ID code: '1QBP' 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' --------------------------------------------------------------------------------- 13 C1' G C 32 beta 8 14 11 36 C1' C+ C 33 beta 31 37 34 56 C1' C+ C 34 beta 51 57 54 76 C1' A C 35 beta 71 77 74 98 C1' G C 36 beta 93 99 96 121 C1' U C 37 beta 116 122 119 141 C1' U C 38 beta 136 142 139 161 C1' C C 39 beta 156 162 159 181 C1' G C 40 beta 176 182 179 204 C1' C C 41 beta 199 205 202 224 C1' U C 42 beta 219 225 222 244 C1' G C 43 beta 239 245 242 267 C1' G C 44 beta 262 268 265 290 C1' C C 45 beta 285 291 288 314 C1' G D 47 beta 309 315 312 337 C1' C+ D 48 beta 332 338 335 357 C1' C+ D 49 beta 352 358 355 377 C1' A D 50 beta 372 378 375 399 C1' G D 51 beta 394 400 397 422 C1' U D 52 beta 417 423 420 442 C1' U D 53 beta 437 443 440 462 C1' C D 54 beta 457 463 460 482 C1' G D 55 beta 477 483 480 505 C1' C D 56 beta 500 506 503 525 C1' U D 57 beta 520 526 523 545 C1' G D 58 beta 540 546 543 568 C1' G D 59 beta 563 569 566 591 C1' C D 60 beta 586 592 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G C 32 OK 13 9 12 34 C2' C+ C 33 OK 36 32 35 54 C2' C+ C 34 OK 56 52 55 74 C2' A C 35 OK 76 72 75 96 C2' G C 36 OK 98 94 97 119 C2' U C 37 OK 121 117 120 139 C2' U C 38 OK 141 137 140 159 C2' C C 39 OK 161 157 160 179 C2' G C 40 OK 181 177 180 202 C2' C C 41 OK 204 200 203 222 C2' U C 42 OK 224 220 223 242 C2' G C 43 OK 244 240 243 265 C2' G C 44 OK 267 263 266 288 C2' C C 45 OK 290 286 289 312 C2' G D 47 OK 314 310 313 335 C2' C+ D 48 OK 337 333 336 355 C2' C+ D 49 OK 357 353 356 375 C2' A D 50 OK 377 373 376 397 C2' G D 51 OK 399 395 398 420 C2' U D 52 OK 422 418 421 440 C2' U D 53 OK 442 438 441 460 C2' C D 54 OK 462 458 461 480 C2' G D 55 OK 482 478 481 503 C2' C D 56 OK 505 501 504 523 C2' U D 57 OK 525 521 524 543 C2' G D 58 OK 545 541 544 566 C2' G D 59 OK 568 564 567 589 C2' C D 60 OK 591 587 590 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G C 32 OK 7 10 11 32 C3' C+ C 33 OK 30 33 34 52 C3' C+ C 34 OK 50 53 54 72 C3' A C 35 OK 70 73 74 94 C3' G C 36 OK 92 95 96 117 C3' U C 37 OK 115 118 119 137 C3' U C 38 OK 135 138 139 157 C3' C C 39 OK 155 158 159 177 C3' G C 40 OK 175 178 179 200 C3' C C 41 OK 198 201 202 220 C3' U C 42 OK 218 221 222 240 C3' G C 43 OK 238 241 242 263 C3' G C 44 OK 261 264 265 286 C3' C C 45 OK 284 287 288 310 C3' G D 47 OK 308 311 312 333 C3' C+ D 48 OK 331 334 335 353 C3' C+ D 49 OK 351 354 355 373 C3' A D 50 OK 371 374 375 395 C3' G D 51 OK 393 396 397 418 C3' U D 52 OK 416 419 420 438 C3' U D 53 OK 436 439 440 458 C3' C D 54 OK 456 459 460 478 C3' G D 55 OK 476 479 480 501 C3' C D 56 OK 499 502 503 521 C3' U D 57 OK 519 522 523 541 C3' G D 58 OK 539 542 543 564 C3' G D 59 OK 562 565 566 587 C3' C D 60 OK 585 588 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G C 32 OK 9 6 8 30 C4' C+ C 33 OK 32 29 31 50 C4' C+ C 34 OK 52 