ID code: '2A9X' 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' --------------------------------------------------------------------------------- 280 C1' G 2 4 alpha beta 275 296 281 278 313 C1' G 2 5 alpha beta 308 329 314 311 345 C1' C 2 6 alpha beta 340 358 346 343 374 C1' U 2 7 alpha beta 369 387 375 372 402 C1' C 2 8 alpha beta 397 415 403 400 431 C1' G 2 9 alpha beta 426 447 432 429 463 C1' U 2 10 alpha beta 458 476 464 461 491 C1' G 2 11 alpha beta 486 507 492 489 523 C1' U 2 12 alpha beta 518 536 524 521 551 C1' A 2 13 alpha beta 546 566 552 549 582 C1' G 2 14 alpha beta 577 598 583 580 614 C1' C 2 15 alpha beta 609 627 615 612 643 C1' U 2 16 alpha beta 638 656 644 641 671 C1' C 2 17 alpha beta 666 684 672 669 700 C1' A 2 18 alpha beta 695 715 701 698 731 C1' U 2 19 alpha beta 726 744 732 729 759 C1' U 2 20 alpha beta 754 772 760 757 787 C1' A 2 21 alpha beta 782 802 788 785 818 C1' G 2 22 alpha beta 813 834 819 816 850 C1' C 2 23 alpha beta 845 863 851 848 879 C1' U 2 24 alpha beta 874 892 880 877 907 C1' C 2 25 alpha beta 902 920 908 905 936 C1' C 2 26 alpha beta 931 949 937 934 965 C1' G 2 27 alpha beta 960 981 966 963 997 C1' A 2 28 alpha beta 992 1012 998 995 1028 C1' G 2 29 alpha beta 1023 1044 1029 1026 1060 C1' C 2 30 alpha beta 1055 1073 1061 1058 1089 C1' C 2 31 alpha beta 1084 1103 1090 1087 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 278 C2' G 2 4 OK OK 280 276 295 279 311 C2' G 2 5 OK OK 313 309 328 312 343 C2' C 2 6 OK OK 345 341 357 344 372 C2' U 2 7 OK OK 374 370 386 373 400 C2' C 2 8 OK OK 402 398 414 401 429 C2' G 2 9 OK OK 431 427 446 430 461 C2' U 2 10 OK OK 463 459 475 462 489 C2' G 2 11 OK OK 491 487 506 490 521 C2' U 2 12 OK OK 523 519 535 522 549 C2' A 2 13 OK OK 551 547 565 550 580 C2' G 2 14 OK OK 582 578 597 581 612 C2' C 2 15 OK OK 614 610 626 613 641 C2' U 2 16 OK OK 643 639 655 642 669 C2' C 2 17 OK OK 671 667 683 670 698 C2' A 2 18 OK OK 700 696 714 699 729 C2' U 2 19 OK OK 731 727 743 730 757 C2' U 2 20 OK OK 759 755 771 758 785 C2' A 2 21 OK OK 787 783 801 786 816 C2' G 2 22 OK OK 818 814 833 817 848 C2' C 2 23 OK OK 850 846 862 849 877 C2' U 2 24 OK OK 879 875 891 878 905 C2' C 2 25 OK OK 907 903 919 906 934 C2' C 2 26 OK OK 936 932 948 935 963 C2' G 2 27 OK OK 965 961 980 964 995 C2' A 2 28 OK OK 997 993 1011 996 1026 C2' G 2 29 OK OK 1028 1024 1043 1027 1058 C2' C 2 30 OK OK 1060 1056 1072 1059 1087 C2' C 2 31 OK OK 1089 1085 1102 1088 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 276 C3' G 2 4 OK OK 274 294 277 278 309 C3' G 2 5 OK OK 307 327 310 311 341 C3' C 2 6 OK OK 339 356 342 343 370 C3' U 2 7 OK OK 368 385 371 372 398 C3' C 2 8 OK OK 396 413 399 400 427 C3' G 2 9 OK OK 425 445 428 429 459 C3' U 2 10 OK OK 457 474 460 461 487 C3' G 2 11 OK OK 485 505 488 489 519 C3' U 2 12 OK OK 517 534 520 521 547 C3' A 2 13 OK OK 545 564 548 549 578 C3' G 2 14 OK OK 576 596 579 580 610 C3' C 2 15 OK OK 608 625 611 612 639 C3' U 2 16 OK OK 637 654 640 641 667 C3' C 2 17 OK OK 665 682 668 669 696 C3' A 2 18 OK OK 694 713 697 698 727 C3' U 2 19 OK OK 725 742 728 729 755 C3' U 2 20 OK OK 753 770 756 757 783 C3' A 2 21 OK OK 781 800 784 785 814 C3' G 2 22 OK OK 812 832 815 816 846 C3' C 2 23 OK OK 844 861 847 848 875 C3' U 2 24 OK OK 873 890 876 877 903 C3' C 2 25 OK OK 901 918 904 905 932 C3' C 2 26 OK OK 930 947 933 934 961 C3' G 2 27 OK OK 959 979 962 963 993 C3' A 2 28 OK OK 991 1010 994 995 1024 C3' G 2 29 OK OK 1022 1042 1025 1026 1056 C3' C 2 30 OK OK 1054 1071 1057 1058 1085 C3' C 2 31 OK OK 