ID code: '5CNR' 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' G A 3 beta 4 10 7 32 C1' U A 4 beta 27 33 30 52 C1' C A 5 beta 47 53 50 72 C1' U A 6 beta 67 73 70 92 C1' A A 7 beta 87 93 90 114 C1' C A 8 beta 109 115 112 134 C1' C A 9 beta 129 135 132 154 C1' C A 10 beta 149 155 152 174 C1' A A 11 beta 169 175 172 196 C1' C A 12 beta 191 197 194 216 C1' C A 13 beta 211 217 214 236 C1' U A 14 beta 231 237 234 256 C1' C A 15 beta 251 257 254 276 C1' G A 16 beta 271 277 274 299 C1' C A 17 beta 294 300 297 319 C1' C A 18 beta 314 320 317 337 C1' A B 37 beta 332 338 335 359 C1' G B 38 beta 354 360 357 382 C1' A B 39 beta 377 383 380 404 C1' G B 40 beta 399 405 402 427 C1' G B 41 beta 422 428 425 450 C1' A B 42 beta 445 451 448 472 C1' C B 43 beta 467 473 470 492 C1' G B 44 beta 487 493 490 515 C1' G B 45 beta 510 516 513 538 C1' C B 46 beta 533 539 536 558 C1' G B 47 beta 553 559 556 579 C1' G E 3 beta 574 580 577 602 C1' U E 4 beta 597 603 600 622 C1' C E 5 beta 617 623 620 642 C1' U E 6 beta 637 643 640 662 C1' A E 7 beta 657 663 660 684 C1' C E 8 beta 679 685 682 704 C1' C E 9 beta 699 705 702 724 C1' C E 10 beta 719 725 722 744 C1' A E 11 beta 739 745 742 766 C1' C E 12 beta 761 767 764 786 C1' C E 13 beta 781 787 784 806 C1' U E 14 beta 801 807 804 826 C1' C E 15 beta 821 827 824 846 C1' G E 16 beta 841 847 844 869 C1' C E 17 beta 864 870 867 889 C1' C E 18 beta 884 890 887 907 C1' A F 37 beta 902 908 905 929 C1' G F 38 beta 924 930 927 952 C1' A F 39 beta 947 953 950 974 C1' G F 40 beta 969 975 972 997 C1' G F 41 beta 992 998 995 1020 C1' A F 42 beta 1015 1021 1018 1042 C1' C F 43 beta 1037 1043 1040 1062 C1' G F 44 beta 1057 1063 1060 1085 C1' G F 45 beta 1080 1086 1083 1108 C1' C F 46 beta 1103 1109 1106 1128 C1' G F 47 beta 1123 1129 1126 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 3 OK 9 5 8 30 C2' U A 4 OK 32 28 31 50 C2' C A 5 OK 52 48 51 70 C2' U A 6 OK 72 68 71 90 C2' A A 7 OK 92 88 91 112 C2' C A 8 OK 114 110 113 132 C2' C A 9 OK 134 130 133 152 C2' C A 10 OK 154 150 153 172 C2' A A 11 OK 174 170 173 194 C2' C A 12 OK 196 192 195 214 C2' C A 13 OK 216 212 215 234 C2' U A 14 OK 236 232 235 254 C2' C A 15 OK 256 252 255 274 C2' G A 16 OK 276 272 275 297 C2' C A 17 OK 299 295 298 317 C2' C A 18 OK 319 315 318 335 C2' A B 37 OK 337 333 336 357 C2' G B 38 OK 359 355 358 380 C2' A B 39 OK 382 378 381 402 C2' G B 40 OK 404 400 403 425 C2' G B 41 OK 427 423 426 448 C2' A B 42 OK 450 446 449 470 C2' C B 43 OK 472 468 471 490 C2' G B 44 OK 492 488 491 513 C2' G B 45 OK 515 511 514 536 C2' C B 46 OK 538 534 537 556 C2' G B 47 OK 558 554 557 577 C2' G E 3 OK 579 575 578 600 C2' U E 