ID code: '1D3U' 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' --------------------------------------------------------------------------------- 8 C1' A C1401 beta 4 9 7 29 C1' G C1402 beta 25 30 28 51 C1' A C1403 beta 47 52 50 72 C1' G C1404 beta 68 73 71 94 C1' T C1405 beta 90 95 93 114 C1' A C1406 beta 110 115 113 135 C1' A C1407 beta 131 136 134 156 C1' A C1408 beta 152 157 155 177 C1' G C1409 beta 173 178 176 199 C1' T C1410 beta 195 200 198 219 C1' T C1411 beta 215 220 218 239 C1' T C1412 beta 235 240 238 259 C1' A C1413 beta 255 260 258 280 C1' A C1414 beta 276 281 279 301 C1' A C1415 beta 297 302 300 322 C1' T C1416 beta 318 323 321 342 C1' A C1417 beta 338 343 341 363 C1' C C1418 beta 359 364 362 382 C1' T C1419 beta 378 383 381 402 C1' T C1420 beta 398 403 401 422 C1' A C1421 beta 418 423 421 443 C1' T C1422 beta 439 444 442 463 C1' A C1423 beta 459 464 462 482 C1' T D1426 beta 478 483 481 502 C1' A D1427 beta 498 503 501 523 C1' T D1428 beta 519 524 522 543 C1' A D1429 beta 539 544 542 564 C1' A D1430 beta 560 565 563 585 C1' G D1431 beta 581 586 584 607 C1' T D1432 beta 603 608 606 627 C1' A D1433 beta 623 628 626 648 C1' T D1434 beta 644 649 647 668 C1' T D1435 beta 664 669 667 688 C1' T D1436 beta 684 689 687 708 C1' A D1437 beta 704 709 707 729 C1' A D1438 beta 725 730 728 750 C1' A D1439 beta 746 751 749 771 C1' C D1440 beta 767 772 770 790 C1' T D1441 beta 786 791 789 810 C1' T D1442 beta 806 811 809 830 C1' T D1443 beta 826 831 829 850 C1' A D1444 beta 846 851 849 871 C1' C D1445 beta 867 872 870 890 C1' T D1446 beta 886 891 889 910 C1' C D1447 beta 906 911 909 929 C1' T D1448 beta 925 930 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C1401 8 5 28 C2' G C1402 29 26 50 C2' A C1403 51 48 71 C2' G C1404 72 69 93 C2' T C1405 94 91 113 C2' A C1406 114 111 134 C2' A C1407 135 132 155 C2' A C1408 156 153 176 C2' G C1409 177 174 198 C2' T C1410 199 196 218 C2' T C1411 219 216 238 C2' T C1412 239 236 258 C2' A C1413 259 256 279 C2' A C1414 280 277 300 C2' A C1415 301 298 321 C2' T C1416 322 319 341 C2' A C1417 342 339 362 C2' C C1418 363 360 381 C2' T C1419 382 379 401 C2' T C1420 402 399 421 C2' A C1421 422 419 442 C2' T C1422 443 440 462 C2' A C1423 463 460 481 C2' T D1426 482 479 501 C2' A D1427 502 499 522 C2' T D1428 523 520 542 C2' A D1429 543 540 563 C2' A D1430 564 561 584 C2' G D1431 585 582 606 C2' T D1432 607 604 626 C2' A D1433 627 624 647 C2' T D1434 648 645 667 C2' T D1435 668 665 687 C2' T D1436 688 685 707 C2' A D1437 708 705 728 C2' A D1438 729 726 749 C2' A D1439 750 747 770 C2' C D1440 771 768 789 C2' T D1441 790 787 809 C2' T D1442 810 807 829 C2' T D1443 830 827 849 C2' A D1444 850 847 870 C2' C D1445 871 868 889 C2' T D1446 890 887 909 C2' C D1447 910 907 928 C2' T D1448 929 926 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C1401 OK 3 6 7 26 C3' G C1402 OK 24 27 28 48 C3' A C1403 OK 46 49 50 69 C3' G C1404 OK 67 70 71 91 C3' T C1405 OK 89 92 93 111 C3' A C1406 OK 109 112 113 132 C3' A C1407 OK 130 133 134 153 C3' A C1408 OK 151 