ID code: '2B3J' 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' U E 28 beta 4 10 7 29 C1' U E 29 beta 24 30 27 49 C1' G E 30 beta 44 50 47 72 C1' A E 31 beta 67 73 70 94 C1' C E 32 beta 89 95 92 114 C1' U E 33 beta 109 115 112 132 C1' P5P E 34 beta 138 131 133 155 C1' C E 35 beta 150 156 153 175 C1' G E 36 beta 170 176 173 198 C1' G E 37 beta 193 199 196 221 C1' A E 38 beta 216 222 219 243 C1' U E 39 beta 238 244 241 263 C1' C E 40 beta 258 264 261 283 C1' A E 41 beta 278 284 281 305 C1' A E 42 beta 300 306 303 325 C1' U F 28 beta 320 326 323 345 C1' U F 29 beta 340 346 343 365 C1' G F 30 beta 360 366 363 388 C1' A F 31 beta 383 389 386 410 C1' C F 32 beta 405 411 408 430 C1' U F 33 beta 425 431 428 448 C1' P5P F 34 beta 454 447 449 471 C1' C F 35 beta 466 472 469 491 C1' G F 36 beta 486 492 489 514 C1' G F 37 beta 509 515 512 537 C1' A F 38 beta 532 538 535 559 C1' U F 39 beta 554 560 557 579 C1' C F 40 beta 574 580 577 599 C1' A F 41 beta 594 600 597 621 C1' A F 42 beta 616 622 619 641 C1' G G 30 beta 636 642 639 664 C1' A G 31 beta 659 665 662 686 C1' C G 32 beta 681 687 684 706 C1' U G 33 beta 701 707 704 724 C1' P5P G 34 beta 730 723 725 747 C1' C G 35 beta 742 748 745 767 C1' G G 36 beta 762 768 765 790 C1' G G 37 beta 785 791 788 811 C1' U H 27 beta 806 812 809 831 C1' U H 28 beta 826 832 829 851 C1' U H 29 beta 846 852 849 871 C1' G H 30 beta 866 872 869 894 C1' A H 31 beta 889 895 892 916 C1' C H 32 beta 911 917 914 936 C1' U H 33 beta 931 937 934 954 C1' P5P H 34 beta 960 953 955 977 C1' C H 35 beta 972 978 975 997 C1' G H 36 beta 992 998 995 1020 C1' G H 37 beta 1015 1021 1018 1043 C1' A H 38 beta 1038 1044 1041 1065 C1' U H 39 beta 1060 1066 1063 1085 C1' C H 40 beta 1080 1086 1083 1105 C1' A H 41 beta 1100 1106 1103 1127 C1' A H 42 beta 1122 1128 1125 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U E 28 OK 9 5 8 27 C2' U E 29 OK 29 25 28 47 C2' G E 30 OK 49 45 48 70 C2' A E 31 OK 72 68 71 92 C2' C E 32 OK 94 90 93 112 C2' U E 33 OK 114 110 113 133 C2' P5P E 34 OK 132 135 134 153 C2' C E 35 OK 155 151 154 173 C2' G E 36 OK 175 171 174 196 C2' G E 37 OK 198 194 197 219 C2' A E 38 OK 221 217 220 241 C2' U E 39 OK 243 239 242 261 C2' C E 40 OK 263 259 262 281 C2' A E 41 OK 283 279 282 303 C2' A E 42 OK 305 301 304 323 C2' U F 28 OK 325 321 324 343 C2' U F 29 OK 345 341 344 363 C2' G F 30 OK 365 361 364 386 C2' A F 31 OK 388 384 387 408 C2' C F 32 OK 410 406 409 428 C2' U F 33 OK 430 426 429 449 C2' P5P F 34 OK 448 451 450 469 C2' C F 35 OK 471 467 470 489 C2' G F 36 OK 491 487 490 512 C2' G F 37 OK 514 510 513 535 C2' A F 38 OK 537 533 536 557 C2' U F 39 OK 559 555 558 577 C2' C F 40 OK 579 575 578 597 C2' A