ID code: '4KZ2' 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 A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' C A 4 beta 67 73 70 92 C1' C A 5 beta 87 93 90 112 C1' A A 6 beta 107 113 110 134 C1' U A 7 beta 129 135 132 154 C1' G A 8 beta 149 155 152 177 C1' U A 9 beta 172 178 175 197 C1' G A 10 beta 192 198 195 220 C1' U A 11 beta 215 221 218 240 C1' A A 12 beta 235 241 238 262 C1' U A 13 beta 257 263 260 282 C1' G A 14 beta 277 283 280 305 C1' U A 15 beta 300 306 303 325 C1' G A 16 beta 320 326 323 348 C1' G A 17 beta 343 349 346 371 C1' G A 18 beta 366 372 369 392 C1' C B 1 beta 387 393 390 412 C1' C B 2 beta 407 413 410 432 C1' C B 3 beta 427 433 430 452 C1' A B 4 beta 447 453 450 474 C1' C B 5 beta 469 475 472 494 C1' A B 6 beta 489 495 492 516 C1' U B 7 beta 511 517 514 536 C1' A B 8 beta 531 537 534 558 C1' C B 9 beta 553 559 556 578 C1' U B 10 beta 573 579 576 598 C1' U B 11 beta 593 599 596 618 C1' U B 12 beta 613 619 616 638 C1' G B 13 beta 633 639 636 661 C1' U B 14 beta 656 662 659 681 C1' U B 15 beta 676 682 679 701 C1' G B 16 beta 696 702 699 724 C1' A B 17 beta 719 725 722 746 C1' U B 18 beta 741 747 744 766 C1' C B 19 beta 761 767 764 786 C1' C B 20 beta 781 787 784 804 C1' G C 1 beta 799 805 802 827 C1' G C 2 beta 822 828 825 850 C1' A C 3 beta 845 851 848 872 C1' U C 4 beta 867 873 870 892 C1' C C 5 beta 887 893 890 912 C1' A C 6 beta 907 913 910 934 C1' A C 7 beta 929 935 932 956 C1' U C 8 beta 951 957 954 976 C1' C C 9 beta 971 977 974 996 C1' A C 10 beta 991 997 994 1018 C1' U C 11 beta 1013 1019 1016 1038 C1' G C 12 beta 1033 1039 1036 1061 C1' G C 13 beta 1056 1062 1059 1084 C1' C C 14 beta 1079 1085 1082 1104 C1' A C 15 beta 1099 1105 1102 1126 C1' A C 16 beta 1121 1127 1124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' C A 4 OK 72 68 71 90 C2' C A 5 OK 92 88 91 110 C2' A A 6 OK 112 108 111 132 C2' U A 7 OK 134 130 133 152 C2' G A 8 OK 154 150 153 175 C2' U A 9 OK 177 173 176 195 C2' G A 10 OK 197 193 196 218 C2' U A 11 OK 220 216 219 238 C2' A A 12 OK 240 236 239 260 C2' U A 13 OK 262 258 261 280 C2' G A 14 OK 282 278 281 303 C2' U A 15 OK 305 301 304 323 C2' G A 16 OK 325 321 324 346 C2' G A 17 OK 348 344 347 369 C2' G A 18 OK 371 367 370 390 C2' C B 1 OK 392 388 391 410 C2' C B 2 OK 412 408 411 430 C2' C B 3 OK 432 428 431 450 C2' A B 4 OK 452 448 451 472 C2' C B 5 OK 474 470 473 492 C2' A B 6 OK 494 490 493 514 C2' U B 7 OK 516 512 515 534 C2' A B 8 OK 536 532 535 556 C2' C B 9 OK 558 554 557 576 C2' U B 10 OK 578 574 577 596 C2' U B 11 OK 598 594 597 616 C2' U B 12 OK 618 614 617 636 C2' G B 13 OK 638 634 637 659 C2' U