ID code: '2AW8' 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 A 1 beta 7 12 10 33 C1' G A 2 beta 29 34 32 55 C1' G A 3 beta 51 56 54 77 C1' G A 4 beta 73 78 76 99 C1' G A 5 beta 95 100 98 121 C1' C A 6 beta 117 122 120 140 C1' C A 7 beta 136 141 139 159 C1' C A 8 beta 155 160 158 178 C1' C A 9 beta 174 179 177 196 C1' C A 10 beta 193 197 195 216 C1' G B 1 beta 212 217 215 238 C1' G B 2 beta 234 239 237 260 C1' G B 3 beta 256 261 259 282 C1' G B 4 beta 278 283 281 304 C1' G B 5 beta 300 305 303 326 C1' C B 6 beta 322 327 325 345 C1' C B 7 beta 341 346 344 364 C1' C B 8 beta 360 365 363 383 C1' C B 9 beta 379 384 382 401 C1' C B 10 beta 398 402 400 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 11 8 32 C2' G A 2 33 30 54 C2' G A 3 55 52 76 C2' G A 4 77 74 98 C2' G A 5 99 96 120 C2' C A 6 121 118 139 C2' C A 7 140 137 158 C2' C A 8 159 156 177 C2' C A 9 178 175 195 C2' C A 10 196 194 215 C2' G B 1 216 213 237 C2' G B 2 238 235 259 C2' G B 3 260 257 281 C2' G B 4 282 279 303 C2' G B 5 304 301 325 C2' C B 6 326 323 344 C2' C B 7 345 342 363 C2' C B 8 364 361 382 C2' C B 9 383 380 400 C2' C B 10 401 399 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 30 C3' G A 2 OK 28 31 32 52 C3' G A 3 OK 50 53 54 74 C3' G A 4 OK 72 75 76 96 C3' G A 5 OK 94 97 98 118 C3' C A 6 OK 116 119 120 137 C3' C A 7 OK 135 138 139 156 C3' C A 8 OK 154 157 158 175 C3' C A 9 OK 173 176 177 194 C3' C A 10 192 195 213 C3' G B 1 OK 211 214 215 235 C3' G B 2 OK 233 236 237 257 C3' G B 3 OK 255 258 259 279 C3' G B 4 OK 277 280 281 301 C3' G B 5 OK 299 302 303 323 C3' C B 6 OK 321 324 325 342 C3' C B 7 OK 340 343 344 361 C3' C B 8 OK 359 362 363 380 C3' C B 9 OK 378 381 382 399 C3' C B 10 397 400 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 28 C4' G A 2 OK 30 27 29 50 C4' G A 3 OK 52 49 51 72 C4' G A 4 OK 74 71 73 94 C4' G A 5 OK 96 93 95 116 C4' C A 6 OK 118 115 117 135 C4' C A 7 OK 137 134 136 154 C4' C A 8 OK 156 153 155 173 C4' C A 9 OK 175 172 174 192 C4' C A 10 OK 194 191 193 211 C4' G B 1 OK 213 210 212 233 C4' G B 2 OK 235 232 234 255 C4' G B 3 OK 257 254 256 277 C4' G B 4 OK 279 276 278 299 C4' G B 5 OK 301 298 300 321 C4' C B 6 OK 323 320 322 340 C4' C B 7 OK 342 339 341 359 C4' C B 8 OK 361 358 360 378 C4' C B 9 OK 380 377 379 397 C4' C B 10 OK 399 396 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 27 C5' G A 2 26 28 49 C5' G A 3 48 50 71 C5' G A 4 70 72 93 C5' G A 5 92 94 115 C5' C A 6 114 116 134 C5' C A 7 133 135 153 C5' C A 8 152 154 172 C5' C A 9 171 173 191 C5' C A 10 190 192 210 C5' G B 1 209 211 232 C5' G B 2 231 233 254 C5' G B 3 253 255 276 C5' G B 4 275 277 298 C5' G B 5 297 299 320 C5' C B 6 319 321 339 C5' C B 7 338 340 358 C5' C B 8 357 359 377 C5' C B 9 376 378 396 C5' C B 10 395 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 23 P G A 2 distorted distorted 9 24 25 26 45 P G A 3 distorted distorted 31 46 47 48 67 P G A 4 distorted distorted 53 68 69 70 89 P G A 5 distorted distorted 75 90 91 92 111 P C A 6 distorted distorted 97 112 113 114 130 P C A 7 distorted distorted 119 131 132 133 149 P C A 8 distorted distorted 138 150 151 152 168 P C A 9 distorted distorted 157 169 170 171 187 P C A 10 distorted distorted 176 188 189 190 206 P G B 1 distorted distorted 207 208 209 228 P G B 2 distorted distorted 214 229 230 231 250 P G B 3 distorted distorted 236 251 252 253 272 P G B 4 distorted distorted 258 273 274 275 294 P G B 5 distorted distorted 280 295 296 297 316 P C B 6 distorted distorted 302 317 318 319 335 P C B 7 distorted distorted 324 336 337 338 354 P C B 8 distorted distorted 343 355 356 357 373 P C B 9 distorted distorted 362 374 375 376 392 P C B 10 distorted distorted 381 393 394 395 ---------------------------------------------------------------------------------