ID code: '1ATW' 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' C A 2 alpha beta 39 59 45 42 75 C1' U A 3 alpha beta 70 90 76 73 105 C1' C A 4 alpha beta 100 120 106 103 136 C1' C A 5 alpha beta 131 151 137 134 167 C1' A A 6 alpha beta 162 184 168 165 200 C1' G A 7 alpha beta 195 218 201 198 234 C1' A A 8 alpha beta 229 251 235 232 267 C1' U A 9 alpha beta 262 282 268 265 297 C1' G A 10 alpha beta 292 315 298 295 331 C1' G A 11 alpha beta 326 349 332 329 365 C1' A A 12 alpha beta 360 382 366 363 398 C1' G A 13 alpha beta 393 416 399 396 432 C1' C A 14 alpha beta 427 447 433 430 463 C1' G A 15 alpha beta 458 482 464 461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK OK 44 40 57 43 73 C2' U A 3 OK OK 75 71 88 74 103 C2' C A 4 OK OK 105 101 118 104 134 C2' C A 5 OK OK 136 132 149 135 165 C2' A A 6 OK OK 167 163 182 166 198 C2' G A 7 OK OK 200 196 216 199 232 C2' A A 8 OK OK 234 230 249 233 265 C2' U A 9 OK OK 267 263 280 266 295 C2' G A 10 OK OK 297 293 313 296 329 C2' G A 11 OK OK 331 327 347 330 363 C2' A A 12 OK OK 365 361 380 364 396 C2' G A 13 OK OK 398 394 414 397 430 C2' C A 14 OK OK 432 428 445 431 461 C2' G A 15 OK OK 463 459 480 462 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' U A 3 OK OK 69 87 72 73 101 C3' C A 4 OK OK 99 117 102 103 132 C3' C A 5 OK OK 130 148 133 134 163 C3' A A 6 OK OK 161 181 164 165 196 C3' G A 7 OK OK 194 215 197 198 230 C3' A A 8 OK OK 228 248 231 232 263 C3' U A 9 OK OK 261 279 264 265 293 C3' G A 10 OK OK 291 312 294 295 327 C3' G A 11 OK OK 325 346 328 329 361 C3' A A 12 OK OK 359 379 362 363 394 C3' G A 13 OK OK 392 413 395 396 428 C3' C A 14 OK OK 426 444 429 430 459 C3' G A 15 OK OK 457 478 460 461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' U A 3 OK OK 71 86 68 70 99 C4' C A 4 OK OK 101 116 98 100 130 C4' C A 5 OK OK 132 147 129 131 161 C4' A A 6 OK OK 163 180 160 162 194 C4' G A 7 OK OK 196 214 193 195 228 C4' A A 8 OK OK 230 247 227 229 261 C4' U A 9 OK OK 263 278 260 262 291 C4' G A 10 OK OK 293 311 290 292 325 C4' G A 11 OK OK 327 345 324 326 359 C4' A A 12 OK OK 361 378 358 360 392 C4' G A 13 OK OK 394 412 391 393 426 C4' C A 14 OK OK 428 443 425 427 457 C4' G A 15 OK OK 459 477 456 458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 36 53 54 38 68 C5' U A 3 OK OK 67 84 85 69 98 C5' C A 4 OK OK 97 114 115 99 129 C5' C A 5 OK OK 128 145 146 130 160 C5' A A 6 OK OK 159 178 179 161 193 C5' G A 7 OK OK 192 212 213 194 227 C5' A A 8 OK OK 226 245 246 228 260 C5' U A 9 OK OK 259 276 277 261 290 C5' G A 10 OK OK 289 309 310 291 324 C5' G A 11 OK OK 323 343 344 325 358 C5' A A 12 OK OK 357 376 377 359 391 C5' G A 13 OK OK 390 410 411 392 425 C5' C A 14 OK OK 424 441 442 426 456 C5' G A 15 OK OK 455 475 476 457 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P U A 3 distorted distorted 41 65 66 67 94 P C A 4 distorted distorted 72 95 96 97 125 P C A 5 distorted distorted 102 126 127 128 156 P A A 6 distorted distorted 133 157 158 159 189 P G A 7 distorted distorted 164 190 191 192 223 P A A 8 distorted distorted 197 224 225 226 256 P U A 9 distorted distorted 231 257 258 259 286 P G A 10 distorted distorted 264 287 288 289 320 P G A 11 distorted distorted 294 321 322 323 354 P A A 12 distorted distorted 328 355 356 357 387 P G A 13 distorted distorted 362 388 389 390 421 P C A 14 distorted distorted 395 422 423 424 452 P G A 15 distorted distorted 429 453 454 455 ---------------------------------------------------------------------------------