue listing
An example of a residue-by-residue listing is given here. The different parts of it are described
in detail below. Some of the key figures are shown on a separate summary page.
The first part of the residue-by-residue listing (the .out file)
deals with a number of stereochemical parameters, as will be described
The first page gives some explanatory notes
about the stereochemical parameters used. These notes include the
"ideal" values, and corresponding standard deviations, against
which the values calculated for your structure are compared. The
"ideals" used here come from an analysis of 118 high-resolution
structures performed by Morris et
al. (1992), and are listed in Table 1 of Appendix A.
Note that, the printing of this explanatory text can be suppressed, if
required, by amending the parameter file procheck.prm (see Customizing the PROCHECK plots).
The explanatory text is followed by an analysis of each of the
stereochemical parameters for each residue in the structure. Each value is
highlighted by asterisks and plus-signs if it deviates from the
"ideal" by more than 1 standard deviation. An asterisk
represents one standard deviation, and a plus-sign represents
half a standard deviation. So, a highlight such as +***
indicates that the value of the parameter is between 3.5 and
4.0 standard deviations from the ideal. Where the deviation is more
than 4.5 standard deviations, its numerical value is shown instead:
for example, *5.5* represents 5.5 standard deviations.
The appearance of the listing can be altered to some extent by editing
the parameter file procheck.prm (see Customizing
the PROCHECK plots). This allows you to show, say, only the asterisks
and not have the values themselves printed. You can also include only those
values that are more than a given number of standard deviations from the
The information shown for each residue is as follows:
At the end of this print-out, the column totals show the maximum deviation
in each column, the column's mean value and standard deviation, and number
of values it contains. If the mean values themselves deviate significantly
from the "ideals", they too are highlighted by asterisks.
1. Residue number
- as given in the original coordinates
2. Chain identifier
- where relevant, picked up from the original
3. Sequential number
- starting at 1 for the first residue and
numbering the residues sequentially from then on. This may differ from the
residue numbering given in the original coordinates file.
4. Kabsch & Sander secondary structure assignment
assignment of secondary structure according to the method of Kabsch & Sander (1983). The codes used
are as follows:
B - residue in isolated beta-bridge S - bend
E - extended strand, participates T - hydrogen-bonded turn
in beta-ladder e - extension of beta-strand
G - 3-helix (3/10 helix) g - extension of 3/10 helix
H - 4-helix (alpha-helix) h - extension of alpha-helix
I - 5-helix (pi-helix)
The lower-case assignments are our extensions of the Kabsch & Sander
definition and are obtained by slightly relaxing their criteria.
5. Region of Ramachandran plot
- a single letter code identifies
which region of the Ramachandran plot the residue is in. For end residues
and glycines this assignment does not apply, so is shown by a hyphen, `-'.
The other codes are as follows:
A - Core alpha L - Core left-handed alpha
a - Allowed alpha l - Allowed left-handed alpha
~a - Generous alpha ~l - Generous left-handed alpha
B - Core beta p - Allowed epsilon
b - Allowed beta ~p - Generous epsilon
~b - Generous beta XX - Outside major areas
6. Chi-1 dihedral angle
- three separate columns are given for
the three possible conformations of chi-1: gauche minus, trans, and gauche
7. Chi-2 dihedral angle
- only the values for the chi-2 dihedral
angles in the trans conformation are shown.
8. Proline phi
- the phi torsion angle for proline residues only.
9. Phi helix
- the phi torsion angle for all residues identified as being
in an alpha-helix by the H of the Kabsch & Sander secondary structure
10. Helix psi
- as above, but for the psi torsion angle.
11. Chi-3 dihedral angle
- being the torsion angle defined by the S-S
bridge in a disulphide bond, with separate columns for the right- and
12. Disulph bond
- sulphur-sulphur distance, in A, between paired cysteine
13. H-bond en.
- estimated strength of the main-chain hydrogen
bond (in kcal/mol), where applicable, calculated using the method of Kabsch & Sander (1983).
14. Chirality C-alpha
- value of the zeta "virtual"
torsion angle, defined by the atoms Calpha, N, C, and Cbeta. This is a
"virtual" torsion angle as it is not defined along an actual
15. Bad contacts
- number of bad contacts for this residue, as
defined by non-bonded atoms at a distance of <= 2.6A. The bad contacts
are listed at the end of the print-out (see Part 3 below).
16. Max dev
- this shows the maximum deviation (in terms of asterisks, etc)
of all the columns in the current row.
The second part of the listing analyses the main-chain bond lengths and
bond angles of your protein structure. As before, any deviations in the
actual bond-lengths and bond angles from the "ideal" values are highlighted
with asterisks and plus signs.
At the end of this print-out, the different bond lengths and bond angles
are summarised in two tables giving the minimum, maximum, and mean values
of each type, together with their standard deviations.
The "ideal" values used are given at the head of the listing
(though the printing of these can be suppressed by amending the parameter
file procheck.prm). The ideals are as determined from the analysis of
small-molecule data by Engh & Huber
(1991) and are shown in Table 2 of Appendix A.
The bad contacts listing shows the
atom-pairs involved, the type of contact, and the separation between the
two atoms. As already mentioned, bad contacts are defined here as any pair
of non-bonded atoms that are at a distance of <=2.6Å from
The final part of the print-out
reproduces the statistics printed on Plots 1, 4 and 5 (Sample Plots). It also gives an overall
assessment of the structure's quality using the Morris et al. (1992) stereochemical
classification scheme. Here a number from 1 to 4 is assigned
to the structure for each of three separate stereochemical parameters
(1 being the best and 4 the worst score). Finally, it prints
an analysis of the various overall G-factors calculated for the
structure. Any G-factors below -1.0 may indicate properties
that need to be investigated more closely.
PROCHECK Operating Manual