ID code: '1F85' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' U A 5 alpha beta 135 155 141 138 170 C1' G A 6 alpha beta 165 188 171 168 204 C1' A A 7 alpha beta 199 221 205 202 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' A A 9 alpha beta 262 284 268 265 300 C1' G A 10 alpha beta 295 318 301 298 334 C1' G A 11 alpha beta 329 352 335 332 368 C1' G A 12 alpha beta 363 386 369 366 402 C1' U A 13 alpha beta 397 417 403 400 432 C1' C A 14 alpha beta 427 448 433 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' U A 5 OK OK 140 136 153 139 168 C2' G A 6 OK OK 170 166 186 169 202 C2' A A 7 OK OK 204 200 219 203 235 C2' U A 8 OK OK 237 233 250 236 265 C2' A A 9 OK OK 267 263 282 266 298 C2' G A 10 OK OK 300 296 316 299 332 C2' G A 11 OK OK 334 330 350 333 366 C2' G A 12 OK OK 368 364 384 367 400 C2' U A 13 OK OK 402 398 415 401 430 C2' C A 14 OK OK 432 428 446 431 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' U A 5 OK OK 134 152 137 138 166 C3' G A 6 OK OK 164 185 167 168 200 C3' A A 7 OK OK 198 218 201 202 233 C3' U A 8 OK OK 231 249 234 235 263 C3' A A 9 OK OK 261 281 264 265 296 C3' G A 10 OK OK 294 315 297 298 330 C3' G A 11 OK OK 328 349 331 332 364 C3' G A 12 OK OK 362 383 365 366 398 C3' U A 13 OK OK 396 414 399 400 428 C3' C A 14 OK OK 426 444 429 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' U A 5 OK OK 136 151 133 135 164 C4' G A 6 OK OK 166 184 163 165 198 C4' A A 7 OK OK 200 217 197 199 231 C4' U A 8 OK OK 233 248 230 232 261 C4' A A 9 OK OK 263 280 260 262 294 C4' G A 10 OK OK 296 314 293 295 328 C4' G A 11 OK OK 330 348 327 329 362 C4' G A 12 OK OK 364 382 361 363 396 C4' U A 13 OK OK 398 413 395 397 426 C4' C A 14 OK OK 428 443 425 427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' U A 5 OK OK 132 149 150 134 163 C5' G A 6 OK OK 162 182 183 164 197 C5' A A 7 OK OK 196 215 216 198 230 C5' U A 8 OK OK 229 246 247 231 260 C5' A A 9 OK OK 259 278 279 261 293 C5' G A 10 OK OK 292 312 313 294 327 C5' G A 11 OK OK 326 346 347 328 361 C5' G A 12 OK OK 360 380 381 362 395 C5' U A 13 OK OK 394 411 412 396 425 C5' C A 14 OK OK 424 441 442 426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P U A 5 distorted distorted 106 130 131 132 159 P G A 6 distorted distorted 137 160 161 162 193 P A A 7 distorted distorted 167 194 195 196 226 P U A 8 distorted distorted 201 227 228 229 256 P A A 9 distorted distorted 234 257 258 259 289 P G A 10 distorted distorted 264 290 291 292 323 P G A 11 distorted distorted 297 324 325 326 357 P G A 12 distorted distorted 331 358 359 360 391 P U A 13 distorted distorted 365 392 393 394 421 P C A 14 distorted distorted 399 422 423 424 ---------------------------------------------------------------------------------