ID code: '4RBQ' 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' A A 1 alpha beta 4 26 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' A A 3 alpha beta 72 94 78 75 110 C1' G A 4 alpha beta 105 128 111 108 144 C1' A A 5 alpha beta 139 161 145 142 177 C1' A A 6 alpha beta 172 194 178 175 210 C1' G A 7 alpha beta 205 228 211 208 244 C1' A A 8 alpha beta 239 261 245 242 277 C1' A A 9 alpha beta 272 294 278 275 310 C1' A A 10 alpha beta 305 327 311 308 343 C1' G A 11 alpha beta 338 361 344 341 377 C1' G A 12 alpha beta 372 395 378 375 411 C1' G A 13 alpha beta 406 429 412 409 445 C1' A A 14 alpha beta 440 462 446 443 478 C1' A A 15 alpha beta 473 495 479 476 511 C1' A A 16 alpha beta 506 528 512 509 544 C1' U A 17 alpha beta 539 559 545 542 574 C1' U A 18 alpha beta 569 589 575 572 604 C1' U A 19 alpha beta 599 619 605 602 634 C1' U A 20 alpha beta 629 649 635 632 664 C1' U A 21 alpha beta 659 679 665 662 694 C1' U A 22 alpha beta 689 709 695 692 724 C1' U A 23 alpha beta 719 739 725 722 754 C1' U A 24 alpha beta 749 769 755 752 784 C1' U A 25 alpha beta 779 799 785 782 814 C1' U A 26 alpha beta 809 829 815 812 844 C1' U A 27 alpha beta 839 859 845 842 874 C1' U A 28 alpha beta 869 889 875 872 904 C1' U A 29 alpha beta 899 919 905 902 934 C1' U A 30 alpha beta 929 949 935 932 964 C1' U A 31 alpha beta 959 979 965 962 994 C1' U A 32 alpha beta 989 1010 995 992 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A A 1 OK OK 9 5 24 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' A A 3 OK OK 77 73 92 76 108 C2' G A 4 OK OK 110 106 126 109 142 C2' A A 5 OK OK 144 140 159 143 175 C2' A A 6 OK OK 177 173 192 176 208 C2' G A 7 OK OK 210 206 226 209 242 C2' A A 8 OK OK 244 240 259 243 275 C2' A A 9 OK OK 277 273 292 276 308 C2' A A 10 OK OK 310 306 325 309 341 C2' G A 11 OK OK 343 339 359 342 375 C2' G A 12 OK OK 377 373 393 376 409 C2' G A 13 OK OK 411 407 427 410 443 C2' A A 14 OK OK 445 441 460 444 476 C2' A A 15 OK OK 478 474 493 477 509 C2' A A 16 OK OK 511 507 526 510 542 C2' U A 17 OK OK 544 540 557 543 572 C2' U A 18 OK OK 574 570 587 573 602 C2' U A 19 OK OK 604 600 617 603 632 C2' U A 20 OK OK 634 630 647 633 662 C2' U A 21 OK OK 664 660 677 663 692 C2' U A 22 OK OK 694 690 707 693 722 C2' U A 23 OK OK 724 720 737 723 752 C2' U A 24 OK OK 754 750 767 753 782 C2' U A 25 OK OK 784 780 797 783 812 C2' U A 26 OK OK 814 810 827 813 842 C2' U A 27 OK OK 844 840 857 843 872 C2' U A 28 OK OK 874 870 887 873 902 C2' U A 29 OK OK 904 900 917 903 932 C2' U A 30 OK OK 934 930 947 933 962 C2' U A 31 OK OK 964 960 977 963 992 C2' U A 32 OK OK 994 990 1008 993 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A A 1 OK OK 3 23 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' A A 3 OK OK 71 91 74 75 106 C3' G A 4 OK OK 104 125 107 108 140 C3' A A 5 OK OK 138 158 141 142 173 C3' A A 6 OK OK 171 191 174 175 206 C3' G A 7 OK OK 204 225 207 208 240 C3' A A 8 OK OK 238 258 241 242 273 C3' A A 9 OK OK 271 291 274 275 306 C3' A A 10 OK OK 304 324 307 308 339 C3' G A 11 OK OK 337 358 340 341 373 C3' G A 12 OK OK 371 392 374 375 407 C3' G A 13 OK OK 405 426 408 409 441 C3' A A 14 OK OK 439 459 442 443 474 C3' A A 15 OK OK 472 492 475 476 507 C3' A A 16 OK OK 505 525 508 509 540 C3' U A 17 OK OK 538 556 541 542 570 C3' U A 18 OK OK 568 586 571 572 600 C3' U A 19 OK OK 598 616 601 602 630 C3' U A 20 OK OK 628 646 631 632 660 C3' U A 21 OK OK 658 676 661 662 690 C3' U A 22 OK OK 688 706 691 692 720 C3' U A 23 OK OK 718 736 721 722 750 C3' U A 24 OK OK 748 766 751 752 780 C3' U A 25 OK OK 778 796 781 782 810 C3' U A 26 OK OK 808 826 811 812 840 C3' U A 27 OK OK 838 856 841 842 870 C3' U A 28 OK OK 868 886 871 872 900 C3' U A 29 OK OK 898 916 901 902 930 C3' U A 30 OK OK 928 946 931 932 960 C3' U A 31 OK OK 958 976 961 962 990 C3' U A 32 OK OK 988 1006 991 992 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A A 1 OK OK 5 22 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' A