ID code: '5J0M' 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' --------------------------------------------------------------------------------- 279 C1' G B 17 alpha beta 274 297 280 277 313 C1' G B 18 alpha beta 308 331 314 311 347 C1' C B 19 alpha beta 342 362 348 345 378 C1' A B 20 alpha beta 373 395 379 376 411 C1' G B 21 alpha beta 406 429 412 409 445 C1' A B 22 alpha beta 440 462 446 443 478 C1' U B 23 alpha beta 473 493 479 476 508 C1' C B 24 alpha beta 503 523 509 506 539 C1' U B 25 alpha beta 534 554 540 537 569 C1' G B 26 alpha beta 564 587 570 567 603 C1' A B 27 alpha beta 598 620 604 601 636 C1' G B 28 alpha beta 631 654 637 634 670 C1' C B 29 alpha beta 665 685 671 668 701 C1' C B 30 alpha beta 696 716 702 699 732 C1' U B 31 alpha beta 727 747 733 730 762 C1' G B 32 alpha beta 757 780 763 760 796 C1' G B 33 alpha beta 791 814 797 794 830 C1' G B 34 alpha beta 825 848 831 828 864 C1' A B 35 alpha beta 859 881 865 862 897 C1' G B 36 alpha beta 892 915 898 895 931 C1' C B 37 alpha beta 926 946 932 929 962 C1' U B 38 alpha beta 957 977 963 960 992 C1' C B 39 alpha beta 987 1007 993 990 1023 C1' U B 40 alpha beta 1018 1038 1024 1021 1053 C1' C B 41 alpha beta 1048 1068 1054 1051 1084 C1' U B 42 alpha beta 1079 1099 1085 1082 1114 C1' G B 43 alpha beta 1109 1132 1115 1112 1148 C1' C B 44 alpha beta 1143 1163 1149 1146 1179 C1' C B 45 alpha beta 1174 1195 1180 1177 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 277 C2' G B 17 OK OK 279 275 295 278 311 C2' G B 18 OK OK 313 309 329 312 345 C2' C B 19 OK OK 347 343 360 346 376 C2' A B 20 OK OK 378 374 393 377 409 C2' G B 21 OK OK 411 407 427 410 443 C2' A B 22 OK OK 445 441 460 444 476 C2' U B 23 OK OK 478 474 491 477 506 C2' C B 24 OK OK 508 504 521 507 537 C2' U B 25 OK OK 539 535 552 538 567 C2' G B 26 OK OK 569 565 585 568 601 C2' A B 27 OK OK 603 599 618 602 634 C2' G B 28 OK OK 636 632 652 635 668 C2' C B 29 OK OK 670 666 683 669 699 C2' C B 30 OK OK 701 697 714 700 730 C2' U B 31 OK OK 732 728 745 731 760 C2' G B 32 OK OK 762 758 778 761 794 C2' G B 33 OK OK 796 792 812 795 828 C2' G B 34 OK OK 830 826 846 829 862 C2' A B 35 OK OK 864 860 879 863 895 C2' G B 36 OK OK 897 893 913 896 929 C2' C B 37 OK OK 931 927 944 930 960 C2' U B 38 OK OK 962 958 975 961 990 C2' C B 39 OK OK 992 988 1005 991 1021 C2' U B 40 OK OK 1023 1019 1036 1022 1051 C2' C B 41 OK OK 1053 1049 1066 1052 1082 C2' U B 42 OK OK 1084 1080 1097 1083 1112 C2' G B 43 OK OK 1114 1110 1130 1113 1146 C2' C B 44 OK OK 1148 1144 1161 1147 1177 C2' C B 45 OK OK 1179 1175 1193 1178 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 275 C3' G B 17 OK OK 273 294 276 277 309 C3' G B 18 OK OK 307 328 310 311 343 C3' C B 19 OK OK 341 359 344 345 374 C3' A B 20 OK OK 372 392 375 376 407 C3' G B 21 OK OK 405 426 408 409 441 C3' A B 22 OK OK 439 459 442 443 474 C3' U B 23 OK OK 472 490 475 476 504 C3' C B 24 OK OK 502 520 505 506 535 C3' U B 25 OK OK 533 551 536 537 565 C3' G B 26 OK OK 563 584 566 567 599 C3' A B 27 OK OK 597 617 600 601 632 C3' G B 28 OK OK 630 651 633 634 666 C3' C B 29 OK OK 664 682 667 668 697 C3' C B 30 OK OK 695 713 698 699 728 C3' U B 31 OK OK 726 744 729 730 758 C3' G B 32 OK OK 756 777 759 760 792 C3' G B 33 OK OK 790 811 793 794 826 C3' G B 34 OK OK 824 845 827 828 860 C3' A B 35 OK OK 858 878 861 862 893 C3' G B 36 OK OK 891 912 894 895 927 C3' C B 37 OK OK 925 943 928 929 958 C3' U B 38 OK OK 956 974 959 960 988 C3' C B 39 OK OK 986 1004 989 990 1019 C3' U B 40 OK OK 1017 1035 1020 1021 1049 C3' C B 41 OK OK 1047 1065 1050 1051 1080 C3' U B 42 OK OK 1078 1096 1081 1082 1110 C3' G B 43 OK OK 1108 1129 1111 1112 1144 C3' C B 44 OK OK 1142 1160 1145 1146 1175 C3' C B 45 OK OK 1173 1191 1176 1177 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 273 C4' G B 