Cremer-Pople parameter calculator

Shinya Fushinobu
Copy and paste lines containing the pyranose sugar ring atoms in your PDB file.
The atom names must be C1, C2, C3, C4, C5, and O5.

Paste PDB data here

Note: This page has been moved from ric.hi-ho.ne.jp (April, 2017).

Fixed: Alternative conformers and anisotropic temperature factor lines are now acceptable (July 27, 2010). Try Sample data 3.

Sample data 1

HETATM 7427  C1  LGC A1001     -22.300 -16.746   8.122  1.00 14.56           C  
HETATM 7428  C2  LGC A1001     -22.433 -15.457   8.963  1.00 13.17           C  
HETATM 7429  O5  LGC A1001     -23.134 -17.808   8.338  1.00 14.74           O  
HETATM 7432  C3  LGC A1001     -23.170 -15.692  10.321  1.00 12.67           C  
HETATM 7434  C4  LGC A1001     -24.378 -16.628  10.123  1.00 14.40           C  
HETATM 7436  C5  LGC A1001     -23.853 -17.984   9.599  1.00 15.99           C  

Sample data 2

HETATM 5164  C1  GAL A 701      24.929   6.486  27.826  1.00 35.16           C  
HETATM 5165  C2  GAL A 701      25.427   7.148  26.520  1.00 33.43           C  
HETATM 5166  C3  GAL A 701      25.873   8.603  26.728  1.00 32.63           C  
HETATM 5167  C4  GAL A 701      24.849   9.386  27.561  1.00 34.51           C  
HETATM 5168  C5  GAL A 701      24.545   8.626  28.849  1.00 35.63           C  
HETATM 5169  C6  GAL A 701      23.520   9.351  29.706  1.00 34.95           C  
HETATM 5170  O1  GAL A 701      25.996   6.224  28.665  1.00 39.00           O  
HETATM 5171  O2  GAL A 701      26.523   6.406  26.001  1.00 27.19           O  
HETATM 5172  O3  GAL A 701      26.043   9.235  25.461  1.00 27.16           O  
HETATM 5173  O4  GAL A 701      23.648   9.550  26.819  1.00 32.17           O  
HETATM 5174  O5  GAL A 701      23.998   7.327  28.528  1.00 36.64           O  
HETATM 5175  O6  GAL A 701      23.858   9.281  31.084  1.00 35.65           O  

Sample data 3

HETATM 3018  C2 ABGC A 403      14.424  34.676  29.808  0.65  6.77           C  
ANISOU 3018  C2 ABGC A 403      791   1025    758    249     40   -117       C  
HETATM 3019  C3 ABGC A 403      15.955  34.650  29.541  0.65  6.29           C  
ANISOU 3019  C3 ABGC A 403      875    789    725    266    128    -16       C  
HETATM 3020  C4 ABGC A 403      16.322  34.593  28.056  0.65  6.17           C  
ANISOU 3020  C4 ABGC A 403      768    862    714     13    107      1       C  
HETATM 3021  C5 ABGC A 403      15.090  34.392  27.191  0.65  6.73           C  
ANISOU 3021  C5 ABGC A 403      776    768   1012    118     -2   -157       C  
HETATM 3022  C6 ABGC A 403      14.556  32.942  27.110  0.65  6.40           C  
ANISOU 3022  C6 ABGC A 403      896    857    678    -66      9     18       C  
HETATM 3023  C1 ABGC A 403      13.514  35.268  28.769  0.65  6.62           C  
ANISOU 3023  C1 ABGC A 403      782    945    789    -89    -38      3       C  
HETATM 3024  O2 ABGC A 403      14.168  35.232  31.046  0.65  4.75           O  
ANISOU 3024  O2 ABGC A 403      476    854    475    109      5    -72       O  
HETATM 3025  O3 ABGC A 403      16.439  33.431  30.209  0.65  5.33           O  
ANISOU 3025  O3 ABGC A 403      492    833    701     89   -136   -171       O  
HETATM 3026  O4 ABGC A 403      16.991  35.846  27.653  0.65  6.19           O  
ANISOU 3026  O4 ABGC A 403      790    772    789     65     65    -61       O  
HETATM 3027  O5 ABGC A 403      14.034  35.297  27.467  0.65  6.98           O  
ANISOU 3027  O5 ABGC A 403      794   1073    784    220     95    -33       O  
HETATM 3028  O6 ABGC A 403      13.604  32.850  26.133  0.65  7.98           O  
ANISOU 3028  O6 ABGC A 403      617   1380   1034   -129    -29    -13       O  

Input lines must follow the PDB guideline.
Do not change the COLUMNS of atom name (13-16), x (31-38), y (39-46), and z (47-54) coordinates.

What's Cremer-Pople parameter?

It is the puckering coordinate system of a six-membered pyranose ring [1]. Spherical polar representation (Fig. left; meridian angle φ, azimuthal angle θ, and radius Q) [2] and Stoddart (or "pseudorotational") diagram (Fig. right; projection of the sphere from the North Pole) are generally used. The radius Q means the magnitude of puckering, measuring the deviation from the perfectly flat six-membered ring (Q = 0).
The 38 basic conformations in the IUPAC nomenclature [3] are used to specify sugar ring conformations. They are 2 chair (θ = 0° or 180° at the Poles), 6 boat (θ = 90° on the Equator), 6 skew-boat (θ = 90° on the Equator), 12 envelope (θ = 54.7° in temperate zones), and 12 half-chair (θ = 50.8° in temperate zones) conformations. The Bérces-Whitfield-Nukada system that calculates the parameters as a linear combination of "ideal" basic conformations of "real" sugar rings is also described [4]. For force calculation during molecular simulation, I recommend the Hill-Reilly system [5].

Figure

References

  1. D. Cremer & J. A. Pople: A General Definition of Ring Puckering Coordinates. J. Am. Chem. Soc. 97, 1354-508 (1975) [doi]
  2. G. A. Jeffrey & J. H. Yates: Stereographic representation of the Cremer-Pople ring-puckering parameters for pyranoid rings. Carbohydr. Res. 74, 319-322 (1979) [doi]
  3. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) Conformational nomenclature for five and six-membered ring forms of monosaccharides and their derivatives, Recommendations 1980. Arch. Biochem. Biophys. 207, 469-472 (1981); Eur. J. Biochem. 111, 295-298 (1980); Pure Appl. Chem. 53, 1901-1905 (1981). [URL]
  4. A. Bérces, D. M. Whitfield & T. Nukada: Quantitative description of six-membered ring conformations following the IUPAC conformational nomenclature. Tetrahedron 57, 477-491 (2001) [doi]: A nice server was once available at http://www.nrc.ca/ibs/6ring.html or http://www.sao.nrc.ca/ibs/6ring.html.
  5. A. D. Hill & P. J. Reilly: Puckering Coordinates of Monocyclic Rings by Triangular Decomposition. J. Chem. Inf. Model. 47, 1031-1035 (2007) [doi] [PubMed]
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Thanks to Tony Hill and people of Reilly's lab at ISU (July-October, 2006).