154 155 174 C3' G C1409 OK 172 175 176 196 C3' T C1410 OK 194 197 198 216 C3' T C1411 OK 214 217 218 236 C3' T C1412 OK 234 237 238 256 C3' A C1413 OK 254 257 258 277 C3' A C1414 OK 275 278 279 298 C3' A C1415 OK 296 299 300 319 C3' T C1416 OK 317 320 321 339 C3' A C1417 OK 337 340 341 360 C3' C C1418 OK 358 361 362 379 C3' T C1419 OK 377 380 381 399 C3' T C1420 OK 397 400 401 419 C3' A C1421 OK 417 420 421 440 C3' T C1422 OK 438 441 442 460 C3' A C1423 OK 458 461 462 479 C3' T D1426 OK 477 480 481 499 C3' A D1427 OK 497 500 501 520 C3' T D1428 OK 518 521 522 540 C3' A D1429 OK 538 541 542 561 C3' A D1430 OK 559 562 563 582 C3' G D1431 OK 580 583 584 604 C3' T D1432 OK 602 605 606 624 C3' A D1433 OK 622 625 626 645 C3' T D1434 OK 643 646 647 665 C3' T D1435 OK 663 666 667 685 C3' T D1436 OK 683 686 687 705 C3' A D1437 OK 703 706 707 726 C3' A D1438 OK 724 727 728 747 C3' A D1439 OK 745 748 749 768 C3' C D1440 OK 766 769 770 787 C3' T D1441 OK 785 788 789 807 C3' T D1442 OK 805 808 809 827 C3' T D1443 OK 825 828 829 847 C3' A D1444 OK 845 848 849 868 C3' C D1445 OK 866 869 870 887 C3' T D1446 OK 885 888 889 907 C3' C D1447 OK 905 908 909 926 C3' T D1448 OK 924 927 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C1401 OK 5 2 4 24 C4' G C1402 OK 26 23 25 46 C4' A C1403 OK 48 45 47 67 C4' G C1404 OK 69 66 68 89 C4' T C1405 OK 91 88 90 109 C4' A C1406 OK 111 108 110 130 C4' A C1407 OK 132 129 131 151 C4' A C1408 OK 153 150 152 172 C4' G C1409 OK 174 171 173 194 C4' T C1410 OK 196 193 195 214 C4' T C1411 OK 216 213 215 234 C4' T C1412 OK 236 233 235 254 C4' A C1413 OK 256 253 255 275 C4' A C1414 OK 277 274 276 296 C4' A C1415 OK 298 295 297 317 C4' T C1416 OK 319 316 318 337 C4' A C1417 OK 339 336 338 358 C4' C C1418 OK 360 357 359 377 C4' T C1419 OK 379 376 378 397 C4' T C1420 OK 399 396 398 417 C4' A C1421 OK 419 416 418 438 C4' T C1422 OK 440 437 439 458 C4' A C1423 OK 460 457 459 477 C4' T D1426 OK 479 476 478 497 C4' A D1427 OK 499 496 498 518 C4' T D1428 OK 520 517 519 538 C4' A D1429 OK 540 537 539 559 C4' A D1430 OK 561 558 560 580 C4' G D1431 OK 582 579 581 602 C4' T D1432 OK 604 601 603 622 C4' A D1433 OK 624 621 623 643 C4' T D1434 OK 645 642 644 663 C4' T D1435 OK 665 662 664 683 C4' T D1436 OK 685 682 684 703 C4' A D1437 OK 705 702 704 724 C4' A D1438 OK 726 723 725 745 C4' A D1439 OK 747 744 746 766 C4' C D1440 OK 768 765 767 785 C4' T D1441 OK 787 784 786 805 C4' T D1442 OK 807 804 806 825 C4' T D1443 OK 827 824 826 845 C4' A D1444 OK 847 844 846 866 C4' C D1445 OK 868 865 867 885 C4' T D1446 OK 887 884 886 905 C4' C D1447 OK 907 904 906 924 C4' T D1448 OK 926 923 925 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C1401 1 3 23 C5' G C1402 22 24 45 C5' A C1403 44 46 66 C5' G C1404 65 67 88 C5' T C1405 87 89 108 C5' A C1406 107 109 129 C5' A C1407 128 130 150 C5' A C1408 149 151 171 C5' G C1409 170 172 193 C5' T C1410 192 194 213 C5' T C1411 212 214 233 C5' T C1412 232 234 253 C5' A C1413 252 254 274 C5' A C1414 273 275 295 C5' A C1415 294 296 316 C5' T C1416 