B 14 OK 661 657 660 679 C2' U B 15 OK 681 677 680 699 C2' G B 16 OK 701 697 700 722 C2' A B 17 OK 724 720 723 744 C2' U B 18 OK 746 742 745 764 C2' C B 19 OK 766 762 765 784 C2' C B 20 OK 786 782 785 802 C2' G C 1 OK 804 800 803 825 C2' G C 2 OK 827 823 826 848 C2' A C 3 OK 850 846 849 870 C2' U C 4 OK 872 868 871 890 C2' C C 5 OK 892 888 891 910 C2' A C 6 OK 912 908 911 932 C2' A C 7 OK 934 930 933 954 C2' U C 8 OK 956 952 955 974 C2' C C 9 OK 976 972 975 994 C2' A C 10 OK 996 992 995 1016 C2' U C 11 OK 1018 1014 1017 1036 C2' G C 12 OK 1038 1034 1037 1059 C2' G C 13 OK 1061 1057 1060 1082 C2' C C 14 OK 1084 1080 1083 1102 C2' A C 15 OK 1104 1100 1103 1124 C2' A C 16 OK 1126 1122 1125 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' C A 4 OK 66 69 70 88 C3' C A 5 OK 86 89 90 108 C3' A A 6 OK 106 109 110 130 C3' U A 7 OK 128 131 132 150 C3' G A 8 OK 148 151 152 173 C3' U A 9 OK 171 174 175 193 C3' G A 10 OK 191 194 195 216 C3' U A 11 OK 214 217 218 236 C3' A A 12 OK 234 237 238 258 C3' U A 13 OK 256 259 260 278 C3' G A 14 OK 276 279 280 301 C3' U A 15 OK 299 302 303 321 C3' G A 16 OK 319 322 323 344 C3' G A 17 OK 342 345 346 367 C3' G A 18 OK 365 368 369 388 C3' C B 1 OK 386 389 390 408 C3' C B 2 OK 406 409 410 428 C3' C B 3 OK 426 429 430 448 C3' A B 4 OK 446 449 450 470 C3' C B 5 OK 468 471 472 490 C3' A B 6 OK 488 491 492 512 C3' U B 7 OK 510 513 514 532 C3' A B 8 OK 530 533 534 554 C3' C B 9 OK 552 555 556 574 C3' U B 10 OK 572 575 576 594 C3' U B 11 OK 592 595 596 614 C3' U B 12 OK 612 615 616 634 C3' G B 13 OK 632 635 636 657 C3' U B 14 OK 655 658 659 677 C3' U B 15 OK 675 678 679 697 C3' G B 16 OK 695 698 699 720 C3' A B 17 OK 718 721 722 742 C3' U B 18 OK 740 743 744 762 C3' C B 19 OK 760 763 764 782 C3' C B 20 OK 780 783 784 800 C3' G C 1 OK 798 801 802 823 C3' G C 2 OK 821 824 825 846 C3' A C 3 OK 844 847 848 868 C3' U C 4 OK 866 869 870 888 C3' C C 5 OK 886 889 890 908 C3' A C 6 OK 906 909 910 930 C3' A C 7 OK 928 931 932 952 C3' U C 8 OK 950 953 954 972 C3' C C 9 OK 970 973 974 992 C3' A C 10 OK 990 993 994 1014 C3' U C 11 OK 1012 1015 1016 1034 C3' G C 12 OK 1032 1035 1036 1057 C3' G C 13 OK 1055 1058 1059 1080 C3' C C 14 OK 1078 1081 1082 1100 C3' A C 15 OK 1098 1101 1102 1122 C3' A C 16 OK 1120 1123 1124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' C A 4 OK 68 65 67 86 C4' C A 5 OK 88 85 87 106 C4' A A 6 OK 108 105 107 128 C4' U A 7 OK 130 127 129 148 C4' G A 8 OK 150 147 149 171 C4' U A 9 OK 173 170 172 191 C4' G A 10 OK 193 190 192 214 C4' U A 11 OK 216 213 215 234 C4' A A 12 OK 236 233 235 256 C4' U A 13 OK 258 255 257 276 C4' G A 14 