ID code: '2ATW' 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' A B 0 beta 4 10 7 31 C1' G B 1 beta 26 32 29 54 C1' A B 2 beta 49 55 52 76 C1' A B 3 beta 71 77 74 98 C1' C B 4 beta 93 99 96 118 C1' U B 5 beta 113 119 116 138 C1' C B 6 beta 133 139 136 158 C1' A B 7 beta 153 159 156 180 C1' A B 8 beta 175 181 178 202 C1' U B 9 beta 197 203 200 222 C1' A B 10 beta 217 223 220 244 C1' G B 11 beta 239 245 242 265 C1' A D 0 beta 260 266 263 287 C1' G D 1 beta 282 288 285 310 C1' A D 2 beta 305 311 308 332 C1' A D 3 beta 327 333 330 354 C1' C D 4 beta 349 355 352 374 C1' U D 5 beta 369 375 372 394 C1' C D 6 beta 389 395 392 414 C1' A D 7 beta 409 415 412 436 C1' A D 8 beta 431 437 434 458 C1' U D 9 beta 453 459 456 478 C1' A D 10 beta 473 479 476 500 C1' G D 11 beta 495 501 498 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A B 0 OK 9 5 8 29 C2' G B 1 OK 31 27 30 52 C2' A B 2 OK 54 50 53 74 C2' A B 3 OK 76 72 75 96 C2' C B 4 OK 98 94 97 116 C2' U B 5 OK 118 114 117 136 C2' C B 6 OK 138 134 137 156 C2' A B 7 OK 158 154 157 178 C2' A B 8 OK 180 176 179 200 C2' U B 9 OK 202 198 201 220 C2' A B 10 OK 222 218 221 242 C2' G B 11 OK 244 240 243 263 C2' A D 0 OK 265 261 264 285 C2' G D 1 OK 287 283 286 308 C2' A D 2 OK 310 306 309 330 C2' A D 3 OK 332 328 331 352 C2' C D 4 OK 354 350 353 372 C2' U D 5 OK 374 370 373 392 C2' C D 6 OK 394 390 393 412 C2' A D 7 OK 414 410 413 434 C2' A D 8 OK 436 432 435 456 C2' U D 9 OK 458 454 457 476 C2' A D 10 OK 478 474 477 498 C2' G D 11 OK 500 496 499 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A B 0 OK 3 6 7 27 C3' G B 1 OK 25 28 29 50 C3' A B 2 OK 48 51 52 72 C3' A B 3 OK 70 73 74 94 C3' C B 4 OK 92 95 96 114 C3' U B 5 OK 112 115 116 134 C3' C B 6 OK 132 135 136 154 C3' A B 7 OK 152 155 156 176 C3' A B 8 OK 174 177 178 198 C3' U B 9 OK 196 199 200 218 C3' A B 10 OK 216 219 220 240 C3' G B 11 OK 238 241 242 261 C3' A D 0 OK 259 262 263 283 C3' G D 1 OK 281 284 285 306 C3' A D 2 OK 304 307 308 328 C3' A D 3 OK 326 329 330 350 C3' C D 4 OK 348 351 352 370 C3' U D 5 OK 368 371 372 390 C3' C D 6 OK 388 391 392 410 C3' A D 7 OK 408 411 412 432 C3' A D 8 OK 430 433 434 454 C3' U D 9 OK 452 455 456 474 C3' A D 10 OK 472 475 476 496 C3' G D 11 OK 494 497 498 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A B 0 OK 5 2 4 25 C4' G B 1 OK 27 24 26 48 C4' A B 2 OK 50 47 49 70 C4' A B 3 OK 72 69 71 92 C4' C B 4 OK 94 91 93 112 C4' U B 5 OK 114 111 113 132 C4' C B 6 OK 134 131 133 152 C4' A B 7 OK 154 151 153 174 C4' A B 8 OK 176 173 175 196 C4' U B 9 OK 198 195 197 216 C4' A B 10 OK 218 215 217 238 C4' G B 11 OK 240 237 239 259 C4' A D 0 OK 261 258 260 281 C4' G D 1 OK 283 280 282 304 C4' A D 2 OK 306 303 305 326 C4' A D 3 OK 328 325 327 348 C4' C D 4 OK 350 347 349 368 C4' U D 5 OK 370 367 369 388 C4' C D 6 OK 390 387 389 408 C4' A D 7 OK 410 407 409 430 C4' A D 8 OK 432 429 431 452 C4' U D 9 OK 454 451 453 472 C4' A D 10 OK 474 471 473 494 C4' G D 11 OK 496 493 495 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A B 0 1 3 24 C5' G B 1 23 25 47 C5' A B 2 46 48 69 C5' A B 3 68 70 91 C5' C B 4 90 92 111 C5' U B 5 110 112 131 C5' C B 6 130 132 151 C5' A B 7 150 152 173 C5' A B 8 172 174 195 C5' U B 9 194 196 215 C5' A B 10 214 216 237 C5' G B 11 236 238 258 C5' A D 0 257 259 280 C5' G D 1 279 281 303 C5' A D 2 302 304 325 C5' A D 3 324 326 347 C5' C D 4 346 348 367 C5' U D 5 366 368 387 C5' C D 6 386 388 407 C5' A D 7 406 408 429 C5' A D 8 428 430 451 C5' U D 9 450 452 471 C5' A D 10 470 472 493 C5' G D 11 492 494 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G B 1 distorted distorted 6 21 22 23 43 P A B 2 distorted distorted 28 44 45 46 65 P A B 3 distorted distorted 51 66 67 68 87 P C B 4 distorted distorted 73 88 89 90 107 P U B 5 distorted distorted 95 108 109 110 127 P C B 6 distorted distorted 115 128 129 130 147 P A B 7 distorted distorted 135 148 149 150 169 P A B 8 distorted distorted 155 170 171 172 191 P U B 9 distorted distorted 177 192 193 194 211 P A B 10 distorted distorted 199 212 213 214 233 P G B 11 distorted distorted 219 234 235 236 276 P G D 1 distorted distorted 262 277 278 279 299 P A D 2 distorted distorted 284 300 301 302 321 P A D 3 distorted distorted 307 322 323 324 343 P C D 4 distorted distorted 329 344 345 346 363 P U D 5 distorted distorted 351 364 365 366 383 P C D 6 distorted distorted 371 384 385 386 403 P A D 7 distorted distorted 391 404 405 406 425 P A D 8 distorted distorted 411 426 427 428 447 P U D 9 distorted distorted 433 448 449 450 467 P A D 10 distorted distorted 455 468 469 470 489 P G D 11 distorted distorted 475 490 491 492 ---------------------------------------------------------------------------------