F 41 OK 599 595 598 619 C2' A F 42 OK 621 617 620 639 C2' G G 30 OK 641 637 640 662 C2' A G 31 OK 664 660 663 684 C2' C G 32 OK 686 682 685 704 C2' U G 33 OK 706 702 705 725 C2' P5P G 34 OK 724 727 726 745 C2' C G 35 OK 747 743 746 765 C2' G G 36 OK 767 763 766 788 C2' G G 37 OK 790 786 789 809 C2' U H 27 OK 811 807 810 829 C2' U H 28 OK 831 827 830 849 C2' U H 29 OK 851 847 850 869 C2' G H 30 OK 871 867 870 892 C2' A H 31 OK 894 890 893 914 C2' C H 32 OK 916 912 915 934 C2' U H 33 OK 936 932 935 955 C2' P5P H 34 OK 954 957 956 975 C2' C H 35 OK 977 973 976 995 C2' G H 36 OK 997 993 996 1018 C2' G H 37 OK 1020 1016 1019 1041 C2' A H 38 OK 1043 1039 1042 1063 C2' U H 39 OK 1065 1061 1064 1083 C2' C H 40 OK 1085 1081 1084 1103 C2' A H 41 OK 1105 1101 1104 1125 C2' A H 42 OK 1127 1123 1126 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U E 28 OK 3 6 7 25 C3' U E 29 OK 23 26 27 45 C3' G E 30 OK 43 46 47 68 C3' A E 31 OK 66 69 70 90 C3' C E 32 OK 88 91 92 110 C3' U E 33 OK 108 111 112 135 C3' P5P E 34 OK 137 136 133 151 C3' C E 35 OK 149 152 153 171 C3' G E 36 OK 169 172 173 194 C3' G E 37 OK 192 195 196 217 C3' A E 38 OK 215 218 219 239 C3' U E 39 OK 237 240 241 259 C3' C E 40 OK 257 260 261 279 C3' A E 41 OK 277 280 281 301 C3' A E 42 OK 299 302 303 321 C3' U F 28 OK 319 322 323 341 C3' U F 29 OK 339 342 343 361 C3' G F 30 OK 359 362 363 384 C3' A F 31 OK 382 385 386 406 C3' C F 32 OK 404 407 408 426 C3' U F 33 OK 424 427 428 451 C3' P5P F 34 OK 453 452 449 467 C3' C F 35 OK 465 468 469 487 C3' G F 36 OK 485 488 489 510 C3' G F 37 OK 508 511 512 533 C3' A F 38 OK 531 534 535 555 C3' U F 39 OK 553 556 557 575 C3' C F 40 OK 573 576 577 595 C3' A F 41 OK 593 596 597 617 C3' A F 42 OK 615 618 619 637 C3' G G 30 OK 635 638 639 660 C3' A G 31 OK 658 661 662 682 C3' C G 32 OK 680 683 684 702 C3' U G 33 OK 700 703 704 727 C3' P5P G 34 OK 729 728 725 743 C3' C G 35 OK 741 744 745 763 C3' G G 36 OK 761 764 765 786 C3' G G 37 OK 784 787 788 807 C3' U H 27 OK 805 808 809 827 C3' U H 28 OK 825 828 829 847 C3' U H 29 OK 845 848 849 867 C3' G H 30 OK 865 868 869 890 C3' A H 31 OK 888 891 892 912 C3' C H 32 OK 910 913 914 932 C3' U H 33 OK 930 933 934 957 C3' P5P H 34 OK 959 958 955 973 C3' C H 35 OK 971 974 975 993 C3' G H 36 OK 991 994 995 1016 C3' G H 37 OK 1014 1017 1018 1039 C3' A H 38 OK 1037 1040 1041 1061 C3' U H 39 OK 1059 1062 1063 1081 C3' C H 40 OK 1079 1082 1083 1101 C3' A H 41 OK 1099 1102 1103 1123 C3' A H 42 OK 1121 1124 1125 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U E 28 OK 5 2 4 23 C4' U E 29 OK 25 22 24 43 C4' G E 30 OK 45 42 44 66 C4' A E 31 OK 68 65 67 88 C4' C E 32 OK 90 87 89 108 C4' U E 33 OK 110 107 109 137 