315 317 336 C5' A C1417 335 337 357 C5' C C1418 356 358 376 C5' T C1419 375 377 396 C5' T C1420 395 397 416 C5' A C1421 415 417 437 C5' T C1422 436 438 457 C5' A C1423 456 458 476 C5' T D1426 475 477 496 C5' A D1427 495 497 517 C5' T D1428 516 518 537 C5' A D1429 536 538 558 C5' A D1430 557 559 579 C5' G D1431 578 580 601 C5' T D1432 600 602 621 C5' A D1433 620 622 642 C5' T D1434 641 643 662 C5' T D1435 661 663 682 C5' T D1436 681 683 702 C5' A D1437 701 703 723 C5' A D1438 722 724 744 C5' A D1439 743 745 765 C5' C D1440 764 766 784 C5' T D1441 783 785 804 C5' T D1442 803 805 824 C5' T D1443 823 825 844 C5' A D1444 843 845 865 C5' C D1445 864 866 884 C5' T D1446 883 885 904 C5' C D1447 903 905 923 C5' T D1448 922 924 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G C1402 distorted distorted 6 20 21 22 41 P A C1403 distorted distorted 27 42 43 44 62 P G C1404 distorted distorted 49 63 64 65 84 P T C1405 distorted distorted 70 85 86 87 104 P A C1406 distorted distorted 92 105 106 107 125 P A C1407 distorted distorted 112 126 127 128 146 P A C1408 distorted distorted 133 147 148 149 167 P G C1409 distorted distorted 154 168 169 170 189 P T C1410 distorted distorted 175 190 191 192 209 P T C1411 distorted distorted 197 210 211 212 229 P T C1412 distorted distorted 217 230 231 232 249 P A C1413 distorted distorted 237 250 251 252 270 P A C1414 distorted distorted 257 271 272 273 291 P A C1415 distorted distorted 278 292 293 294 312 P T C1416 distorted distorted 299 313 314 315 332 P A C1417 distorted distorted 320 333 334 335 353 P C C1418 distorted distorted 340 354 355 356 372 P T C1419 distorted distorted 361 373 374 375 392 P T C1420 distorted distorted 380 393 394 395 412 P A C1421 distorted distorted 400 413 414 415 433 P T C1422 distorted distorted 420 434 435 436 453 P A C1423 distorted distorted 441 454 455 456 492 P A D1427 distorted distorted 480 493 494 495 513 P T D1428 distorted distorted 500 514 515 516 533 P A D1429 distorted distorted 521 534 535 536 554 P A D1430 distorted distorted 541 555 556 557 575 P G D1431 distorted distorted 562 576 577 578 597 P T D1432 distorted distorted 583 598 599 600 617 P A D1433 distorted distorted 605 618 619 620 638 P T D1434 distorted distorted 625 639 640 641 658 P T D1435 distorted distorted 646 659 660 661 678 P T D1436 distorted distorted 666 679 680 681 698 P A D1437 distorted distorted 686 699 700 701 719 P A D1438 distorted distorted 706 720 721 722 740 P A D1439 distorted distorted 727 741 742 743 761 P C D1440 distorted distorted 748 762 763 764 780 P T D1441 distorted distorted 769 781 782 783 800 P T D1442 distorted distorted 788 801 802 803 820 P T D1443 distorted distorted 808 821 822 823 840 P A D1444 distorted distorted 828 841 842 843 861 P C D1445 distorted distorted 848 862 863 864 880 P T D1446 distorted distorted 869 881 882 883 900 P C D1447 distorted distorted 888 901 902 903 919 P T D1448 distorted distorted 908 920 921 922 ---------------------------------------------------------------------------------