* B-DNA Cylindrical Polar Coordinates * * File: bdna * updated 1999 October 22 by Tom Schneider * use: in program dnag * https://alum.mit.edu/www/toms/delila/dnag.html * * reference: * * S. Arnott and D. W. L. Hukins * Biochem. and Biophys. Res. Comm 47: 1504-1509 (1972) * "Optimised Parameters for A-DNA and B-DNA" * * This is Table 5 on page 1508. The legend reads: * * Cylindrical polar coordinates of a nucleotide residue in B-DNA. The * coordinate origin is at the intersection of the helix axis and the base-pair * dyad axis. Coordinates of successive nucleotide residues may be obtained by * adding 36.0 degrees to theta and 3.38 angstroms to Z. All base coordinates * refer to one residue: to generate coordinates of the dyadically related * base-pair negate theta and Z. * * group - atom - radius (angstrom) - theta (angle, degrees) - z axis (angstrom) * P = phosphate, D = deoxyribose * A = adenine, G = guanine, C = cytosine, T = thymine * P O1 8.75 97.4 3.63 P O2 10.20 91.1 1.86 P O3 8.82 103.3 1.29 P P1 8.91 95.2 2.08 P O4 7.73 88.0 1.83 D C5 7.70 79.8 2.77 D O5 6.22 66.0 1.83 D C4 7.59 69.9 2.04 D C3 8.20 69.9 0.64 D C2 7.04 73.2 -0.24 D C1 5.86 67.4 0.47 A N9 4.63 76.6 0.42 A C8 4.84 93.0 0.50 A N7 3.95 105.4 0.43 A C5 2.74 94.0 0.28 A N6 1.83 154.0 0.14 A C6 1.41 107.2 0.15 A N1 0.86 40.1 0.03 A C2 2.17 30.6 0.04 A N3 3.24 47.0 0.16 A C4 3.33 70.5 0.28 G N9 4.63 76.6 0.42 G C8 4.82 93.2 0.50 G N7 3.92 105.7 0.42 G C5 2.70 94.0 0.28 G O6 1.71 154.6 0.13 G C6 1.39 109.3 0.15 G N1 0.92 37.9 0.03 G N2 3.01 4.2 -0.10 G C2 2.28 28.7 0.03 G N3 3.29 46.7 0.16 G C4 3.33 70.3 0.28 C N1 4.63 76.6 0.42 C C6 4.99 92.2 0.52 C C5 4.35 107.0 0.47 C N4 2.76 136.6 0.27 C C4 2.94 110.0 0.32 C N3 2.31 83.9 0.22 C O2 3.69 47.9 0.18 C C2 3.40 67.4 0.27 T N1 4.63 76.6 0.42 T C6 5.01 92.3 0.52 T Me 5.40 119.8 0.58 T C5 4.38 106.9 0.47 T O4 2.82 136.3 0.27 T C4 2.98 111.9 0.32 T N3 2.36 85.2 0.23 T O2 3.64 47.8 0.18 T C2 3.42 67.3 0.27