C4' P5P E 34 OK 135 139 138 149 C4' C E 35 OK 151 148 150 169 C4' G E 36 OK 171 168 170 192 C4' G E 37 OK 194 191 193 215 C4' A E 38 OK 217 214 216 237 C4' U E 39 OK 239 236 238 257 C4' C E 40 OK 259 256 258 277 C4' A E 41 OK 279 276 278 299 C4' A E 42 OK 301 298 300 319 C4' U F 28 OK 321 318 320 339 C4' U F 29 OK 341 338 340 359 C4' G F 30 OK 361 358 360 382 C4' A F 31 OK 384 381 383 404 C4' C F 32 OK 406 403 405 424 C4' U F 33 OK 426 423 425 453 C4' P5P F 34 OK 451 455 454 465 C4' C F 35 OK 467 464 466 485 C4' G F 36 OK 487 484 486 508 C4' G F 37 OK 510 507 509 531 C4' A F 38 OK 533 530 532 553 C4' U F 39 OK 555 552 554 573 C4' C F 40 OK 575 572 574 593 C4' A F 41 OK 595 592 594 615 C4' A F 42 OK 617 614 616 635 C4' G G 30 OK 637 634 636 658 C4' A G 31 OK 660 657 659 680 C4' C G 32 OK 682 679 681 700 C4' U G 33 OK 702 699 701 729 C4' P5P G 34 OK 727 731 730 741 C4' C G 35 OK 743 740 742 761 C4' G G 36 OK 763 760 762 784 C4' G G 37 OK 786 783 785 805 C4' U H 27 OK 807 804 806 825 C4' U H 28 OK 827 824 826 845 C4' U H 29 OK 847 844 846 865 C4' G H 30 OK 867 864 866 888 C4' A H 31 OK 890 887 889 910 C4' C H 32 OK 912 909 911 930 C4' U H 33 OK 932 929 931 959 C4' P5P H 34 OK 957 961 960 971 C4' C H 35 OK 973 970 972 991 C4' G H 36 OK 993 990 992 1014 C4' G H 37 OK 1016 1013 1015 1037 C4' A H 38 OK 1039 1036 1038 1059 C4' U H 39 OK 1061 1058 1060 1079 C4' C H 40 OK 1081 1078 1080 1099 C4' A H 41 OK 1101 1098 1100 1121 C4' A H 42 OK 1123 1120 1122 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U E 28 1 3 22 C5' U E 29 21 23 42 C5' G E 30 41 43 65 C5' A E 31 64 66 87 C5' C E 32 86 88 107 C5' U E 33 106 108 139 C5' P5P E 34 140 137 148 C5' C E 35 147 149 168 C5' G E 36 167 169 191 C5' G E 37 190 192 214 C5' A E 38 213 215 236 C5' U E 39 235 237 256 C5' C E 40 255 257 276 C5' A E 41 275 277 298 C5' A E 42 297 299 318 C5' U F 28 317 319 338 C5' U F 29 337 339 358 C5' G F 30 357 359 381 C5' A F 31 380 382 403 C5' C F 32 402 404 423 C5' U F 33 422 424 455 C5' P5P F 34 456 453 464 C5' C F 35 463 465 484 C5' G F 36 483 485 507 C5' G F 37 506 508 530 C5' A F 38 529 531 552 C5' U F 39 551 553 572 C5' C F 40 571 573 592 C5' A F 41 591 593 614 C5' A F 42 613 615 634 C5' G G 30 633 635 657 C5' A G 31 656 658 679 C5' C G 32 678 680 699 C5' U G 33 698 700 731 C5' P5P G 34 732 729 740 C5' C G 35 739 741 760 C5' G G 36 759 761 783 C5' G G 37 782 784 804 C5' U H 27 803 805 824 C5' U H 28 823 825 844 C5' U H 29 843 845 864 C5' G H 30 863 865 887 C5' A H 31 886 888 909 C5' C H 32 908 910 929 C5' U H 33 928 930 961 C5' P5P H 34 962 959 970 C5' C H 35 969 971 990 C5' G H 36 989 991 1013 C5' G H 37 1012 1014 1036 C5' A H 38 1035 1037 1058 C5' U H 39 