ID code: '2KDQ' 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 274 297 280 277 314 C1' G B 18 alpha beta 309 332 315 312 348 C1' C B 19 alpha beta 343 363 349 346 379 C1' A B 20 alpha beta 374 396 380 377 412 C1' G B 21 alpha beta 407 430 413 410 446 C1' A B 22 alpha beta 441 463 447 444 479 C1' U B 23 alpha beta 474 494 480 477 509 C1' C B 24 alpha beta 504 524 510 507 540 C1' U B 25 alpha beta 535 555 541 538 570 C1' G B 26 alpha beta 565 588 571 568 604 C1' A B 27 alpha beta 599 621 605 602 637 C1' G B 28 alpha beta 632 655 638 635 671 C1' C B 29 alpha beta 666 686 672 669 702 C1' C B 30 alpha beta 697 717 703 700 733 C1' U B 31 alpha beta 728 748 734 731 763 C1' G B 32 alpha beta 758 781 764 761 797 C1' G B 33 alpha beta 792 815 798 795 831 C1' G B 34 alpha beta 826 849 832 829 865 C1' A B 35 alpha beta 860 882 866 863 898 C1' G B 36 alpha beta 893 916 899 896 932 C1' C B 37 alpha beta 927 947 933 930 963 C1' U B 38 alpha beta 958 978 964 961 993 C1' C B 39 alpha beta 988 1008 994 991 1024 C1' U B 40 alpha beta 1019 1039 1025 1022 1054 C1' C B 41 alpha beta 1049 1069 1055 1052 1085 C1' U B 42 alpha beta 1080 1100 1086 1083 1115 C1' G B 43 alpha beta 1110 1133 1116 1113 1149 C1' C B 44 alpha beta 1144 1164 1150 1147 1180 C1' C B 45 alpha beta 1175 1196 1181 1178 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 279 275 295 278 312 C2' G B 18 OK OK 314 310 330 313 346 C2' C B 19 OK OK 348 344 361 347 377 C2' A B 20 OK OK 379 375 394 378 410 C2' G B 21 OK OK 412 408 428 411 444 C2' A B 22 OK OK 446 442 461 445 477 C2' U B 23 OK OK 479 475 492 478 507 C2' C B 24 OK OK 509 505 522 508 538 C2' U B 25 OK OK 540 536 553 539 568 C2' G B 26 OK OK 570 566 586 569 602 C2' A B 27 OK OK 604 600 619 603 635 C2' G B 28 OK OK 637 633 653 636 669 C2' C B 29 OK OK 671 667 684 670 700 C2' C B 30 OK OK 702 698 715 701 731 C2' U B 31 OK OK 733 729 746 732 761 C2' G B 32 OK OK 763 759 779 762 795 C2' G B 33 OK OK 797 793 813 796 829 C2' G B 34 OK OK 831 827 847 830 863 C2' A B 35 OK OK 865 861 880 864 896 C2' G B 36 OK OK 898 894 914 897 930 C2' C B 37 OK OK 932 928 945 931 961 C2' U B 38 OK OK 963 959 976 962 991 C2' C B 39 OK OK 993 989 1006 992 1022 C2' U B 40 OK OK 1024 1020 1037 1023 1052 C2' C B 41 OK OK 1054 1050 1067 1053 1083 C2' U B 42 OK OK 1085 1081 1098 1084 1113 C2' G B 43 OK OK 1115 1111 1131 1114 1147 C2' C B 44 OK OK 1149 1145 1162 1148 1178 C2' C B 45 OK OK 1180 1176 1194 1179 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 275 C3' G B 17 OK OK 273 294 276 277 310 C3' G B 18 OK OK 308 329 311 312 344 C3' C B 19 OK OK 342 360 345 346 375 C3' A B 20 OK OK 373 393 376 377 408 C3' G B 21 OK OK 406 427 409 410 442 C3' A B 22 OK OK 440 460 443 444 475 C3' U B 23 OK OK 473 491 476 477 505 C3' C B 24 OK OK 503 521 506 507 536 C3' U B 25 OK OK 534 552 537 538 566 C3' G B 26 OK OK 564 585 567 568 600 C3' A B 27 OK OK 598 618 601 602 633 C3' G B 28 OK OK 631 652 634 635 667 C3' C B 29 OK OK 665 683 668 669 698 C3' C B 30 OK OK 696 714 699 700 729 C3' U B 31 OK OK 727 745 730 731 759 C3' G B 32 OK OK 757 778 760 761 793 C3' G B 33 OK OK 791 812 794 795 827 C3' G B 34 OK OK 825 846 828 829 861 C3' A B 35 OK OK 859 879 862 863 894 C3' G B 36 OK OK 892 913 895 896 928 C3' C B 37 OK OK 926 944 929 930 959 C3' U B 38 OK OK 957 975 960 961 989 C3' C B 39 OK OK 987 1005 990 991 1020 C3' U B 40 OK OK 1018 1036 1021 1022 1050 C3' C B 41 OK OK 1048 1066 1051 1052 1081 C3' U B 42 OK OK 1079 1097 1082 1083 1111 C3' G B 43 OK OK 1109 1130 1112 1113 1145 C3' C B 44 OK OK 1143 1161 1146 1147 1176 C3' C B 45 OK OK 1174 1192 1177 1178 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 273 C4' G B 17 OK OK 275 293 272 274 308 C4' G B 18 OK OK 310 328 307 309 342 