ID code: '1O9M' 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 A1403 beta 4 10 7 32 C1' C A1404 beta 27 33 30 52 C1' G A1405 beta 47 53 50 75 C1' U A1406 beta 70 76 73 95 C1' C A1407 beta 90 96 93 115 C1' A A1408 beta 110 116 113 137 C1' C A1409 beta 132 138 135 157 C1' A A1410 beta 152 158 155 179 C1' C A1411 beta 174 180 177 199 C1' C A1412 beta 194 200 197 219 C1' G A1488 beta 214 220 217 242 C1' G A1489 beta 237 243 240 265 C1' U A1490 beta 260 266 263 285 C1' G A1491 beta 280 286 283 308 C1' A A1492 beta 303 309 306 330 C1' A A1493 beta 325 331 328 352 C1' G A1494 beta 347 353 350 375 C1' U A1495 beta 370 376 373 395 C1' C A1496 beta 390 396 393 415 C1' G A1497 beta 410 416 413 438 C1' C A1498 beta 433 439 436 456 C1' G B1403 beta 451 457 454 479 C1' C B1404 beta 474 480 477 499 C1' G B1405 beta 494 500 497 522 C1' U B1406 beta 517 523 520 542 C1' C B1407 beta 537 543 540 562 C1' A B1408 beta 557 563 560 584 C1' C B1409 beta 579 585 582 604 C1' A B1410 beta 599 605 602 626 C1' C B1411 beta 621 627 624 646 C1' C B1412 beta 641 647 644 666 C1' G B1488 beta 661 667 664 689 C1' G B1489 beta 684 690 687 712 C1' U B1490 beta 707 713 710 732 C1' G B1491 beta 727 733 730 755 C1' A B1492 beta 750 756 753 777 C1' A B1493 beta 772 778 775 799 C1' G B1494 beta 794 800 797 822 C1' U B1495 beta 817 823 820 842 C1' C B1496 beta 837 843 840 862 C1' G B1497 beta 857 863 860 885 C1' C B1498 beta 880 886 883 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A1403 OK 9 5 8 30 C2' C A1404 OK 32 28 31 50 C2' G A1405 OK 52 48 51 73 C2' U A1406 OK 75 71 74 93 C2' C A1407 OK 95 91 94 113 C2' A A1408 OK 115 111 114 135 C2' C A1409 OK 137 133 136 155 C2' A A1410 OK 157 153 156 177 C2' C A1411 OK 179 175 178 197 C2' C A1412 OK 199 195 198 217 C2' G A1488 OK 219 215 218 240 C2' G A1489 OK 242 238 241 263 C2' U A1490 OK 265 261 264 283 C2' G A1491 OK 285 281 284 306 C2' A A1492 OK 308 304 307 328 C2' A A1493 OK 330 326 329 350 C2' G A1494 OK 352 348 351 373 C2' U A1495 OK 375 371 374 393 C2' C A1496 OK 395 391 394 413 C2' G A1497 OK 415 411 414 436 C2' C A1498 OK 438 434 437 454 C2' G B1403 OK 456 452 455 477 C2' C B1404 OK 479 475 478 497 C2' G B1405 OK 499 495 498 520 C2' U B1406 OK 522 518 521 540 C2' C B1407 OK 542 538 541 560 C2' A B1408 OK 562 558 561 582 C2' C B1409 OK 584 580 583 602 C2' A B1410 OK 604 600 603 624 C2' C B1411 OK 626 622 625 644 C2' C B1412 OK 646 642 645 664 C2' G B1488 OK 666 662 665 687 C2' G B1489 OK 689 685 688 710 C2' U B1490 OK 712 708 711 730 C2' G B1491 OK 732 728 731 753 C2' A B1492 OK 755 751 754 775 C2' A B1493 OK 777 773 776 797 C2' G B1494 OK 799 795 798 820 C2' U B1495 OK 822 818 821 840 C2' C B1496 OK 842 838 841 860 C2' G B1497 OK 862 858 861 883 C2' C B1498 OK 885 881 884 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A1403 OK 3 6 7 28 C3' C A1404 OK 26 29 30 48 