ID code: '5DA6' 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' --------------------------------------------------------------------------------- 274 C1' A A 5 alpha beta 269 291 275 272 307 C1' A A 6 alpha beta 302 324 308 305 340 C1' G A 7 alpha beta 335 358 341 338 374 C1' A A 8 alpha beta 369 391 375 372 407 C1' A A 9 alpha beta 402 424 408 405 440 C1' A A 10 alpha beta 435 457 441 438 473 C1' G A 11 alpha beta 468 491 474 471 507 C1' G A 12 alpha beta 502 525 508 505 541 C1' G A 13 alpha beta 536 559 542 539 575 C1' A A 14 alpha beta 570 592 576 573 608 C1' A A 15 alpha beta 603 625 609 606 641 C1' A A 16 alpha beta 636 658 642 639 674 C1' U A 17 alpha beta 669 689 675 672 704 C1' U A 18 alpha beta 699 719 705 702 734 C1' U A 19 alpha beta 729 749 735 732 764 C1' U A 20 alpha beta 759 779 765 762 794 C1' U A 21 alpha beta 789 809 795 792 824 C1' U A 22 alpha beta 819 839 825 822 854 C1' U A 23 alpha beta 849 869 855 852 884 C1' U A 24 alpha beta 879 899 885 882 914 C1' U A 25 alpha beta 909 929 915 912 944 C1' U A 26 alpha beta 939 959 945 942 974 C1' U A 27 alpha beta 969 989 975 972 1004 C1' U A 28 alpha beta 999 1019 1005 1002 1034 C1' U A 29 alpha beta 1029 1049 1035 1032 1064 C1' U A 30 alpha beta 1059 1079 1065 1062 1094 C1' U A 31 alpha beta 1089 1109 1095 1092 1124 C1' U A 32 alpha beta 1119 1140 1125 1122 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 272 C2' A A 5 OK OK 274 270 289 273 305 C2' A A 6 OK OK 307 303 322 306 338 C2' G A 7 OK OK 340 336 356 339 372 C2' A A 8 OK OK 374 370 389 373 405 C2' A A 9 OK OK 407 403 422 406 438 C2' A A 10 OK OK 440 436 455 439 471 C2' G A 11 OK OK 473 469 489 472 505 C2' G A 12 OK OK 507 503 523 506 539 C2' G A 13 OK OK 541 537 557 540 573 C2' A A 14 OK OK 575 571 590 574 606 C2' A A 15 OK OK 608 604 623 607 639 C2' A A 16 OK OK 641 637 656 640 672 C2' U A 17 OK OK 674 670 687 673 702 C2' U A 18 OK OK 704 700 717 703 732 C2' U A 19 OK OK 734 730 747 733 762 C2' U A 20 OK OK 764 760 777 763 792 C2' U A 21 OK OK 794 790 807 793 822 C2' U A 22 OK OK 824 820 837 823 852 C2' U A 23 OK OK 854 850 867 853 882 C2' U A 24 OK OK 884 880 897 883 912 C2' U A 25 OK OK 914 910 927 913 942 C2' U A 26 OK OK 944 940 957 943 972 C2' U A 27 OK OK 974 970 987 973 1002 C2' U A 28 OK OK 1004 1000 1017 1003 1032 C2' U A 29 OK OK 1034 1030 1047 1033 1062 C2' U A 30 OK OK 1064 1060 1077 1063 1092 C2' U A 31 OK OK 1094 1090 1107 1093 1122 C2' U A 32 OK OK 1124 1120 1138 1123 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 270 C3' A A 5 OK OK 268 288 271 272 303 C3' A A 6 OK OK 301 321 304 305 336 C3' G A 7 OK OK 334 355 337 338 370 C3' A A 8 OK OK 368 388 371 372 403 C3' A A 9 OK OK 401 421 404 405 436 C3' A A 10 OK OK 434 454 437 438 469 C3' G A 11 OK OK 467 488 470 471 503 C3' G A 12 OK OK 501 522 504 505 537 C3' G A 13 OK OK 535 556 538 539 571 C3' A A 14 OK OK 569 589 572 573 604 C3' A A 15 OK OK 602 622 605 606 637 C3' A A 16 OK OK 635 655 638 639 670 C3' U A 17 OK OK 668 686 671 672 700 C3' U A 18 OK OK 698 716 701 702 730 C3' U A 19 OK OK 728 746 731 732 760 C3' U A 20 OK OK 758 776 761 762 790 C3' U A 21 OK OK 788 806 791 792 820 C3' U A 22 OK OK 818 836 821 822 850 C3' U A 23 OK OK 848 866 851 852 880 C3' U A 24 OK OK 878 896 881 882 910 C3' U A 25 OK OK 908 926 911 912 940 C3' U A 26 OK OK 938 956 941 942 970 C3' U A 27 OK OK 968 986 971 972 1000 C3' U A 28 OK OK 998 1016 1001 1002 1030 C3' U A 29 OK OK 1028 1046 1031 1032 1060 C3' U A 30 OK OK 1058 1076 1061 1062 1090 C3' U A 31 OK OK 1088 1106 1091 1092 1120 C3' U A 32 OK OK 1118 1136 1121 1122 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 268 C4' A A 5 OK OK 270 287 267 269 301 C4' A A 6 OK OK 303 320 