ID code: '2L8F' 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' U A 2 alpha beta 39 59 45 42 74 C1' G A 3 alpha beta 69 92 75 72 108 C1' A A 4 alpha beta 103 125 109 106 141 C1' A A 5 alpha beta 136 158 142 139 174 C1' G A 6 alpha beta 169 192 175 172 208 C1' C A 7 alpha beta 203 223 209 206 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' C A 9 alpha beta 265 285 271 268 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' U A 11 alpha beta 330 351 336 333 364 C1' C B 12 alpha beta 359 379 365 362 396 C1' G B 13 alpha beta 391 414 397 394 430 C1' G B 14 alpha beta 425 448 431 428 464 C1' A B 15 alpha beta 459 481 465 462 497 C1' G B 16 alpha beta 492 515 498 495 531 C1' G B 17 alpha beta 526 549 532 529 565 C1' A B 18 alpha beta 560 582 566 563 598 C1' C B 19 alpha beta 593 613 599 596 629 C1' A B 20 alpha beta 624 646 630 627 662 C1' C B 21 alpha beta 657 677 663 660 693 C1' U B 22 alpha beta 688 709 694 691 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 2 OK OK 44 40 57 43 72 C2' G A 3 OK OK 74 70 90 73 106 C2' A A 4 OK OK 108 104 123 107 139 C2' A A 5 OK OK 141 137 156 140 172 C2' G A 6 OK OK 174 170 190 173 206 C2' C A 7 OK OK 208 204 221 207 237 C2' C A 8 OK OK 239 235 252 238 268 C2' C A 9 OK OK 270 266 283 269 299 C2' G A 10 OK OK 301 297 317 300 333 C2' U A 11 OK OK 335 331 349 334 362 C2' C B 12 OK OK 364 360 377 363 394 C2' G B 13 OK OK 396 392 412 395 428 C2' G B 14 OK OK 430 426 446 429 462 C2' A B 15 OK OK 464 460 479 463 495 C2' G B 16 OK OK 497 493 513 496 529 C2' G B 17 OK OK 531 527 547 530 563 C2' A B 18 OK OK 565 561 580 564 596 C2' C B 19 OK OK 598 594 611 597 627 C2' A B 20 OK OK 629 625 644 628 660 C2' C B 21 OK OK 662 658 675 661 691 C2' U B 22 OK OK 693 689 707 692 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' U A 2 OK OK 38 56 41 42 70 C3' G A 3 OK OK 68 89 71 72 104 C3' A A 4 OK OK 102 122 105 106 137 C3' A A 5 OK OK 135 155 138 139 170 C3' G A 6 OK OK 168 189 171 172 204 C3' C A 7 OK OK 202 220 205 206 235 C3' C A 8 OK OK 233 251 236 237 266 C3' C A 9 OK OK 264 282 267 268 297 C3' G A 10 OK OK 295 316 298 299 331 C3' U A 11 OK OK 329 347 332 333 360 C3' C B 12 OK OK 358 376 361 362 392 C3' G B 13 OK OK 390 411 393 394 426 C3' G B 14 OK OK 424 445 427 428 460 C3' A B 15 OK OK 458 478 461 462 493 C3' G B 16 OK OK 491 512 494 495 527 C3' G B 17 OK OK 525 546 528 529 561 C3' A B 18 OK OK 559 579 562 563 594 C3' C B 19 OK OK 592 610 595 596 625 C3' A B 20 OK OK 623 643 626 627 658 C3' C B 21 OK OK 656 674 659 660 689 C3' U B 22 OK OK 687 705 690 691 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' U A 2 OK OK 40 55 37 39 68 C4' G A 3 OK OK 70 88 67 69 102 C4' A A 4 OK OK 104 121 101 103 135 C4' A A 5 OK OK 137 154 134 136 168 C4' G A 6 OK OK 170 188 167 169 202 C4' C A 7 OK OK 204 219 201 203 233 C4' C A 8 OK OK 235 250 232 234 264 C4' C A 9 OK OK 266 281 263 265 295 C4' G A 10 OK OK 297 315 294 296 329 C4' U A 11 OK OK 331 346 328 330 358 C4' C B 12 OK OK 360 375 357 359 390 C4' G B 13 OK OK 392 410 389 391 424 C4' G B 14 OK OK 426 444 423 425 458 C4' A B 15 OK OK 460 477 457 459 491 C4' G B 16 OK OK 493 511 490 492 525 C4' G B 17 OK OK 527 545 524 526 559 C4' A B 18 OK OK 561 578 558 560 592 C4' C B 19 OK OK 594 609 591 593 623 C4' A B 20 OK OK 625 642 622 624 656 C4' C B 21 OK OK 658 673 655 657 687 C4' U B 22 OK OK 689 704 686 688 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 2 OK OK 36 53 54 38 67 C5' G A 3 OK OK 66 86 87 68 101 C5' A A 4 OK OK 100 119 120 102 134 C5' A A 5 OK OK 133 152 153 135 167 C5' G A 6 OK OK 166 186 187 168 201 C5' C A 7 OK OK 200 217 218 202 232 C5' C A 8 OK OK 231 248 249 233 263 C5' C A 9 OK OK 262 279 280 264 294 C5' G A 10 OK OK 293 313 314 295 328 C5' U A 11 OK OK 327 344 345 329 357 C5' C B 12 OK OK 356 373 374 358 389 C5' G B 13 OK OK 388 408 409 390 423 C5' G B 14 OK OK 422 442 443 424 457 C5' A B 15 OK OK 456 475 476 458 490 C5' G B 16 OK OK 489 509 510 491 524 C5' G B 17 OK OK 523 543 544 525 558 C5' A B 18 OK OK 557 576 577 559 591 C5' C B 19 OK OK 590 607 608 592 622 C5' A B 20 OK OK 621 640 641 623 655 C5' C B 21 OK OK 654 671 672 656 686 C5' U B 22 OK OK 685 702 703 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P U A 2 distorted distorted 6 34 35 36 63 P G A 3 distorted distorted 41 64 65 66 97 P A A 4 distorted distorted 71 98 99 100 130 P A A 5 distorted distorted 105 131 132 133 163 P G A 6 distorted distorted 138 164 165 166 197 P C A 7 distorted distorted 171 198 199 200 228 P C A 8 distorted distorted 205 229 230 231 259 P C A 9 distorted distorted 236 260 261 262 290 P G A 10 distorted distorted 267 291 292 293 324 P U A 11 distorted distorted 298 325 326 327 385 P G B 13 distorted distorted 361 386 387 388 419 P G B 14 distorted distorted 393 420 421 422 453 P A B 15 distorted distorted 427 454 455 456 486 P G B 16 distorted distorted 461 487 488 489 520 P G B 17 distorted distorted 494 521 522 523 554 P A B 18 distorted distorted 528 555 556 557 587 P C B 19 distorted distorted 562 588 589 590 618 P A B 20 distorted distorted 595 619 620 621 651 P C B 21 distorted distorted 626 652 653 654 682 P U B 22 distorted distorted 659 683 684 685 ---------------------------------------------------------------------------------