C3' G A1405 OK 46 49 50 71 C3' U A1406 OK 69 72 73 91 C3' C A1407 OK 89 92 93 111 C3' A A1408 OK 109 112 113 133 C3' C A1409 OK 131 134 135 153 C3' A A1410 OK 151 154 155 175 C3' C A1411 OK 173 176 177 195 C3' C A1412 OK 193 196 197 215 C3' G A1488 OK 213 216 217 238 C3' G A1489 OK 236 239 240 261 C3' U A1490 OK 259 262 263 281 C3' G A1491 OK 279 282 283 304 C3' A A1492 OK 302 305 306 326 C3' A A1493 OK 324 327 328 348 C3' G A1494 OK 346 349 350 371 C3' U A1495 OK 369 372 373 391 C3' C A1496 OK 389 392 393 411 C3' G A1497 OK 409 412 413 434 C3' C A1498 OK 432 435 436 452 C3' G B1403 OK 450 453 454 475 C3' C B1404 OK 473 476 477 495 C3' G B1405 OK 493 496 497 518 C3' U B1406 OK 516 519 520 538 C3' C B1407 OK 536 539 540 558 C3' A B1408 OK 556 559 560 580 C3' C B1409 OK 578 581 582 600 C3' A B1410 OK 598 601 602 622 C3' C B1411 OK 620 623 624 642 C3' C B1412 OK 640 643 644 662 C3' G B1488 OK 660 663 664 685 C3' G B1489 OK 683 686 687 708 C3' U B1490 OK 706 709 710 728 C3' G B1491 OK 726 729 730 751 C3' A B1492 OK 749 752 753 773 C3' A B1493 OK 771 774 775 795 C3' G B1494 OK 793 796 797 818 C3' U B1495 OK 816 819 820 838 C3' C B1496 OK 836 839 840 858 C3' G B1497 OK 856 859 860 881 C3' C B1498 OK 879 882 883 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A1403 OK 5 2 4 26 C4' C A1404 OK 28 25 27 46 C4' G A1405 OK 48 45 47 69 C4' U A1406 OK 71 68 70 89 C4' C A1407 OK 91 88 90 109 C4' A A1408 OK 111 108 110 131 C4' C A1409 OK 133 130 132 151 C4' A A1410 OK 153 150 152 173 C4' C A1411 OK 175 172 174 193 C4' C A1412 OK 195 192 194 213 C4' G A1488 OK 215 212 214 236 C4' G A1489 OK 238 235 237 259 C4' U A1490 OK 261 258 260 279 C4' G A1491 OK 281 278 280 302 C4' A A1492 OK 304 301 303 324 C4' A A1493 OK 326 323 325 346 C4' G A1494 OK 348 345 347 369 C4' U A1495 OK 371 368 370 389 C4' C A1496 OK 391 388 390 409 C4' G A1497 OK 411 408 410 432 C4' C A1498 OK 434 431 433 450 C4' G B1403 OK 452 449 451 473 C4' C B1404 OK 475 472 474 493 C4' G B1405 OK 495 492 494 516 C4' U B1406 OK 518 515 517 536 C4' C B1407 OK 538 535 537 556 C4' A B1408 OK 558 555 557 578 C4' C B1409 OK 580 577 579 598 C4' A B1410 OK 600 597 599 620 C4' C B1411 OK 622 619 621 640 C4' C B1412 OK 642 639 641 660 C4' G B1488 OK 662 659 661 683 C4' G B1489 OK 685 682 684 706 C4' U B1490 OK 708 705 707 726 C4' G B1491 OK 728 725 727 749 C4' A B1492 OK 751 748 750 771 C4' A B1493 OK 773 770 772 793 C4' G B1494 OK 795 792 794 816 C4' U B1495 OK 818 815 817 836 C4' C B1496 OK 838 835 837 856 C4' G B1497 OK 858 855 857 879 C4' C B1498 OK 881 878 880 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A1403 1 3 25 C5' C A1404 24 26 45 C5' G A1405 44 46 68 C5' U A1406 67 69 88 C5' C A1407 87 89 108 C5' A A1408 107 109 130 C5' C A1409 129 131 150 C5' A A1410 149 151 172 C5' C A1411 171 173 192 C5' C A1412 191 193 212 C5' G A1488 211 213 235 