ID code: '2KBP' 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' U A 1 alpha beta 4 24 10 7 40 C1' A A 2 alpha beta 35 57 41 38 73 C1' G A 3 alpha beta 68 91 74 71 107 C1' G A 4 alpha beta 102 125 108 105 141 C1' G A 5 alpha beta 136 159 142 139 175 C1' U A 6 alpha beta 170 190 176 173 205 C1' U A 7 alpha beta 200 220 206 203 235 C1' A A 8 alpha beta 230 252 236 233 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' G A 11 alpha beta 331 354 337 334 370 C1' U A 12 alpha beta 365 386 371 368 399 C1' U B 13 alpha beta 394 414 400 397 430 C1' A B 14 alpha beta 425 447 431 428 463 C1' G B 15 alpha beta 458 481 464 461 497 C1' G B 16 alpha beta 492 515 498 495 531 C1' G B 17 alpha beta 526 549 532 529 565 C1' U B 18 alpha beta 560 580 566 563 595 C1' U B 19 alpha beta 590 610 596 593 625 C1' A B 20 alpha beta 620 642 626 623 658 C1' G B 21 alpha beta 653 676 659 656 692 C1' G B 22 alpha beta 687 710 693 690 726 C1' G B 23 alpha beta 721 744 727 724 760 C1' U B 24 alpha beta 755 776 761 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' A A 2 OK OK 40 36 55 39 71 C2' G A 3 OK OK 73 69 89 72 105 C2' G A 4 OK OK 107 103 123 106 139 C2' G A 5 OK OK 141 137 157 140 173 C2' U A 6 OK OK 175 171 188 174 203 C2' U A 7 OK OK 205 201 218 204 233 C2' A A 8 OK OK 235 231 250 234 266 C2' G A 9 OK OK 268 264 284 267 300 C2' G A 10 OK OK 302 298 318 301 334 C2' G A 11 OK OK 336 332 352 335 368 C2' U A 12 OK OK 370 366 384 369 397 C2' U B 13 OK OK 399 395 412 398 428 C2' A B 14 OK OK 430 426 445 429 461 C2' G B 15 OK OK 463 459 479 462 495 C2' G B 16 OK OK 497 493 513 496 529 C2' G B 17 OK OK 531 527 547 530 563 C2' U B 18 OK OK 565 561 578 564 593 C2' U B 19 OK OK 595 591 608 594 623 C2' A B 20 OK OK 625 621 640 624 656 C2' G B 21 OK OK 658 654 674 657 690 C2' G B 22 OK OK 692 688 708 691 724 C2' G B 23 OK OK 726 722 742 725 758 C2' U B 24 OK OK 760 756 774 759 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' A A 2 OK OK 34 54 37 38 69 C3' G A 3 OK OK 67 88 70 71 103 C3' G A 4 OK OK 101 122 104 105 137 C3' G A 5 OK OK 135 156 138 139 171 C3' U A 6 OK OK 169 187 172 173 201 C3' U A 7 OK OK 199 217 202 203 231 C3' A A 8 OK OK 229 249 232 233 264 C3' G A 9 OK OK 262 283 265 266 298 C3' G A 10 OK OK 296 317 299 300 332 C3' G A 11 OK OK 330 351 333 334 366 C3' U A 12 OK OK 364 382 367 368 395 C3' U B 13 OK OK 393 411 396 397 426 C3' A B 14 OK OK 424 444 427 428 459 C3' G B 15 OK OK 457 478 460 461 493 C3' G B 16 OK OK 491 512 494 495 527 C3' G B 17 OK OK 525 546 528 529 561 C3' U B 18 OK OK 559 577 562 563 591 C3' U B 19 OK OK 589 607 592 593 621 C3' A B 20 OK OK 619 639 622 623 654 C3' G B 21 OK OK 652 673 655 656 688 C3' G B 22 OK OK 686 707 689 690 722 C3' G B 23 OK OK 720 741 723 724 756 C3' U B 24 OK OK 754 772 757 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' A A 2 OK OK 36 53 33 35 67 C4' G A 