4 OK 602 598 601 620 C2' C E 5 OK 622 618 621 640 C2' U E 6 OK 642 638 641 660 C2' A E 7 OK 662 658 661 682 C2' C E 8 OK 684 680 683 702 C2' C E 9 OK 704 700 703 722 C2' C E 10 OK 724 720 723 742 C2' A E 11 OK 744 740 743 764 C2' C E 12 OK 766 762 765 784 C2' C E 13 OK 786 782 785 804 C2' U E 14 OK 806 802 805 824 C2' C E 15 OK 826 822 825 844 C2' G E 16 OK 846 842 845 867 C2' C E 17 OK 869 865 868 887 C2' C E 18 OK 889 885 888 905 C2' A F 37 OK 907 903 906 927 C2' G F 38 OK 929 925 928 950 C2' A F 39 OK 952 948 951 972 C2' G F 40 OK 974 970 973 995 C2' G F 41 OK 997 993 996 1018 C2' A F 42 OK 1020 1016 1019 1040 C2' C F 43 OK 1042 1038 1041 1060 C2' G F 44 OK 1062 1058 1061 1083 C2' G F 45 OK 1085 1081 1084 1106 C2' C F 46 OK 1108 1104 1107 1126 C2' G F 47 OK 1128 1124 1127 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 3 OK 3 6 7 28 C3' U A 4 OK 26 29 30 48 C3' C A 5 OK 46 49 50 68 C3' U A 6 OK 66 69 70 88 C3' A A 7 OK 86 89 90 110 C3' C A 8 OK 108 111 112 130 C3' C A 9 OK 128 131 132 150 C3' C A 10 OK 148 151 152 170 C3' A A 11 OK 168 171 172 192 C3' C A 12 OK 190 193 194 212 C3' C A 13 OK 210 213 214 232 C3' U A 14 OK 230 233 234 252 C3' C A 15 OK 250 253 254 272 C3' G A 16 OK 270 273 274 295 C3' C A 17 OK 293 296 297 315 C3' C A 18 OK 313 316 317 333 C3' A B 37 OK 331 334 335 355 C3' G B 38 OK 353 356 357 378 C3' A B 39 OK 376 379 380 400 C3' G B 40 OK 398 401 402 423 C3' G B 41 OK 421 424 425 446 C3' A B 42 OK 444 447 448 468 C3' C B 43 OK 466 469 470 488 C3' G B 44 OK 486 489 490 511 C3' G B 45 OK 509 512 513 534 C3' C B 46 OK 532 535 536 554 C3' G B 47 OK 552 555 556 575 C3' G E 3 OK 573 576 577 598 C3' U E 4 OK 596 599 600 618 C3' C E 5 OK 616 619 620 638 C3' U E 6 OK 636 639 640 658 C3' A E 7 OK 656 659 660 680 C3' C E 8 OK 678 681 682 700 C3' C E 9 OK 698 701 702 720 C3' C E 10 OK 718 721 722 740 C3' A E 11 OK 738 741 742 762 C3' C E 12 OK 760 763 764 782 C3' C E 13 OK 780 783 784 802 C3' U E 14 OK 800 803 804 822 C3' C E 15 OK 820 823 824 842 C3' G E 16 OK 840 843 844 865 C3' C E 17 OK 863 866 867 885 C3' C E 18 OK 883 886 887 903 C3' A F 37 OK 901 904 905 925 C3' G F 38 OK 923 926 927 948 C3' A F 39 OK 946 949 950 970 C3' G F 40 OK 968 971 972 993 C3' G F 41 OK 991 994 995 1016 C3' A F 42 OK 1014 1017 1018 1038 C3' C F 43 OK 1036 1039 1040 1058 C3' G F 44 OK 1056 1059 1060 1081 C3' G F 45 OK 1079 1082 1083 1104 C3' C F 46 OK 1102 1105 1106 1124 C3' G F 47 OK 1122 1125 1126 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 3 OK 5 2 4 26 C4' U A 4 OK 28 25 27 46 C4' C A 5 OK 48 45 47 66 C4' U A 6 OK 68 65 67 86 C4' A A 7 OK 88 85 87 108 C4' C A 8 OK 110 107 109 128 C4' C A 