17 OK OK 275 293 272 274 307 C4' G B 18 OK OK 309 327 306 308 341 C4' C B 19 OK OK 343 358 340 342 372 C4' A B 20 OK OK 374 391 371 373 405 C4' G B 21 OK OK 407 425 404 406 439 C4' A B 22 OK OK 441 458 438 440 472 C4' U B 23 OK OK 474 489 471 473 502 C4' C B 24 OK OK 504 519 501 503 533 C4' U B 25 OK OK 535 550 532 534 563 C4' G B 26 OK OK 565 583 562 564 597 C4' A B 27 OK OK 599 616 596 598 630 C4' G B 28 OK OK 632 650 629 631 664 C4' C B 29 OK OK 666 681 663 665 695 C4' C B 30 OK OK 697 712 694 696 726 C4' U B 31 OK OK 728 743 725 727 756 C4' G B 32 OK OK 758 776 755 757 790 C4' G B 33 OK OK 792 810 789 791 824 C4' G B 34 OK OK 826 844 823 825 858 C4' A B 35 OK OK 860 877 857 859 891 C4' G B 36 OK OK 893 911 890 892 925 C4' C B 37 OK OK 927 942 924 926 956 C4' U B 38 OK OK 958 973 955 957 986 C4' C B 39 OK OK 988 1003 985 987 1017 C4' U B 40 OK OK 1019 1034 1016 1018 1047 C4' C B 41 OK OK 1049 1064 1046 1048 1078 C4' U B 42 OK OK 1080 1095 1077 1079 1108 C4' G B 43 OK OK 1110 1128 1107 1109 1142 C4' C B 44 OK OK 1144 1159 1141 1143 1173 C4' C B 45 OK OK 1175 1190 1172 1174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 272 C5' G B 17 OK OK 271 291 292 273 306 C5' G B 18 OK OK 305 325 326 307 340 C5' C B 19 OK OK 339 356 357 341 371 C5' A B 20 OK OK 370 389 390 372 404 C5' G B 21 OK OK 403 423 424 405 438 C5' A B 22 OK OK 437 456 457 439 471 C5' U B 23 OK OK 470 487 488 472 501 C5' C B 24 OK OK 500 517 518 502 532 C5' U B 25 OK OK 531 548 549 533 562 C5' G B 26 OK OK 561 581 582 563 596 C5' A B 27 OK OK 595 614 615 597 629 C5' G B 28 OK OK 628 648 649 630 663 C5' C B 29 OK OK 662 679 680 664 694 C5' C B 30 OK OK 693 710 711 695 725 C5' U B 31 OK OK 724 741 742 726 755 C5' G B 32 OK OK 754 774 775 756 789 C5' G B 33 OK OK 788 808 809 790 823 C5' G B 34 OK OK 822 842 843 824 857 C5' A B 35 OK OK 856 875 876 858 890 C5' G B 36 OK OK 889 909 910 891 924 C5' C B 37 OK OK 923 940 941 925 955 C5' U B 38 OK OK 954 971 972 956 985 C5' C B 39 OK OK 984 1001 1002 986 1016 C5' U B 40 OK OK 1015 1032 1033 1017 1046 C5' C B 41 OK OK 1045 1062 1063 1047 1077 C5' U B 42 OK OK 1076 1093 1094 1078 1107 C5' G B 43 OK OK 1106 1126 1127 1108 1141 C5' C B 44 OK OK 1140 1157 1158 1142 1172 C5' C B 45 OK OK 1171 1188 1189 1173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 302 P G B 18 distorted distorted 276 303 304 305 336 P C B 19 distorted distorted 310 337 338 339 367 P A B 20 distorted distorted 344 368 369 370 400 P G B 21 distorted distorted 375 401 402 403 434 P A B 22 distorted distorted 408 435 436 437 467 P U B 23 distorted distorted 442 468 469 470 497 P C B 24 distorted distorted 475 498 499 500 528 P U B 25 distorted distorted 505 529 530 531 558 P G B 26 distorted distorted 536 559 560 561 592 P A B 27 distorted distorted 566 593 594 595 625 P G B 28 distorted distorted 600 626 627 628 659 P C B 29 distorted distorted 633 660 661 662 690 P C B 30 distorted distorted 667 691 692 693 721 P U B 31 distorted distorted 698 722 723 724 751 P G B 32 distorted distorted 729 752 753 754 785 P G B 33 distorted distorted 759 786 787 788 819 P G B 34 distorted distorted 793 820 821 822 853 P A B 35 distorted distorted 827 854 855 856 886 P G B 36 distorted distorted 861 887 888 889 920 P C B 37 distorted distorted 894 921 922 923 951 P U B 38 distorted distorted 928 952 953 954 981 P C B 39 distorted distorted 959 982 983 984 1012 P U B 40 distorted distorted 989 1013 1014 1015 1042 P C B 41 distorted distorted 1020 1043 1044 1045 1073 P U B 42 distorted distorted 1050 1074 1075 1076 1103 P G B 43 distorted distorted 1081 1104 1105 1106 1137 P C B 44 distorted distorted 1111 1138 1139 1140 1168 P C B 45 distorted distorted 1145 1169 1170 1171 ---------------------------------------------------------------------------------