49 51 70 C4' A C 35 OK 72 69 71 92 C4' G C 36 OK 94 91 93 115 C4' U C 37 OK 117 114 116 135 C4' U C 38 OK 137 134 136 155 C4' C C 39 OK 157 154 156 175 C4' G C 40 OK 177 174 176 198 C4' C C 41 OK 200 197 199 218 C4' U C 42 OK 220 217 219 238 C4' G C 43 OK 240 237 239 261 C4' G C 44 OK 263 260 262 284 C4' C C 45 OK 286 283 285 308 C4' G D 47 OK 310 307 309 331 C4' C+ D 48 OK 333 330 332 351 C4' C+ D 49 OK 353 350 352 371 C4' A D 50 OK 373 370 372 393 C4' G D 51 OK 395 392 394 416 C4' U D 52 OK 418 415 417 436 C4' U D 53 OK 438 435 437 456 C4' C D 54 OK 458 455 457 476 C4' G D 55 OK 478 475 477 499 C4' C D 56 OK 501 498 500 519 C4' U D 57 OK 521 518 520 539 C4' G D 58 OK 541 538 540 562 C4' G D 59 OK 564 561 563 585 C4' C D 60 OK 587 584 586 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G C 32 5 7 29 C5' C+ C 33 28 30 49 C5' C+ C 34 48 50 69 C5' A C 35 68 70 91 C5' G C 36 90 92 114 C5' U C 37 113 115 134 C5' U C 38 133 135 154 C5' C C 39 153 155 174 C5' G C 40 173 175 197 C5' C C 41 196 198 217 C5' U C 42 216 218 237 C5' G C 43 236 238 260 C5' G C 44 259 261 283 C5' C C 45 282 284 307 C5' G D 47 306 308 330 C5' C+ D 48 329 331 350 C5' C+ D 49 349 351 370 C5' A D 50 369 371 392 C5' G D 51 391 393 415 C5' U D 52 414 416 435 C5' U D 53 434 436 455 C5' C D 54 454 456 475 C5' G D 55 474 476 498 C5' C D 56 497 499 518 C5' U D 57 517 519 538 C5' G D 58 537 539 561 C5' G D 59 560 562 584 C5' C D 60 583 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G C 32 OK OK 3 4 5 25 P C+ C 33 distorted distorted 10 26 27 28 45 P C+ C 34 distorted distorted 33 46 47 48 65 P A C 35 distorted distorted 53 66 67 68 87 P G C 36 distorted distorted 73 88 89 90 110 P U C 37 distorted distorted 95 111 112 113 130 P U C 38 distorted distorted 118 131 132 133 150 P C C 39 distorted distorted 138 151 152 153 170 P G C 40 distorted distorted 158 171 172 173 193 P C C 41 distorted distorted 178 194 195 196 213 P U C 42 distorted distorted 201 214 215 216 233 P G C 43 distorted distorted 221 234 235 236 256 P G C 44 distorted distorted 241 257 258 259 279 P C C 45 distorted distorted 264 280 281 282 303 P G D 47 distorted distorted 304 305 306 326 P C+ D 48 distorted distorted 311 327 328 329 346 P C+ D 49 distorted distorted 334 347 348 349 366 P A D 50 distorted distorted 354 367 368 369 388 P G D 51 distorted distorted 374 389 390 391 411 P U D 52 distorted distorted 396 412 413 414 431 P U D 53 distorted distorted 419 432 433 434 451 P C D 54 distorted distorted 439 452 453 454 471 P G D 55 distorted distorted 459 472 473 474 494 P C D 56 distorted distorted 479 495 496 497 514 P U D 57 distorted distorted 502 515 516 517 534 P G D 58 distorted distorted 522 535 536 537 557 P G D 59 distorted distorted 542 558 559 560 580 P C D 60 distorted distorted 565 581 582 583 ---------------------------------------------------------------------------------