C4' C B 19 OK OK 344 359 341 343 373 C4' A B 20 OK OK 375 392 372 374 406 C4' G B 21 OK OK 408 426 405 407 440 C4' A B 22 OK OK 442 459 439 441 473 C4' U B 23 OK OK 475 490 472 474 503 C4' C B 24 OK OK 505 520 502 504 534 C4' U B 25 OK OK 536 551 533 535 564 C4' G B 26 OK OK 566 584 563 565 598 C4' A B 27 OK OK 600 617 597 599 631 C4' G B 28 OK OK 633 651 630 632 665 C4' C B 29 OK OK 667 682 664 666 696 C4' C B 30 OK OK 698 713 695 697 727 C4' U B 31 OK OK 729 744 726 728 757 C4' G B 32 OK OK 759 777 756 758 791 C4' G B 33 OK OK 793 811 790 792 825 C4' G B 34 OK OK 827 845 824 826 859 C4' A B 35 OK OK 861 878 858 860 892 C4' G B 36 OK OK 894 912 891 893 926 C4' C B 37 OK OK 928 943 925 927 957 C4' U B 38 OK OK 959 974 956 958 987 C4' C B 39 OK OK 989 1004 986 988 1018 C4' U B 40 OK OK 1020 1035 1017 1019 1048 C4' C B 41 OK OK 1050 1065 1047 1049 1079 C4' U B 42 OK OK 1081 1096 1078 1080 1109 C4' G B 43 OK OK 1111 1129 1108 1110 1143 C4' C B 44 OK OK 1145 1160 1142 1144 1174 C4' C B 45 OK OK 1176 1191 1173 1175 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 272 C5' G B 17 OK OK 271 291 292 273 307 C5' G B 18 OK OK 306 326 327 308 341 C5' C B 19 OK OK 340 357 358 342 372 C5' A B 20 OK OK 371 390 391 373 405 C5' G B 21 OK OK 404 424 425 406 439 C5' A B 22 OK OK 438 457 458 440 472 C5' U B 23 OK OK 471 488 489 473 502 C5' C B 24 OK OK 501 518 519 503 533 C5' U B 25 OK OK 532 549 550 534 563 C5' G B 26 OK OK 562 582 583 564 597 C5' A B 27 OK OK 596 615 616 598 630 C5' G B 28 OK OK 629 649 650 631 664 C5' C B 29 OK OK 663 680 681 665 695 C5' C B 30 OK OK 694 711 712 696 726 C5' U B 31 OK OK 725 742 743 727 756 C5' G B 32 OK OK 755 775 776 757 790 C5' G B 33 OK OK 789 809 810 791 824 C5' G B 34 OK OK 823 843 844 825 858 C5' A B 35 OK OK 857 876 877 859 891 C5' G B 36 OK OK 890 910 911 892 925 C5' C B 37 OK OK 924 941 942 926 956 C5' U B 38 OK OK 955 972 973 957 986 C5' C B 39 OK OK 985 1002 1003 987 1017 C5' U B 40 OK OK 1016 1033 1034 1018 1047 C5' C B 41 OK OK 1046 1063 1064 1048 1078 C5' U B 42 OK OK 1077 1094 1095 1079 1108 C5' G B 43 OK OK 1107 1127 1128 1109 1142 C5' C B 44 OK OK 1141 1158 1159 1143 1173 C5' C B 45 OK OK 1172 1189 1190 1174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 303 P G B 18 distorted distorted 276 304 305 306 337 P C B 19 distorted distorted 311 338 339 340 368 P A B 20 distorted distorted 345 369 370 371 401 P G B 21 distorted distorted 376 402 403 404 435 P A B 22 distorted distorted 409 436 437 438 468 P U B 23 distorted distorted 443 469 470 471 498 P C B 24 distorted distorted 476 499 500 501 529 P U B 25 distorted distorted 506 530 531 532 559 P G B 26 distorted distorted 537 560 561 562 593 P A B 27 distorted distorted 567 594 595 596 626 P G B 28 distorted distorted 601 627 628 629 660 P C B 29 distorted distorted 634 661 662 663 691 P C B 30 distorted distorted 668 692 693 694 722 P U B 31 distorted distorted 699 723 724 725 752 P G B 32 distorted distorted 730 753 754 755 786 P G B 33 distorted distorted 760 787 788 789 820 P G B 34 distorted distorted 794 821 822 823 854 P A B 35 distorted distorted 828 855 856 857 887 P G B 36 distorted distorted 862 888 889 890 921 P C B 37 distorted distorted 895 922 923 924 952 P U B 38 distorted distorted 929 953 954 955 982 P C B 39 distorted distorted 960 983 984 985 1013 P U B 40 distorted distorted 990 1014 1015 1016 1043 P C B 41 distorted distorted 1021 1044 1045 1046 1074 P U B 42 distorted distorted 1051 1075 1076 1077 1104 P G B 43 distorted distorted 1082 1105 1106 1107 1138 P C B 44 distorted distorted 1112 1139 1140 1141 1169 P C B 45 distorted distorted 1146 1170 1171 1172 ---------------------------------------------------------------------------------