1057 1059 1078 C5' C H 40 1077 1079 1098 C5' A H 41 1097 1099 1120 C5' A H 42 1119 1121 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U E 29 distorted distorted 6 19 20 21 38 P G E 30 distorted distorted 26 39 40 41 61 P A E 31 distorted distorted 46 62 63 64 83 P C E 32 distorted distorted 69 84 85 86 103 P U E 33 distorted distorted 91 104 105 106 141 P P5P E 34 distorted distorted 111 142 143 140 144 P C E 35 distorted distorted 136 145 146 147 164 P G E 36 distorted distorted 152 165 166 167 187 P G E 37 distorted distorted 172 188 189 190 210 P A E 38 distorted distorted 195 211 212 213 232 P U E 39 distorted distorted 218 233 234 235 252 P C E 40 distorted distorted 240 253 254 255 272 P A E 41 distorted distorted 260 273 274 275 294 P A E 42 distorted distorted 280 295 296 297 334 P U F 29 distorted distorted 322 335 336 337 354 P G F 30 distorted distorted 342 355 356 357 377 P A F 31 distorted distorted 362 378 379 380 399 P C F 32 distorted distorted 385 400 401 402 419 P U F 33 distorted distorted 407 420 421 422 457 P P5P F 34 distorted distorted 427 458 459 456 460 P C F 35 distorted distorted 452 461 462 463 480 P G F 36 distorted distorted 468 481 482 483 503 P G F 37 distorted distorted 488 504 505 506 526 P A F 38 distorted distorted 511 527 528 529 548 P U F 39 distorted distorted 534 549 550 551 568 P C F 40 distorted distorted 556 569 570 571 588 P A F 41 distorted distorted 576 589 590 591 610 P A F 42 distorted distorted 596 611 612 613 653 P A G 31 distorted distorted 638 654 655 656 675 P C G 32 distorted distorted 661 676 677 678 695 P U G 33 distorted distorted 683 696 697 698 733 P P5P G 34 distorted distorted 703 734 735 732 736 P C G 35 distorted distorted 728 737 738 739 756 P G G 36 distorted distorted 744 757 758 759 779 P G G 37 distorted distorted 764 780 781 782 820 P U H 28 distorted distorted 808 821 822 823 840 P U H 29 distorted distorted 828 841 842 843 860 P G H 30 distorted distorted 848 861 862 863 883 P A H 31 distorted distorted 868 884 885 886 905 P C H 32 distorted distorted 891 906 907 908 925 P U H 33 distorted distorted 913 926 927 928 963 P P5P H 34 distorted distorted 933 964 965 962 966 P C H 35 distorted distorted 958 967 968 969 986 P G H 36 distorted distorted 974 987 988 989 1009 P G H 37 distorted distorted 994 1010 1011 1012 1032 P A H 38 distorted distorted 1017 1033 1034 1035 1054 P U H 39 distorted distorted 1040 1055 1056 1057 1074 P C H 40 distorted distorted 1062 1075 1076 1077 1094 P A H 41 distorted distorted 1082 1095 1096 1097 1116 P A H 42 distorted distorted 1102 1117 1118 1119 ---------------------------------------------------------------------------------