ID code: '1N39' 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' G B 2 beta 26 31 29 52 C1' T B 3 beta 48 53 51 72 C1' A B 4 beta 68 73 71 93 C1' G B 5 beta 89 94 92 115 C1' A B 6 beta 111 116 114 136 C1' C B 7 beta 132 137 135 156 C1' G C 24 beta 152 157 155 178 C1' T C 25 beta 174 179 177 198 C1' C C 26 beta 194 199 197 217 C1' T C 27 beta 213 218 216 237 C1' A C 28 beta 233 238 236 258 C1' C C 29 beta 254 259 257 277 C1' C C 30 beta 273 278 276 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G B 2 30 27 51 C2' T B 3 52 49 71 C2' A B 4 72 69 92 C2' G B 5 93 90 114 C2' A B 6 115 112 135 C2' C B 7 136 133 155 C2' G C 24 156 153 177 C2' T C 25 178 175 197 C2' C C 26 198 195 216 C2' T C 27 217 214 236 C2' A C 28 237 234 257 C2' C C 29 258 255 276 C2' C C 30 277 274 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 27 C3' G B 2 OK 25 28 29 49 C3' T B 3 OK 47 50 51 69 C3' A B 4 OK 67 70 71 90 C3' G B 5 OK 88 91 92 112 C3' A B 6 OK 110 113 114 133 C3' C B 7 OK 131 134 135 153 C3' G C 24 OK 151 154 155 175 C3' T C 25 OK 173 176 177 195 C3' C C 26 OK 193 196 197 214 C3' T C 27 OK 212 215 216 234 C3' A C 28 OK 232 235 236 255 C3' C C 29 OK 253 256 257 274 C3' C C 30 OK 272 275 276 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 25 C4' G B 2 OK 27 24 26 47 C4' T B 3 OK 49 46 48 67 C4' A B 4 OK 69 66 68 88 C4' G B 5 OK 90 87 89 110 C4' A B 6 OK 112 109 111 131 C4' C B 7 OK 133 130 132 151 C4' G C 24 OK 153 150 152 173 C4' T C 25 OK 175 172 174 193 C4' C C 26 OK 195 192 194 212 C4' T C 27 OK 214 211 213 232 C4' A C 28 OK 234 231 233 253 C4' C C 29 OK 255 252 254 272 C4' C C 30 OK 274 271 273 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 24 C5' G B 2 23 25 46 C5' T B 3 45 47 66 C5' A B 4 65 67 87 C5' G B 5 86 88 109 C5' A B 6 108 110 130 C5' C B 7 129 131 150 C5' G C 24 149 151 172 C5' T C 25 171 173 192 C5' C C 26 191 193 211 C5' T C 27 210 212 231 C5' A C 28 230 232 252 C5' C C 29 251 253 271 C5' C C 30 270 272 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G B 2 distorted distorted 6 21 22 23 42 P T B 3 distorted distorted 28 43 44 45 62 P A B 4 distorted distorted 50 63 64 65 83 P G B 5 distorted distorted 70 84 85 86 105 P A B 6 distorted distorted 91 106 107 108 126 P C B 7 distorted distorted 113 127 128 129 146 P G C 24 distorted distorted 147 148 149 168 P T C 25 distorted distorted 154 169 170 171 188 P C C 26 distorted distorted 176 189 190 191 207 P T C 27 distorted distorted 196 208 209 210 227 P A C 28 distorted distorted 215 228 229 230 248 P C C 29 distorted distorted 235 249 250 251 267 P C C 30 distorted distorted 256 268 269 270 ---------------------------------------------------------------------------------