1083 1100 1086 1087 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 274 C4' G 2 4 OK OK 276 293 273 275 307 C4' G 2 5 OK OK 309 326 306 308 339 C4' C 2 6 OK OK 341 355 338 340 368 C4' U 2 7 OK OK 370 384 367 369 396 C4' C 2 8 OK OK 398 412 395 397 425 C4' G 2 9 OK OK 427 444 424 426 457 C4' U 2 10 OK OK 459 473 456 458 485 C4' G 2 11 OK OK 487 504 484 486 517 C4' U 2 12 OK OK 519 533 516 518 545 C4' A 2 13 OK OK 547 563 544 546 576 C4' G 2 14 OK OK 578 595 575 577 608 C4' C 2 15 OK OK 610 624 607 609 637 C4' U 2 16 OK OK 639 653 636 638 665 C4' C 2 17 OK OK 667 681 664 666 694 C4' A 2 18 OK OK 696 712 693 695 725 C4' U 2 19 OK OK 727 741 724 726 753 C4' U 2 20 OK OK 755 769 752 754 781 C4' A 2 21 OK OK 783 799 780 782 812 C4' G 2 22 OK OK 814 831 811 813 844 C4' C 2 23 OK OK 846 860 843 845 873 C4' U 2 24 OK OK 875 889 872 874 901 C4' C 2 25 OK OK 903 917 900 902 930 C4' C 2 26 OK OK 932 946 929 931 959 C4' G 2 27 OK OK 961 978 958 960 991 C4' A 2 28 OK OK 993 1009 990 992 1022 C4' G 2 29 OK OK 1024 1041 1021 1023 1054 C4' C 2 30 OK OK 1056 1070 1053 1055 1083 C4' C 2 31 OK OK 1085 1099 1082 1084 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 273 C5' G 2 4 OK 272 292 274 306 C5' G 2 5 OK 305 325 307 338 C5' C 2 6 OK 337 354 339 367 C5' U 2 7 OK 366 383 368 395 C5' C 2 8 OK 394 411 396 424 C5' G 2 9 OK 423 443 425 456 C5' U 2 10 OK 455 472 457 484 C5' G 2 11 OK 483 503 485 516 C5' U 2 12 OK 515 532 517 544 C5' A 2 13 OK 543 562 545 575 C5' G 2 14 OK 574 594 576 607 C5' C 2 15 OK 606 623 608 636 C5' U 2 16 OK 635 652 637 664 C5' C 2 17 OK 663 680 665 693 C5' A 2 18 OK 692 711 694 724 C5' U 2 19 OK 723 740 725 752 C5' U 2 20 OK 751 768 753 780 C5' A 2 21 OK 779 798 781 811 C5' G 2 22 OK 810 830 812 843 C5' C 2 23 OK 842 859 844 872 C5' U 2 24 OK 871 888 873 900 C5' C 2 25 OK 899 916 901 929 C5' C 2 26 OK 928 945 930 958 C5' G 2 27 OK 957 977 959 990 C5' A 2 28 OK 989 1008 991 1021 C5' G 2 29 OK 1020 1040 1022 1053 C5' C 2 30 OK 1052 1069 1054 1082 C5' C 2 31 OK 1081 1098 1083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 269 P G 2 4 OK OK 270 271 272 302 P G 2 5 distorted distorted 277 303 304 305 334 P C 2 6 distorted distorted 310 335 336 337 363 P U 2 7 distorted distorted 342 364 365 366 391 P C 2 8 distorted distorted 371 392 393 394 420 P G 2 9 distorted distorted 399 421 422 423 452 P U 2 10 distorted distorted 428 453 454 455 480 P G 2 11 distorted distorted 460 481 482 483 512 P U 2 12 distorted distorted 488 513 514 515 540 P A 2 13 distorted distorted 520 541 542 543 571 P G 2 14 distorted distorted 548 572 573 574 603 P C 2 15 distorted distorted 579 604 605 606 632 P U 2 16 distorted distorted 611 633 634 635 660 P C 2 17 distorted distorted 640 661 662 663 689 P A 2 18 distorted distorted 668 690 691 692 720 P U 2 19 distorted distorted 697 721 722 723 748 P U 2 20 distorted distorted 728 749 750 751 776 P A 2 21 distorted distorted 756 777 778 779 807 P G 2 22 distorted distorted 784 808 809 810 839 P C 2 23 distorted distorted 815 840 841 842 868 P U 2 24 distorted distorted 847 869 870 871 896 P C 2 25 distorted distorted 876 897 898 899 925 P C 2 26 distorted distorted 904 926 927 928 954 P G 2 27 distorted distorted 933 955 956 957 986 P A 2 28 distorted distorted 962 987 988 989 1017 P G 2 29 distorted distorted 994 1018 1019 1020 1049 P C 2 30 distorted distorted 1025 1050 1051 1052 1078 P C 2 31 distorted distorted 1057 1079 1080 1081 ---------------------------------------------------------------------------------