9 OK 130 127 129 148 C4' C A 10 OK 150 147 149 168 C4' A A 11 OK 170 167 169 190 C4' C A 12 OK 192 189 191 210 C4' C A 13 OK 212 209 211 230 C4' U A 14 OK 232 229 231 250 C4' C A 15 OK 252 249 251 270 C4' G A 16 OK 272 269 271 293 C4' C A 17 OK 295 292 294 313 C4' C A 18 OK 315 312 314 331 C4' A B 37 OK 333 330 332 353 C4' G B 38 OK 355 352 354 376 C4' A B 39 OK 378 375 377 398 C4' G B 40 OK 400 397 399 421 C4' G B 41 OK 423 420 422 444 C4' A B 42 OK 446 443 445 466 C4' C B 43 OK 468 465 467 486 C4' G B 44 OK 488 485 487 509 C4' G B 45 OK 511 508 510 532 C4' C B 46 OK 534 531 533 552 C4' G B 47 OK 554 551 553 573 C4' G E 3 OK 575 572 574 596 C4' U E 4 OK 598 595 597 616 C4' C E 5 OK 618 615 617 636 C4' U E 6 OK 638 635 637 656 C4' A E 7 OK 658 655 657 678 C4' C E 8 OK 680 677 679 698 C4' C E 9 OK 700 697 699 718 C4' C E 10 OK 720 717 719 738 C4' A E 11 OK 740 737 739 760 C4' C E 12 OK 762 759 761 780 C4' C E 13 OK 782 779 781 800 C4' U E 14 OK 802 799 801 820 C4' C E 15 OK 822 819 821 840 C4' G E 16 OK 842 839 841 863 C4' C E 17 OK 865 862 864 883 C4' C E 18 OK 885 882 884 901 C4' A F 37 OK 903 900 902 923 C4' G F 38 OK 925 922 924 946 C4' A F 39 OK 948 945 947 968 C4' G F 40 OK 970 967 969 991 C4' G F 41 OK 993 990 992 1014 C4' A F 42 OK 1016 1013 1015 1036 C4' C F 43 OK 1038 1035 1037 1056 C4' G F 44 OK 1058 1055 1057 1079 C4' G F 45 OK 1081 1078 1080 1102 C4' C F 46 OK 1104 1101 1103 1122 C4' G F 47 OK 1124 1121 1123 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 3 1 3 25 C5' U A 4 24 26 45 C5' C A 5 44 46 65 C5' U A 6 64 66 85 C5' A A 7 84 86 107 C5' C A 8 106 108 127 C5' C A 9 126 128 147 C5' C A 10 146 148 167 C5' A A 11 166 168 189 C5' C A 12 188 190 209 C5' C A 13 208 210 229 C5' U A 14 228 230 249 C5' C A 15 248 250 269 C5' G A 16 268 270 292 C5' C A 17 291 293 312 C5' C A 18 311 313 330 C5' A B 37 329 331 352 C5' G B 38 351 353 375 C5' A B 39 374 376 397 C5' G B 40 396 398 420 C5' G B 41 419 421 443 C5' A B 42 442 444 465 C5' C B 43 464 466 485 C5' G B 44 484 486 508 C5' G B 45 507 509 531 C5' C B 46 530 532 551 C5' G B 47 550 552 572 C5' G E 3 571 573 595 C5' U E 4 594 596 615 C5' C E 5 614 616 635 C5' U E 6 634 636 655 C5' A E 7 654 656 677 C5' C E 8 676 678 697 C5' C E 9 696 698 717 C5' C E 10 716 718 737 C5' A E 11 736 738 759 C5' C E 12 758 760 779 C5' C E 13 778 780 799 C5' U E 14 798 800 819 C5' C E 15 818 820 839 C5' G E 16 838 840 862 C5' C E 17 861 863 882 C5' C E 18 881 883 900 C5' A F 37 899 901 922 C5' G F 38 921 923 945 C5' A F 39 944 946 967 C5' G F 40 966 968 990 C5' G F 41 989 991 1013 C5' A F 42 1012 1014 1035 C5' C F 43 1034 1036 1055 C5' G F 44 1054 1056 1078 