ID code: '1K8S' 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' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' A A 6 alpha beta 171 193 177 174 209 C1' G A 7 alpha beta 204 227 210 207 243 C1' U A 8 alpha beta 238 258 244 241 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' C A 10 alpha beta 302 322 308 305 338 C1' C A 11 alpha beta 333 353 339 336 369 C1' G A 12 alpha beta 364 387 370 367 403 C1' C A 13 alpha beta 398 419 404 401 433 C1' G B 14 alpha beta 428 451 434 431 468 C1' C B 15 alpha beta 463 483 469 466 499 C1' G B 16 alpha beta 494 517 500 497 533 C1' G B 17 alpha beta 528 551 534 531 567 C1' C B 18 alpha beta 562 582 568 565 598 C1' A B 19 alpha beta 593 615 599 596 631 C1' C B 20 alpha beta 626 646 632 629 662 C1' C B 21 alpha beta 657 677 663 660 693 C1' U B 22 alpha beta 688 708 694 691 723 C1' G B 23 alpha beta 718 741 724 721 757 C1' C B 24 alpha beta 752 772 758 755 788 C1' C B 25 alpha beta 783 804 789 786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' G A 5 OK OK 142 138 158 141 174 C2' A A 6 OK OK 176 172 191 175 207 C2' G A 7 OK OK 209 205 225 208 241 C2' U A 8 OK OK 243 239 256 242 271 C2' G A 9 OK OK 273 269 289 272 305 C2' C A 10 OK OK 307 303 320 306 336 C2' C A 11 OK OK 338 334 351 337 367 C2' G A 12 OK OK 369 365 385 368 401 C2' C A 13 OK OK 403 399 417 402 431 C2' G B 14 OK OK 433 429 449 432 466 C2' C B 15 OK OK 468 464 481 467 497 C2' G B 16 OK OK 499 495 515 498 531 C2' G B 17 OK OK 533 529 549 532 565 C2' C B 18 OK OK 567 563 580 566 596 C2' A B 19 OK OK 598 594 613 597 629 C2' C B 20 OK OK 631 627 644 630 660 C2' C B 21 OK OK 662 658 675 661 691 C2' U B 22 OK OK 693 689 706 692 721 C2' G B 23 OK OK 723 719 739 722 755 C2' C B 24 OK OK 757 753 770 756 786 C2' C B 25 OK OK 788 784 802 787 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' G A 5 OK OK 136 157 139 140 172 C3' A A 6 OK OK 170 190 173 174 205 C3' G A 7 OK OK 203 224 206 207 239 C3' U A 8 OK OK 237 255 240 241 269 C3' G A 9 OK OK 267 288 270 271 303 C3' C A 10 OK OK 301 319 304 305 334 C3' C A 11 OK OK 332 350 335 336 365 C3' G A 12 OK OK 363 384 366 367 399 C3' C A 13 OK OK 397 415 400 401 429 C3' G B 14 OK OK 427 448 430 431 464 C3' C B 15 OK OK 462 480 465 466 495 C3' G B 16 OK OK 493 514 496 497 529 C3' G B 17 OK OK 527 548 530 531 563 C3' C B 18 OK OK 561 579 564 565 594 C3' A B 19 OK OK 592 612 595 596 627 C3' C B 20 OK OK 625 643 628 629 658 C3' C B 21 OK OK 656 674 659 660 689 C3' U B 22 OK OK 687 705 690 691 719 C3' G B 23 OK OK 717 738 720 721 753 C3' C B 24 OK OK 751 769 754 755 784 C3' C B 25 OK OK 782 800 785 786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' G A 5 OK OK 138 156 135 137 170 C4' A A 6 OK OK 172 189 169 171 203 C4' G A 7 OK OK 205 223 202 204 237 C4' U A 8 OK OK 239 254 236 238 267 C4' G A 9 OK OK 269 287 266 268 301 C4' C A 10 OK OK 303 318 300 302 332 C4' C A 11 OK OK 334 349 331 333 363 C4' G A 12 OK OK 365 383 362 364 397 C4' C A 13 OK OK 399 414 396 398 427 C4' G B 14 OK OK 429 447 426 428 462 C4' C B 15 OK OK 464 479 461 463 493 C4' G B 16 OK OK 495 513 492 494 527 C4' G B 17 OK OK 529 547 526 528 561 C4' C B 18 OK OK 563 578 560 562 592 C4' A B 19 OK OK 594 611 591 593 625 C4' C B 20 OK OK 627 642 624 626 656 C4' C B 21 OK OK 658 673 655 657 687 C4' U B 22 OK OK 689 704 686 688 717 C4' G B 23 OK OK 719 737 716 718 751 C4' C B 24 OK OK 753 768 750 752 782 C4' C B 25 OK OK 784 799 781 783 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' G A 5 OK OK 134 154 155 136 169 C5' A A 6 OK OK 168 187 188 170 202 C5' G A 7 OK OK 201 221 222 203 236 C5' U A 8 OK OK 235 252 253 237 266 C5' G A 9 OK OK 265 285 286 267 300 C5' C A 10 OK OK 299 316 317 301 331 C5' C A 11 OK OK 330 347 348 332 362 C5' G A 12 OK OK 361 381 382 363 396 C5' C A 13 OK OK 395 412 413 397 426 C5' G B 14 OK OK 425 445 446 427 461 C5' C B 15 OK OK 460 477 478 462 492 C5' G B 16 OK OK 491 511 512 493 526 C5' G B 17 OK OK 525 545 546 527 560 C5' C B 18 OK OK 559 576 577 561 591 C5' A B 19 OK OK 590 609 610 592 624 C5' C B 20 OK OK 623 640 641 625 655 C5' C B 21 OK OK 654 671 672 656 686 C5' U B 22 OK OK 685 702 703 687 716 C5' G B 23 OK OK 715 735 736 717 750 C5' C B 24 OK OK 749 766 767 751 781 C5' C B 25 OK OK 780 797 798 782 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P G A 5 distorted distorted 106 132 133 134 165 P A A 6 distorted distorted 139 166 167 168 198 P G A 7 distorted distorted 173 199 200 201 232 P U A 8 distorted distorted 206 233 234 235 262 P G A 9 distorted distorted 240 263 264 265 296 P C A 10 distorted distorted 270 297 298 299 327 P C A 11 distorted distorted 304 328 329 330 358 P G A 12 distorted distorted 335 359 360 361 392 P C A 13 distorted distorted 366 393 394 395 457 P C B 15 distorted distorted 430 458 459 460 488 P G B 16 distorted distorted 465 489 490 491 522 P G B 17 distorted distorted 496 523 524 525 556 P C B 18 distorted distorted 530 557 558 559 587 P A B 19 distorted distorted 564 588 589 590 620 P C B 20 distorted distorted 595 621 622 623 651 P C B 21 distorted distorted 628 652 653 654 682 P U B 22 distorted distorted 659 683 684 685 712 P G B 23 distorted distorted 690 713 714 715 746 P C B 24 distorted distorted 720 747 748 749 777 P C B 25 distorted distorted 754 778 779 780 ---------------------------------------------------------------------------------