A 3 OK OK 73 90 70 72 104 C4' G A 4 OK OK 106 124 103 105 138 C4' A A 5 OK OK 140 157 137 139 171 C4' A A 6 OK OK 173 190 170 172 204 C4' G A 7 OK OK 206 224 203 205 238 C4' A A 8 OK OK 240 257 237 239 271 C4' A A 9 OK OK 273 290 270 272 304 C4' A A 10 OK OK 306 323 303 305 337 C4' G A 11 OK OK 339 357 336 338 371 C4' G A 12 OK OK 373 391 370 372 405 C4' G A 13 OK OK 407 425 404 406 439 C4' A A 14 OK OK 441 458 438 440 472 C4' A A 15 OK OK 474 491 471 473 505 C4' A A 16 OK OK 507 524 504 506 538 C4' U A 17 OK OK 540 555 537 539 568 C4' U A 18 OK OK 570 585 567 569 598 C4' U A 19 OK OK 600 615 597 599 628 C4' U A 20 OK OK 630 645 627 629 658 C4' U A 21 OK OK 660 675 657 659 688 C4' U A 22 OK OK 690 705 687 689 718 C4' U A 23 OK OK 720 735 717 719 748 C4' U A 24 OK OK 750 765 747 749 778 C4' U A 25 OK OK 780 795 777 779 808 C4' U A 26 OK OK 810 825 807 809 838 C4' U A 27 OK OK 840 855 837 839 868 C4' U A 28 OK OK 870 885 867 869 898 C4' U A 29 OK OK 900 915 897 899 928 C4' U A 30 OK OK 930 945 927 929 958 C4' U A 31 OK OK 960 975 957 959 988 C4' U A 32 OK OK 990 1005 987 989 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A A 1 OK OK 1 20 21 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' A A 3 OK OK 69 88 89 71 103 C5' G A 4 OK OK 102 122 123 104 137 C5' A A 5 OK OK 136 155 156 138 170 C5' A A 6 OK OK 169 188 189 171 203 C5' G A 7 OK OK 202 222 223 204 237 C5' A A 8 OK OK 236 255 256 238 270 C5' A A 9 OK OK 269 288 289 271 303 C5' A A 10 OK OK 302 321 322 304 336 C5' G A 11 OK OK 335 355 356 337 370 C5' G A 12 OK OK 369 389 390 371 404 C5' G A 13 OK OK 403 423 424 405 438 C5' A A 14 OK OK 437 456 457 439 471 C5' A A 15 OK OK 470 489 490 472 504 C5' A A 16 OK OK 503 522 523 505 537 C5' U A 17 OK OK 536 553 554 538 567 C5' U A 18 OK OK 566 583 584 568 597 C5' U A 19 OK OK 596 613 614 598 627 C5' U A 20 OK OK 626 643 644 628 657 C5' U A 21 OK OK 656 673 674 658 687 C5' U A 22 OK OK 686 703 704 688 717 C5' U A 23 OK OK 716 733 734 718 747 C5' U A 24 OK OK 746 763 764 748 777 C5' U A 25 OK OK 776 793 794 778 807 C5' U A 26 OK OK 806 823 824 808 837 C5' U A 27 OK OK 836 853 854 838 867 C5' U A 28 OK OK 866 883 884 868 897 C5' U A 29 OK OK 896 913 914 898 927 C5' U A 30 OK OK 926 943 944 928 957 C5' U A 31 OK OK 956 973 974 958 987 C5' U A 32 OK OK 986 1003 1004 988 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P A A 3 distorted distorted 40 67 68 69 99 P G A 4 distorted distorted 74 100 101 102 133 P A A 5 distorted distorted 107 134 135 136 166 P A A 6 distorted distorted 141 167 168 169 199 P G A 7 distorted distorted 174 200 201 202 233 P A A 8 distorted distorted 207 234 235 236 266 P A A 9 distorted distorted 241 267 268 269 299 P A A 10 distorted distorted 274 300 301 302 332 P G A 11 distorted distorted 307 333 334 335 366 P G A 12 distorted distorted 340 367 368 369 400 P G A 13 distorted distorted 374 401 402 403 434 P A A 14 distorted distorted 408 435 436 437 467 P A A 15 distorted distorted 442 468 469 470 500 P A A 16 distorted distorted 475 501 502 503 533 P U A 17 distorted distorted 508 534 535 536 563 P U A 18 distorted distorted 541 564 565 566 593 P U A 19 distorted distorted 571 594 595 596 623 P U A 20 distorted distorted 601 624 625 626 653 P U A 21 distorted distorted 631 654 655 656 683 P U A 22 distorted distorted 661 684 685 686 713 P U A 23 distorted distorted 691 714 715 716 743 P U A 24 distorted distorted 721 744 745 746 773 P U A 25 distorted distorted 751 774 775 776 803 P U A 26 distorted distorted 781 804 805 806 833 P U A 27 distorted distorted 811 834 835 836 863 P U A 28 distorted distorted 841 864 865 866 893 P U A 29 distorted distorted 871 894 895 896 923 P U A 30 distorted distorted 901 924 925 926 953 P U A 31 distorted distorted 931 954 955 956 983 P U A 32 distorted distorted 961 984 985 986 ---------------------------------------------------------------------------------