Altona-Sundaralingam parameter calculator

Shinya Fushinobu

This site calculates the parameters of furanose ring conformation.
Copy and paste lines containing furanose sugar ring atoms in your PDB file.
The atom names must be C1-4, and O4 for a standard aldofuranose (ribose, xylofuranose, or arabinofuranose). For a ketofuranose (e.g., fructose), the ring atom names must be C2-5 and O5.

Select furanose type:

Standard
(C1, C2, C3, C4, and O4)

Fructose
(C2, C3, C4, C5 and O5)

Nucleotides (DNA, RNA, ATP etc.)
(C1', C2', C3', C4' and O4')

NADH adenosine ribose
(C1B, C2B, C3B, C4B and O4B)

NADH nicotinamide ribose
(C1D, C2D, C3D, C4D and O4D)

Paste PDB data ->

Note: Error reports are welcome (Semtember, 2021).

Sample data 1 (Standard)

HETATM 3632  C1  BXX A 602      20.048  19.283   5.331  1.00 32.19           C
HETATM 3639  C2  BXX A 602      19.621  18.280   4.247  1.00 30.41           C
HETATM 3637  C3  BXX A 602      18.523  19.023   3.508  1.00 31.64           C
HETATM 3634  C4  BXX A 602      18.885  20.497   3.706  1.00 30.78           C
HETATM 3633  O4  BXX A 602      19.404  20.538   5.023  1.00 32.68           O
HETATM 3631  O1  BXX A 602      19.720  18.886   6.687  1.00 34.55           O
HETATM 3635  C5  BXX A 602      17.763  21.513   3.515  1.00 30.88           C
HETATM 3636  O5  BXX A 602      16.688  21.216   4.401  1.00 28.49           O
HETATM 3638  O3  BXX A 602      18.416  18.667   2.097  1.00 26.17           O
HETATM 3640  O2  BXX A 602      19.296  16.928   4.714  1.00 25.23           O

Sample data 2 (Fructose)

HETATM 3639  C2  FRU A 702      20.290  19.543   5.543  1.00 25.30           C
HETATM 3636  C3  FRU A 702      20.076  18.440   4.492  1.00 22.03           C
HETATM 3634  C4  FRU A 702      18.960  19.071   3.628  1.00 21.36           C
HETATM 3633  C5  FRU A 702      19.094  20.577   3.834  1.00 21.41           C
HETATM 3638  O5  FRU A 702      19.405  20.619   5.184  1.00 22.23           O
HETATM 3631  O6  FRU A 702      16.779  21.110   4.404  1.00 20.39           O
HETATM 3632  C6  FRU A 702      17.891  21.458   3.553  1.00 21.24           C
HETATM 3635  O4  FRU A 702      18.915  18.625   2.220  1.00 19.36           O
HETATM 3637  O3  FRU A 702      19.723  17.060   4.944  1.00 19.69           O
HETATM 3640  O2  FRU A 702      20.089  19.046   6.903  1.00 23.16           O
HETATM 3641  C1  FRU A 702      21.659  20.281   5.378  1.00 27.10           C
HETATM 3642  O1  FRU A 702      22.737  19.429   5.694  1.00 29.49           O

Sample data 3 (DNA)

