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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.

Part 1. Residue information

The first part of the residue-by-residue listing (the .out file) deals with a number of stereochemical parameters, as will be described below.

Explanatory notes. 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).

Residue-by-residue information. 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 ideal.

The information shown for each residue is as follows:

1. Residue number
as given in the original coordinates file.
2. Chain identifier
where relevant, picked up from the original coordinates file.
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     
                                 (ie disallowed)
6. Chi-1 dihedral angle
three separate columns are given for the three possible conformations of chi-1: gauche minus, trans, and gauche plus.
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 assignment code.
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 left-handed conformations.
12. Disulph bond
sulphur-sulphur distance, in A, between paired cysteine residues.
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 bond.
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.
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.

Part 2. Main-chain bond lengths and bond angles

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.

Part 3. Bad contacts listing

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 one another.

Part 4. Summary statistics and quality assessment

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.

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