ID code: '1L2D' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 8 C1' G B 1 beta 4 9 7 30 C1' T B 2 beta 26 31 29 50 C1' A B 3 beta 46 51 49 71 C1' G B 4 beta 67 72 70 93 C1' A B 5 beta 89 94 92 114 C1' C B 6 beta 110 115 113 134 C1' G C 19 beta 130 135 133 156 C1' T C 20 beta 152 157 155 176 C1' C C 21 beta 172 177 175 195 C1' T C 22 beta 191 196 194 215 C1' A C 23 beta 211 216 214 236 C1' C C 24 beta 232 237 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 1 8 5 29 C2' T B 2 30 27 49 C2' A B 3 50 47 70 C2' G B 4 71 68 92 C2' A B 5 93 90 113 C2' C B 6 114 111 133 C2' G C 19 134 131 155 C2' T C 20 156 153 175 C2' C C 21 176 173 194 C2' T C 22 195 192 214 C2' A C 23 215 212 235 C2' C C 24 236 233 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 27 C3' T B 2 OK 25 28 29 47 C3' A B 3 OK 45 48 49 68 C3' G B 4 OK 66 69 70 90 C3' A B 5 OK 88 91 92 111 C3' C B 6 OK 109 112 113 131 C3' G C 19 OK 129 132 133 153 C3' T C 20 OK 151 154 155 173 C3' C C 21 OK 171 174 175 192 C3' T C 22 OK 190 193 194 212 C3' A C 23 OK 210 213 214 233 C3' C C 24 OK 231 234 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 25 C4' T B 2 OK 27 24 26 45 C4' A B 3 OK 47 44 46 66 C4' G B 4 OK 68 65 67 88 C4' A B 5 OK 90 87 89 109 C4' C B 6 OK 111 108 110 129 C4' G C 19 OK 131 128 130 151 C4' T C 20 OK 153 150 152 171 C4' C C 21 OK 173 170 172 190 C4' T C 22 OK 192 189 191 210 C4' A C 23 OK 212 209 211 231 C4' C C 24 OK 233 230 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 24 C5' T B 2 23 25 44 C5' A B 3 43 45 65 C5' G B 4 64 66 87 C5' A B 5 86 88 108 C5' C B 6 107 109 128 C5' G C 19 127 129 150 C5' T C 20 149 151 170 C5' C C 21 169 171 189 C5' T C 22 188 190 209 C5' A C 23 208 210 230 C5' C C 24 229 231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P T B 2 distorted distorted 6 21 22 23 40 P A B 3 distorted distorted 28 41 42 43 61 P G B 4 distorted distorted 48 62 63 64 83 P A B 5 distorted distorted 69 84 85 86 104 P C B 6 distorted distorted 91 105 106 107 124 P G C 19 distorted distorted 125 126 127 146 P T C 20 distorted distorted 132 147 148 149 166 P C C 21 distorted distorted 154 167 168 169 185 P T C 22 distorted distorted 174 186 187 188 205 P A C 23 distorted distorted 193 206 207 208 226 P C C 24 distorted distorted 213 227 228 229 ---------------------------------------------------------------------------------