ATOM   2129  O5'  DT N   1      -6.208  19.857  60.270  1.00 93.16           O  
ANISOU 2129  O5'  DT N   1    12950  11912  10532   -829   2239   -113       O  
ATOM   2130  C5'  DT N   1      -7.045  21.005  60.455  1.00 94.56           C  
ANISOU 2130  C5'  DT N   1    12944  12325  10659   -601   2291   -124       C  
ATOM   2131  C4'  DT N   1      -6.454  22.019  61.428  1.00 93.35           C  
ANISOU 2131  C4'  DT N   1    13035  11887  10544   -435   2285      9       C  
ATOM   2132  O4'  DT N   1      -6.137  21.394  62.702  1.00 92.77           O  
ANISOU 2132  O4'  DT N   1    13231  11548  10468   -668   2343      6       O  
ATOM   2133  C3'  DT N   1      -5.132  22.665  61.028  1.00 91.45           C  
ANISOU 2133  C3'  DT N   1    12975  11371  10398   -258   2159    159       C  
ATOM   2134  O3'  DT N   1      -5.328  23.666  60.024  1.00 92.03           O  
ANISOU 2134  O3'  DT N   1    12903  11606  10456     40   2132    205       O  
ATOM   2135  C2'  DT N   1      -4.734  23.268  62.371  1.00 90.86           C  
ANISOU 2135  C2'  DT N   1    13153  11041  10329   -249   2205    218       C  
ATOM   2136  C1'  DT N   1      -5.140  22.167  63.359  1.00 91.31           C  
ANISOU 2136  C1'  DT N   1    13293  11061  10337   -534   2285    133       C  
ATOM   2137  N1   DT N   1      -3.995  21.282  63.846  1.00 89.91           N  
ANISOU 2137  N1   DT N   1    13400  10574  10186   -688   2214    172       N  
ATOM   2138  C2   DT N   1      -2.965  21.810  64.626  1.00 88.97           C  
ANISOU 2138  C2   DT N   1    13510  10202  10089   -610   2156    251       C  
ATOM   2139  O2   DT N   1      -2.885  22.983  64.969  1.00 88.78           O  
ANISOU 2139  O2   DT N   1    13504  10146  10080   -462   2176    292       O  
ATOM   2140  N3   DT N   1      -1.990  20.906  64.998  1.00 88.14           N  
ANISOU 2140  N3   DT N   1    13630   9890   9966   -702   2078    264       N  
ATOM   2141  C4   DT N   1      -1.933  19.554  64.691  1.00 88.57           C  
ANISOU 2141  C4   DT N   1    13762   9909   9979   -852   2070    228       C  
ATOM   2142  O4   DT N   1      -1.011  18.832  65.076  1.00 87.86           O  
ANISOU 2142  O4   DT N   1    13913   9626   9841   -863   2000    251       O  
ATOM   2143  C5   DT N   1      -3.031  19.064  63.883  1.00 89.53           C  
ANISOU 2143  C5   DT N   1    13668  10257  10092   -978   2158    147       C  
ATOM   2144  C7   DT N   1      -3.091  17.619  63.480  1.00 89.97           C  
ANISOU 2144  C7   DT N   1    13821  10272  10089  -1185   2193     85       C  
ATOM   2145  C6   DT N   1      -3.988  19.935  63.507  1.00 90.20           C  
ANISOU 2145  C6   DT N   1    13474  10601  10195   -895   2215    114       C

Sample data 4 (NADH)

