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Appendix A - Stereochemical parameters

The two tables in this appendix list the stereochemical parameters used in the PROCHECK programs.

TABLE A.1

Stereochemical parameters of Morris et al. (1992), derived from high-resolution protein structures.
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Stereochemical parameter       |     Mean value     | Standard deviation
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                               |                    |                  
phi-psi in most favoured       |                    |                  
regions of Ramachandran plot   |        >90%        |                  
                               |                    |                  
chi1 dihedral angle:           |                    |                  
   gauche minus                |     64.1 degrees   |   15.7 degrees
   trans                       |    183.6 degrees   |   16.8 degrees
   gauce plus                  |    -66.7 degrees   |   15.0 degrees
                               |                    |                  
chi2 dihedral angle            |    177.4 degrees   |   18.5 degrees
                               |                    |                  
Proline phi torsion angle      |    -65.4 degrees   |   11.2 degrees
                               |                    |                  
Helix phi torsion angle        |    -65.3 degrees   |   11.9 degrees
Helix psi torsion angle        |    -39.4 degrees   |   11.3 degrees
                               |                    |                  
chi3 (S-S bridge):             |                    |                  
   right-handed                |    96.8 degrees    |   14.8 degrees
   left-handed                 |   -85.8 degrees    |   10.7 degrees
                               |                    |                  
Disulphide bond separation     |      2.0A          |    0.1A
                               |                    |                  
omega dihedral angle           |   180.0 degrees    |    5.8 degrees
                               |                    |                  
Main-chain hydrogen            |                    |                  
bond energy (kcal/mol)*        |     -2.03          |    0.75            
                               |                    |                  
Calpha chirality: zeta         |                    |                  
``virtual'' torsion angle      | 33.9 degrees       |    3.5 degrees
(Calpha-N-C-Cbeta              |                    |                  
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* Evaluated using the Kabsch & Sander (1983) method.

TABLE A.2

Main-chain bond lengths and bond angles, and their standard deviations, as observed in small molecules (Engh & Huber, 1991). The atom-labelling follows that used in the X-PLOR dictionary, with some additional atom types (marked with an asterisk) as defined by Engh & Huber (1991).

a. Bond lengths

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Bond                    | X-PLOR labelling}                 | Value | sigma 
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C-N                     | C-NH1          | (except Pro)     | 1.329 | 0.014
                        | C-N            | (Pro)            | 1.341 | 0.016
                        |                |                  |       |      
C-O                     | C-O            |                  | 1.231 | 0.020
                        |                |                  |       |      
Calpha-C                | CH1E-C         | (except Gly)     | 1.525 | 0.021
                        | CH2G*-C        | (Gly)            | 1.516 | 0.018
                        |                |                  |       |      
Calpha-Cbeta            | CH1E-CH3E      | (Ala)            | 1.521 | 0.033
                        | CH1E-CH1E      | (Ile,Thr,Val)    | 1.540 | 0.027
                        | CH1E-CH2E      | (the rest)       | 1.530 | 0.020
                        |                |                  |       |      
N-Calpha                | NH1-CH1E       | (except Gly,Pro) | 1.458 | 0.019
                        | NH1-CH2G*      | (Gly)            | 1.451 | 0.016
                        | N-CH1E         | (Pro)            | 1.466 | 0.015
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b. Bond angles

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Angle                   | X-PLOR labelling                  | Value | sigma 
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C-N-Calpha              | C-NH1-CH1E     | (except Gly,Pro) | 121.7 | 1.8
                        | C-NH1-CH2G*    | (Gly)            | 120.6 | 1.7
                        | C-N-CH1E       | (Pro)            | 122.6 | 5.0
                        |                |                  |       |    
Calpha-C-N              | CH1E-C-NH1     | (except Gly,Pro) | 116.2 | 2.0
                        | CH2G*-C-NH1    | (Gly)            | 116.4 | 2.1
                        | CH1E-C-N       | (Pro)            | 116.9 | 1.5
                        |                |                  |       |    
Calpha-C-O              | CH1E-C-O       | (except Gly)     | 120.8 | 1.7
                        | CH2G*-C-O      | (Gly)            | 120.8 | 2.1
                        |                |                  |       |    
Cbeta-Calpha-C          | CH3E-CH1E-C    | (Ala)            | 110.5 | 1.5
                        | CH1E-CH1E-C    | (Ile,Thr,Val)    | 109.1 | 2.2
                        | CH2E-CH1E-C    | (the rest)       | 110.1 | 1.9
                        |                |                  |       |    
N-Calpha-C              | NH1-CH1E-C     | (except Gly,Pro) | 111.2 | 2.8
                        | NH1-CH2G*-C    | (Gly)            | 112.5 | 2.9
                        | N-CH1E-C       | (Pro)            | 111.8 | 2.5
                        |                |                  |       |    
N-Calpha-Cbeta          | NH1-CH1E-CH3E  | (Ala)            | 110.4 | 1.5
                        | NH1-CH1E-CH1E  | (Ile,Thr,Val)    | 111.5 | 1.7
                        | N-CH1E-CH2E    | (Pro)            | 103.0 | 1.1
                        | NH1-CH1E-CH2E  | (the rest)       | 110.5 | 1.7
                        |                |                  |       |    
O-C-N                   | O-C-NH1        | (except Pro)     | 123.0 | 1.6
                        | O-C-N          | (Pro)            | 122.0 | 1.4
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