ID code: '1M97' 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' --------------------------------------------------------------------------------- 11 C1' G B 21 beta 7 12 10 33 C1' C B 22 beta 29 34 32 52 C1' T B 23 beta 48 53 51 72 C1' A B 24 beta 68 73 71 93 C1' T B 25 beta 89 94 92 113 C1' A B 26 beta 109 114 112 134 C1' C B 27 beta 130 135 133 153 C1' G B 28 beta 149 154 152 175 C1' A B 29 beta 171 176 174 197 C1' T C 8 beta 193 198 196 217 C1' C C 9 beta 213 218 216 236 C1' G C 10 beta 232 237 235 258 C1' T C 11 beta 254 259 257 278 C1' A C 12 beta 274 279 277 299 C1' T C 13 beta 295 300 298 319 C1' A C 14 beta 315 320 318 340 C1' G C 15 beta 336 341 339 362 C1' C C 16 beta 358 363 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 21 11 8 32 C2' C B 22 33 30 51 C2' T B 23 52 49 71 C2' A B 24 72 69 92 C2' T B 25 93 90 112 C2' A B 26 113 110 133 C2' C B 27 134 131 152 C2' G B 28 153 150 174 C2' A B 29 175 172 196 C2' T C 8 197 194 216 C2' C C 9 217 214 235 C2' G C 10 236 233 257 C2' T C 11 258 255 277 C2' A C 12 278 275 298 C2' T C 13 299 296 318 C2' A C 14 319 316 339 C2' G C 15 340 337 361 C2' C C 16 362 359 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 21 OK 6 9 10 30 C3' C B 22 OK 28 31 32 49 C3' T B 23 OK 47 50 51 69 C3' A B 24 OK 67 70 71 90 C3' T B 25 OK 88 91 92 110 C3' A B 26 OK 108 111 112 131 C3' C B 27 OK 129 132 133 150 C3' G B 28 OK 148 151 152 172 C3' A B 29 OK 170 173 174 194 C3' T C 8 OK 192 195 196 214 C3' C C 9 OK 212 215 216 233 C3' G C 10 OK 231 234 235 255 C3' T C 11 OK 253 256 257 275 C3' A C 12 OK 273 276 277 296 C3' T C 13 OK 294 297 298 316 C3' A C 14 OK 314 317 318 337 C3' G C 15 OK 335 338 339 359 C3' C C 16 OK 357 360 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 21 OK 8 5 7 28 C4' C B 22 OK 30 27 29 47 C4' T B 23 OK 49 46 48 67 C4' A B 24 OK 69 66 68 88 C4' T B 25 OK 90 87 89 108 C4' A B 26 OK 110 107 109 129 C4' C B 27 OK 131 128 130 148 C4' G B 28 OK 150 147 149 170 C4' A B 29 OK 172 169 171 192 C4' T C 8 OK 194 191 193 212 C4' C C 9 OK 214 211 213 231 C4' G C 10 OK 233 230 232 253 C4' T C 11 OK 255 252 254 273 C4' A C 12 OK 275 272 274 294 C4' T C 13 OK 296 293 295 314 C4' A C 14 OK 316 313 315 335 C4' G C 15 OK 337 334 336 357 C4' C C 16 OK 359 356 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 21 4 6 27 C5' C B 22 26 28 46 C5' T B 23 45 47 66 C5' A B 24 65 67 87 C5' T B 25 86 88 107 C5' A B 26 106 108 128 C5' C B 27 127 129 147 C5' G B 28 146 148 169 C5' A B 29 168 170 191 C5' T C 8 190 192 211 C5' C C 9 210 212 230 C5' G C 10 229 231 252 C5' T C 11 251 253 272 C5' A C 12 271 273 293 C5' T C 13 292 294 313 C5' A C 14 312 314 334 C5' G C 15 333 335 356 C5' C C 16 355 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 21 distorted distorted 2 3 4 23 P C B 22 distorted distorted 9 24 25 26 42 P T B 23 distorted distorted 31 43 44 45 62 P A B 24 distorted distorted 50 63 64 65 83 P T B 25 distorted distorted 70 84 85 86 103 P A B 26 distorted distorted 91 104 105 106 124 P C B 27 distorted distorted 111 125 126 127 143 P G B 28 distorted distorted 132 144 145 146 165 P A B 29 distorted distorted 151 166 167 168 187 P T C 8 distorted distorted 188 189 190 207 P C C 9 distorted distorted 195 208 209 210 226 P G C 10 distorted distorted 215 227 228 229 248 P T C 11 distorted distorted 234 249 250 251 268 P A C 12 distorted distorted 256 269 270 271 289 P T C 13 distorted distorted 276 290 291 292 309 P A C 14 distorted distorted 297 310 311 312 330 P G C 15 distorted distorted 317 331 332 333 352 P C C 16 distorted distorted 338 353 354 355 ---------------------------------------------------------------------------------