C5' G F 45 1077 1079 1101 C5' C F 46 1100 1102 1121 C5' G F 47 1120 1122 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 4 distorted distorted 6 22 23 24 41 P C A 5 distorted distorted 29 42 43 44 61 P U A 6 distorted distorted 49 62 63 64 81 P A A 7 distorted distorted 69 82 83 84 103 P C A 8 distorted distorted 89 104 105 106 123 P C A 9 distorted distorted 111 124 125 126 143 P C A 10 distorted distorted 131 144 145 146 163 P A A 11 distorted distorted 151 164 165 166 185 P C A 12 distorted distorted 171 186 187 188 205 P C A 13 distorted distorted 193 206 207 208 225 P U A 14 distorted distorted 213 226 227 228 245 P C A 15 distorted distorted 233 246 247 248 265 P G A 16 distorted distorted 253 266 267 268 288 P C A 17 distorted distorted 273 289 290 291 308 P C A 18 distorted distorted 296 309 310 311 348 P G B 38 distorted distorted 334 349 350 351 371 P A B 39 distorted distorted 356 372 373 374 393 P G B 40 distorted distorted 379 394 395 396 416 P G B 41 distorted distorted 401 417 418 419 439 P A B 42 distorted distorted 424 440 441 442 461 P C B 43 distorted distorted 447 462 463 464 481 P G B 44 distorted distorted 469 482 483 484 504 P G B 45 distorted distorted 489 505 506 507 527 P C B 46 distorted distorted 512 528 529 530 547 P G B 47 distorted distorted 535 548 549 550 591 P U E 4 distorted distorted 576 592 593 594 611 P C E 5 distorted distorted 599 612 613 614 631 P U E 6 distorted distorted 619 632 633 634 651 P A E 7 distorted distorted 639 652 653 654 673 P C E 8 distorted distorted 659 674 675 676 693 P C E 9 distorted distorted 681 694 695 696 713 P C E 10 distorted distorted 701 714 715 716 733 P A E 11 distorted distorted 721 734 735 736 755 P C E 12 distorted distorted 741 756 757 758 775 P C E 13 distorted distorted 763 776 777 778 795 P U E 14 distorted distorted 783 796 797 798 815 P C E 15 distorted distorted 803 816 817 818 835 P G E 16 distorted distorted 823 836 837 838 858 P C E 17 distorted distorted 843 859 860 861 878 P C E 18 distorted distorted 866 879 880 881 918 P G F 38 distorted distorted 904 919 920 921 941 P A F 39 distorted distorted 926 942 943 944 963 P G F 40 distorted distorted 949 964 965 966 986 P G F 41 distorted distorted 971 987 988 989 1009 P A F 42 distorted distorted 994 1010 1011 1012 1031 P C F 43 distorted distorted 1017 1032 1033 1034 1051 P G F 44 distorted distorted 1039 1052 1053 1054 1074 P G F 45 distorted distorted 1059 1075 1076 1077 1097 P C F 46 distorted distorted 1082 1098 1099 1100 1117 P G F 47 distorted distorted 1105 1118 1119 1120 ---------------------------------------------------------------------------------