300 302 334 C4' G A 7 OK OK 336 354 333 335 368 C4' A A 8 OK OK 370 387 367 369 401 C4' A A 9 OK OK 403 420 400 402 434 C4' A A 10 OK OK 436 453 433 435 467 C4' G A 11 OK OK 469 487 466 468 501 C4' G A 12 OK OK 503 521 500 502 535 C4' G A 13 OK OK 537 555 534 536 569 C4' A A 14 OK OK 571 588 568 570 602 C4' A A 15 OK OK 604 621 601 603 635 C4' A A 16 OK OK 637 654 634 636 668 C4' U A 17 OK OK 670 685 667 669 698 C4' U A 18 OK OK 700 715 697 699 728 C4' U A 19 OK OK 730 745 727 729 758 C4' U A 20 OK OK 760 775 757 759 788 C4' U A 21 OK OK 790 805 787 789 818 C4' U A 22 OK OK 820 835 817 819 848 C4' U A 23 OK OK 850 865 847 849 878 C4' U A 24 OK OK 880 895 877 879 908 C4' U A 25 OK OK 910 925 907 909 938 C4' U A 26 OK OK 940 955 937 939 968 C4' U A 27 OK OK 970 985 967 969 998 C4' U A 28 OK OK 1000 1015 997 999 1028 C4' U A 29 OK OK 1030 1045 1027 1029 1058 C4' U A 30 OK OK 1060 1075 1057 1059 1088 C4' U A 31 OK OK 1090 1105 1087 1089 1118 C4' U A 32 OK OK 1120 1135 1117 1119 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 267 C5' A A 5 OK OK 266 285 286 268 300 C5' A A 6 OK OK 299 318 319 301 333 C5' G A 7 OK OK 332 352 353 334 367 C5' A A 8 OK OK 366 385 386 368 400 C5' A A 9 OK OK 399 418 419 401 433 C5' A A 10 OK OK 432 451 452 434 466 C5' G A 11 OK OK 465 485 486 467 500 C5' G A 12 OK OK 499 519 520 501 534 C5' G A 13 OK OK 533 553 554 535 568 C5' A A 14 OK OK 567 586 587 569 601 C5' A A 15 OK OK 600 619 620 602 634 C5' A A 16 OK OK 633 652 653 635 667 C5' U A 17 OK OK 666 683 684 668 697 C5' U A 18 OK OK 696 713 714 698 727 C5' U A 19 OK OK 726 743 744 728 757 C5' U A 20 OK OK 756 773 774 758 787 C5' U A 21 OK OK 786 803 804 788 817 C5' U A 22 OK OK 816 833 834 818 847 C5' U A 23 OK OK 846 863 864 848 877 C5' U A 24 OK OK 876 893 894 878 907 C5' U A 25 OK OK 906 923 924 908 937 C5' U A 26 OK OK 936 953 954 938 967 C5' U A 27 OK OK 966 983 984 968 997 C5' U A 28 OK OK 996 1013 1014 998 1027 C5' U A 29 OK OK 1026 1043 1044 1028 1057 C5' U A 30 OK OK 1056 1073 1074 1058 1087 C5' U A 31 OK OK 1086 1103 1104 1088 1117 C5' U A 32 OK OK 1116 1133 1134 1118 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 63 P G A 2 64 P G A 2 131 P A A 3 132 P A A 3 197 P G A 4 198 P G A 4 263 P A A 5 distorted distorted 264 265 266 296 P A A 6 distorted distorted 271 297 298 299 329 P G A 7 distorted distorted 304 330 331 332 363 P A A 8 distorted distorted 337 364 365 366 396 P A A 9 distorted distorted 371 397 398 399 429 P A A 10 distorted distorted 404 430 431 432 462 P G A 11 distorted distorted 437 463 464 465 496 P G A 12 distorted distorted 470 497 498 499 530 P G A 13 distorted distorted 504 531 532 533 564 P A A 14 distorted distorted 538 565 566 567 597 P A A 15 distorted distorted 572 598 599 600 630 P A A 16 distorted distorted 605 631 632 633 663 P U A 17 distorted distorted 638 664 665 666 693 P U A 18 distorted distorted 671 694 695 696 723 P U A 19 distorted distorted 701 724 725 726 753 P U A 20 distorted distorted 731 754 755 756 783 P U A 21 distorted distorted 761 784 785 786 813 P U A 22 distorted distorted 791 814 815 816 843 P U A 23 distorted distorted 821 844 845 846 873 P U A 24 distorted distorted 851 874 875 876 903 P U A 25 distorted distorted 881 904 905 906 933 P U A 26 distorted distorted 911 934 935 936 963 P U A 27 distorted distorted 941 964 965 966 993 P U A 28 distorted distorted 971 994 995 996 1023 P U A 29 distorted distorted 1001 1024 1025 1026 1053 P U A 30 distorted distorted 1031 1054 1055 1056 1083 P U A 31 distorted distorted 1061 1084 1085 1086 1113 P U A 32 distorted distorted 1091 1114 1115 1116 ---------------------------------------------------------------------------------