3 OK OK 69 87 66 68 101 C4' G A 4 OK OK 103 121 100 102 135 C4' G A 5 OK OK 137 155 134 136 169 C4' U A 6 OK OK 171 186 168 170 199 C4' U A 7 OK OK 201 216 198 200 229 C4' A A 8 OK OK 231 248 228 230 262 C4' G A 9 OK OK 264 282 261 263 296 C4' G A 10 OK OK 298 316 295 297 330 C4' G A 11 OK OK 332 350 329 331 364 C4' U A 12 OK OK 366 381 363 365 393 C4' U B 13 OK OK 395 410 392 394 424 C4' A B 14 OK OK 426 443 423 425 457 C4' G B 15 OK OK 459 477 456 458 491 C4' G B 16 OK OK 493 511 490 492 525 C4' G B 17 OK OK 527 545 524 526 559 C4' U B 18 OK OK 561 576 558 560 589 C4' U B 19 OK OK 591 606 588 590 619 C4' A B 20 OK OK 621 638 618 620 652 C4' G B 21 OK OK 654 672 651 653 686 C4' G B 22 OK OK 688 706 685 687 720 C4' G B 23 OK OK 722 740 719 721 754 C4' U B 24 OK OK 756 771 753 755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' A A 2 OK OK 32 51 52 34 66 C5' G A 3 OK OK 65 85 86 67 100 C5' G A 4 OK OK 99 119 120 101 134 C5' G A 5 OK OK 133 153 154 135 168 C5' U A 6 OK OK 167 184 185 169 198 C5' U A 7 OK OK 197 214 215 199 228 C5' A A 8 OK OK 227 246 247 229 261 C5' G A 9 OK OK 260 280 281 262 295 C5' G A 10 OK OK 294 314 315 296 329 C5' G A 11 OK OK 328 348 349 330 363 C5' U A 12 OK OK 362 379 380 364 392 C5' U B 13 OK OK 391 408 409 393 423 C5' A B 14 OK OK 422 441 442 424 456 C5' G B 15 OK OK 455 475 476 457 490 C5' G B 16 OK OK 489 509 510 491 524 C5' G B 17 OK OK 523 543 544 525 558 C5' U B 18 OK OK 557 574 575 559 588 C5' U B 19 OK OK 587 604 605 589 618 C5' A B 20 OK OK 617 636 637 619 651 C5' G B 21 OK OK 650 670 671 652 685 C5' G B 22 OK OK 684 704 705 686 719 C5' G B 23 OK OK 718 738 739 720 753 C5' U B 24 OK OK 752 769 770 754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P A A 2 distorted distorted 6 30 31 32 62 P G A 3 distorted distorted 37 63 64 65 96 P G A 4 distorted distorted 70 97 98 99 130 P G A 5 distorted distorted 104 131 132 133 164 P U A 6 distorted distorted 138 165 166 167 194 P U A 7 distorted distorted 172 195 196 197 224 P A A 8 distorted distorted 202 225 226 227 257 P G A 9 distorted distorted 232 258 259 260 291 P G A 10 distorted distorted 265 292 293 294 325 P G A 11 distorted distorted 299 326 327 328 359 P U A 12 distorted distorted 333 360 361 362 419 P A B 14 distorted distorted 396 420 421 422 452 P G B 15 distorted distorted 427 453 454 455 486 P G B 16 distorted distorted 460 487 488 489 520 P G B 17 distorted distorted 494 521 522 523 554 P U B 18 distorted distorted 528 555 556 557 584 P U B 19 distorted distorted 562 585 586 587 614 P A B 20 distorted distorted 592 615 616 617 647 P G B 21 distorted distorted 622 648 649 650 681 P G B 22 distorted distorted 655 682 683 684 715 P G B 23 distorted distorted 689 716 717 718 749 P U B 24 distorted distorted 723 750 751 752 ---------------------------------------------------------------------------------