HETATM11465  PA  NAI A 401     -32.220 -16.579   6.480  1.00 21.60           P  
HETATM11466  O1A NAI A 401     -30.874 -16.161   5.916  1.00 22.93           O  
HETATM11467  O2A NAI A 401     -32.770 -17.924   6.155  1.00 23.29           O  
HETATM11468  O5B NAI A 401     -32.170 -16.364   8.047  1.00 22.56           O  
HETATM11469  C5B NAI A 401     -33.301 -16.505   8.885  1.00 23.85           C  
HETATM11470  C4B NAI A 401     -32.881 -16.983  10.262  1.00 21.56           C  
HETATM11471  O4B NAI A 401     -34.076 -17.051  11.054  1.00 22.54           O  
HETATM11472  C3B NAI A 401     -32.205 -18.340  10.280  1.00 21.39           C  
HETATM11473  O3B NAI A 401     -30.851 -18.199  10.715  1.00 20.03           O  
HETATM11474  C2B NAI A 401     -33.046 -19.145  11.241  1.00 22.62           C  
HETATM11475  O2B NAI A 401     -32.323 -20.027  12.115  1.00 23.85           O  
HETATM11476  C1B NAI A 401     -33.769 -18.045  12.015  1.00 22.36           C  
HETATM11477  N9A NAI A 401     -34.951 -18.594  12.674  1.00 21.39           N  
HETATM11478  C8A NAI A 401     -35.825 -19.493  12.181  1.00 23.94           C  
HETATM11479  N7A NAI A 401     -36.747 -19.794  13.117  1.00 24.54           N  
HETATM11480  C5A NAI A 401     -36.476 -19.056  14.209  1.00 22.64           C  
HETATM11481  C6A NAI A 401     -37.021 -18.884  15.572  1.00 22.90           C  
HETATM11482  N6A NAI A 401     -38.121 -19.536  15.956  1.00 22.37           N  
HETATM11483  N1A NAI A 401     -36.405 -18.031  16.427  1.00 22.75           N  
HETATM11484  C2A NAI A 401     -35.319 -17.336  16.062  1.00 24.15           C  
HETATM11485  N3A NAI A 401     -34.757 -17.436  14.836  1.00 22.97           N  
HETATM11486  C4A NAI A 401     -35.281 -18.282  13.905  1.00 22.35           C  
HETATM11487  O3  NAI A 401     -33.349 -15.510   6.011  1.00 19.91           O  
HETATM11488  PN  NAI A 401     -32.967 -13.988   5.619  1.00 19.27           P  
HETATM11489  O1N NAI A 401     -32.107 -13.369   6.682  1.00 17.81           O  
HETATM11490  O2N NAI A 401     -32.539 -13.943   4.164  1.00 19.26           O  
HETATM11491  O5D NAI A 401     -34.477 -13.415   5.609  1.00 17.59           O  
HETATM11492  C5D NAI A 401     -35.131 -13.085   6.851  1.00 17.27           C  
HETATM11493  C4D NAI A 401     -36.259 -12.086   6.537  1.00 17.94           C  
HETATM11494  O4D NAI A 401     -35.695 -10.969   5.857  1.00 20.00           O  
HETATM11495  C3D NAI A 401     -37.298 -12.632   5.572  1.00 18.07           C  
HETATM11496  O3D NAI A 401     -38.580 -12.213   5.999  1.00 16.78           O  
HETATM11497  C2D NAI A 401     -36.909 -12.074   4.191  1.00 19.24           C  
HETATM11498  O2D NAI A 401     -38.019 -11.859   3.340  1.00 18.10           O  
HETATM11499  C1D NAI A 401     -36.271 -10.745   4.564  1.00 20.72           C  
HETATM11500  N1N NAI A 401     -35.214 -10.256   3.724  1.00 23.44           N  
HETATM11501  C2N NAI A 401     -35.129  -8.932   3.501  1.00 30.76           C  
HETATM11502  C3N NAI A 401     -34.113  -8.334   2.694  1.00 31.80           C  
HETATM11503  C7N NAI A 401     -34.069  -6.831   2.411  1.00 30.30           C  
HETATM11504  O7N NAI A 401     -33.383  -6.329   1.494  1.00 27.00           O  
HETATM11505  N7N NAI A 401     -34.809  -6.019   3.196  1.00 29.60           N  
HETATM11506  C4N NAI A 401     -33.144  -9.222   2.161  1.00 36.58           C  
HETATM11507  C5N NAI A 401     -33.221 -10.606   2.465  1.00 34.36           C  
HETATM11508  C6N NAI A 401     -34.263 -11.090   3.254  1.00 30.54           C

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 Altona-Sundaralingam parameter?

It is the puckering coordinate system of a five-membered furanose ring [1,2]. φ_m (or γ_m) means the magnitude of puckering. P means the phase angle. Ribose of nucleic acids frequently takes C2'-endo (²E, P ~ 160°) or C3'-endo (³E, P ~ 18°) conformation.

References

C. Altona & M. Sundaralingam: Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94, 8205-12 (1972) [doi ]

H.A. Taha, M.R. Richards & T.L. Lowary: Conformational analysis of furanoside-containing mono- and oligosaccharides. Chem. Rev. 113, 1851-76 (2013) [doi ]

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