ID code: '1DCR' 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' C A 2 beta 7 12 10 30 C1' G A 3 beta 26 31 29 52 C1' A A 4 beta 48 53 51 73 C1' A A 5 beta 69 74 72 94 C1' +U A 6 beta 90 95 93 113 C1' G A 7 beta 109 114 112 135 C1' A A 8 beta 131 136 134 156 C1' G A 9 beta 152 157 155 178 C1' G A 10 beta 174 179 177 198 C1' C B 11 beta 194 199 197 217 C1' C B 12 beta 213 218 216 236 C1' G B 13 beta 232 237 235 258 C1' A B 14 beta 254 259 257 279 C1' A B 15 beta 275 280 278 300 C1' +U B 16 beta 296 301 299 319 C1' G B 17 beta 315 320 318 341 C1' A B 18 beta 337 342 340 362 C1' G B 19 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' C A 2 11 8 29 C2' G A 3 30 27 51 C2' A A 4 52 49 72 C2' A A 5 73 70 93 C2' +U A 6 94 91 112 C2' G A 7 113 110 134 C2' A A 8 135 132 155 C2' G A 9 156 153 177 C2' G A 10 178 175 197 C2' C B 11 198 195 216 C2' C B 12 217 214 235 C2' G B 13 236 233 257 C2' A B 14 258 255 278 C2' A B 15 279 276 299 C2' +U B 16 300 297 318 C2' G B 17 319 316 340 C2' A B 18 341 338 361 C2' G B 19 362 359 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 2 OK 6 9 10 27 C3' G A 3 OK 25 28 29 49 C3' A A 4 OK 47 50 51 70 C3' A A 5 OK 68 71 72 91 C3' +U A 6 OK 89 92 93 110 C3' G A 7 OK 108 111 112 132 C3' A A 8 OK 130 133 134 153 C3' G A 9 OK 151 154 155 175 C3' G A 10 OK 173 176 177 195 C3' C B 11 OK 193 196 197 214 C3' C B 12 OK 212 215 216 233 C3' G B 13 OK 231 234 235 255 C3' A B 14 OK 253 256 257 276 C3' A B 15 OK 274 277 278 297 C3' +U B 16 OK 295 298 299 316 C3' G B 17 OK 314 317 318 338 C3' A B 18 OK 336 339 340 359 C3' G B 19 OK 357 360 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 2 OK 8 5 7 25 C4' G A 3 OK 27 24 26 47 C4' A A 4 OK 49 46 48 68 C4' A A 5 OK 70 67 69 89 C4' +U A 6 OK 91 88 90 108 C4' G A 7 OK 110 107 109 130 C4' A A 8 OK 132 129 131 151 C4' G A 9 OK 153 150 152 173 C4' G A 10 OK 175 172 174 193 C4' C B 11 OK 195 192 194 212 C4' C B 12 OK 214 211 213 231 C4' G B 13 OK 233 230 232 253 C4' A B 14 OK 255 252 254 274 C4' A B 15 OK 276 273 275 295 C4' +U B 16 OK 297 294 296 314 C4' G B 17 OK 316 313 315 336 C4' A B 18 OK 338 335 337 357 C4' G B 19 OK 359 356 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 2 4 6 24 C5' G A 3 23 25 46 C5' A A 4 45 47 67 C5' A A 5 66 68 88 C5' +U A 6 87 89 107 C5' G A 7 106 108 129 C5' A A 8 128 130 150 C5' G A 9 149 151 172 C5' G A 10 171 173 192 C5' C B 11 191 193 211 C5' C B 12 210 212 230 C5' G B 13 229 231 252 C5' A B 14 251 253 273 C5' A B 15 272 274 294 C5' +U B 16 293 295 313 C5' G B 17 312 314 335 C5' A B 18 334 336 356 C5' G B 19 355 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 2 distorted distorted 2 3 4 20 P G A 3 distorted distorted 9 21 22 23 42 P A A 4 distorted distorted 28 43 44 45 63 P A A 5 distorted distorted 50 64 65 66 84 P +U A 6 OK OK 71 85 86 87 103 P G A 7 distorted distorted 92 104 105 106 125 P A A 8 distorted distorted 111 126 127 128 146 P G A 9 distorted distorted 133 147 148 149 168 P G A 10 distorted distorted 154 169 170 171 207 P C B 12 distorted distorted 196 208 209 210 226 P G B 13 distorted distorted 215 227 228 229 248 P A B 14 distorted distorted 234 249 250 251 269 P A B 15 distorted distorted 256 270 271 272 290 P +U B 16 OK OK 277 291 292 293 309 P G B 17 distorted distorted 298 310 311 312 331 P A B 18 distorted distorted 317 332 333 334 352 P G B 19 distorted distorted 339 353 354 355 ---------------------------------------------------------------------------------