C5' G A1489 234 236 258 C5' U A1490 257 259 278 C5' G A1491 277 279 301 C5' A A1492 300 302 323 C5' A A1493 322 324 345 C5' G A1494 344 346 368 C5' U A1495 367 369 388 C5' C A1496 387 389 408 C5' G A1497 407 409 431 C5' C A1498 430 432 449 C5' G B1403 448 450 472 C5' C B1404 471 473 492 C5' G B1405 491 493 515 C5' U B1406 514 516 535 C5' C B1407 534 536 555 C5' A B1408 554 556 577 C5' C B1409 576 578 597 C5' A B1410 596 598 619 C5' C B1411 618 620 639 C5' C B1412 638 640 659 C5' G B1488 658 660 682 C5' G B1489 681 683 705 C5' U B1490 704 706 725 C5' G B1491 724 726 748 C5' A B1492 747 749 770 C5' A B1493 769 771 792 C5' G B1494 791 793 815 C5' U B1495 814 816 835 C5' C B1496 834 836 855 C5' G B1497 854 856 878 C5' C B1498 877 879 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A1404 distorted distorted 6 22 23 24 41 P G A1405 distorted distorted 29 42 43 44 64 P U A1406 distorted distorted 49 65 66 67 84 P C A1407 distorted distorted 72 85 86 87 104 P A A1408 distorted distorted 92 105 106 107 126 P C A1409 distorted distorted 112 127 128 129 146 P A A1410 distorted distorted 134 147 148 149 168 P C A1411 distorted distorted 154 169 170 171 188 P C A1412 distorted distorted 176 189 190 191 208 P G A1488 distorted distorted 196 209 210 211 231 P G A1489 distorted distorted 216 232 233 234 254 P U A1490 distorted distorted 239 255 256 257 274 P G A1491 distorted distorted 262 275 276 277 297 P A A1492 distorted distorted 282 298 299 300 319 P A A1493 distorted distorted 305 320 321 322 341 P G A1494 distorted distorted 327 342 343 344 364 P U A1495 distorted distorted 349 365 366 367 384 P C A1496 distorted distorted 372 385 386 387 404 P G A1497 distorted distorted 392 405 406 407 427 P C A1498 distorted distorted 412 428 429 430 468 P C B1404 distorted distorted 453 469 470 471 488 P G B1405 distorted distorted 476 489 490 491 511 P U B1406 distorted distorted 496 512 513 514 531 P C B1407 distorted distorted 519 532 533 534 551 P A B1408 distorted distorted 539 552 553 554 573 P C B1409 distorted distorted 559 574 575 576 593 P A B1410 distorted distorted 581 594 595 596 615 P C B1411 distorted distorted 601 616 617 618 635 P C B1412 distorted distorted 623 636 637 638 655 P G B1488 distorted distorted 643 656 657 658 678 P G B1489 distorted distorted 663 679 680 681 701 P U B1490 distorted distorted 686 702 703 704 721 P G B1491 distorted distorted 709 722 723 724 744 P A B1492 distorted distorted 729 745 746 747 766 P A B1493 distorted distorted 752 767 768 769 788 P G B1494 distorted distorted 774 789 790 791 811 P U B1495 distorted distorted 796 812 813 814 831 P C B1496 distorted distorted 819 832 833 834 851 P G B1497 distorted distorted 839 852 853 854 874 P C B1498 distorted distorted 859 875 876 877 ---------------------------------------------------------------------------------