OK 278 275 277 299 C4' U A 15 OK 301 298 300 319 C4' G A 16 OK 321 318 320 342 C4' G A 17 OK 344 341 343 365 C4' G A 18 OK 367 364 366 386 C4' C B 1 OK 388 385 387 406 C4' C B 2 OK 408 405 407 426 C4' C B 3 OK 428 425 427 446 C4' A B 4 OK 448 445 447 468 C4' C B 5 OK 470 467 469 488 C4' A B 6 OK 490 487 489 510 C4' U B 7 OK 512 509 511 530 C4' A B 8 OK 532 529 531 552 C4' C B 9 OK 554 551 553 572 C4' U B 10 OK 574 571 573 592 C4' U B 11 OK 594 591 593 612 C4' U B 12 OK 614 611 613 632 C4' G B 13 OK 634 631 633 655 C4' U B 14 OK 657 654 656 675 C4' U B 15 OK 677 674 676 695 C4' G B 16 OK 697 694 696 718 C4' A B 17 OK 720 717 719 740 C4' U B 18 OK 742 739 741 760 C4' C B 19 OK 762 759 761 780 C4' C B 20 OK 782 779 781 798 C4' G C 1 OK 800 797 799 821 C4' G C 2 OK 823 820 822 844 C4' A C 3 OK 846 843 845 866 C4' U C 4 OK 868 865 867 886 C4' C C 5 OK 888 885 887 906 C4' A C 6 OK 908 905 907 928 C4' A C 7 OK 930 927 929 950 C4' U C 8 OK 952 949 951 970 C4' C C 9 OK 972 969 971 990 C4' A C 10 OK 992 989 991 1012 C4' U C 11 OK 1014 1011 1013 1032 C4' G C 12 OK 1034 1031 1033 1055 C4' G C 13 OK 1057 1054 1056 1078 C4' C C 14 OK 1080 1077 1079 1098 C4' A C 15 OK 1100 1097 1099 1120 C4' A C 16 OK 1122 1119 1121 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' U A 2 21 23 42 C5' G A 3 41 43 65 C5' C A 4 64 66 85 C5' C A 5 84 86 105 C5' A A 6 104 106 127 C5' U A 7 126 128 147 C5' G A 8 146 148 170 C5' U A 9 169 171 190 C5' G A 10 189 191 213 C5' U A 11 212 214 233 C5' A A 12 232 234 255 C5' U A 13 254 256 275 C5' G A 14 274 276 298 C5' U A 15 297 299 318 C5' G A 16 317 319 341 C5' G A 17 340 342 364 C5' G A 18 363 365 385 C5' C B 1 384 386 405 C5' C B 2 404 406 425 C5' C B 3 424 426 445 C5' A B 4 444 446 467 C5' C B 5 466 468 487 C5' A B 6 486 488 509 C5' U B 7 508 510 529 C5' A B 8 528 530 551 C5' C B 9 550 552 571 C5' U B 10 570 572 591 C5' U B 11 590 592 611 C5' U B 12 610 612 631 C5' G B 13 630 632 654 C5' U B 14 653 655 674 C5' U B 15 673 675 694 C5' G B 16 693 695 717 C5' A B 17 716 718 739 C5' U B 18 738 740 759 C5' C B 19 758 760 779 C5' C B 20 778 780 797 C5' G C 1 796 798 820 C5' G C 2 819 821 843 C5' A C 3 842 844 865 C5' U C 4 864 866 885 C5' C C 5 884 886 905 C5' A C 6 904 906 927 C5' A C 7 926 928 949 C5' U C 8 948 950 969 C5' C C 9 968 970 989 C5' A C 10 988 990 1011 C5' U C 11 1010 1012 1031 C5' G C 12 1030 1032 1054 C5' G C 13 1053 1055 1077 C5' C C 14 1076 1078 1097 C5' A C 15 1096 1098 1119 C5' A C 16 1118 1120 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P C A 4 distorted distorted 46 62 63 64 81 P C A 5 distorted distorted 69 82 83 84 101 P A A 6 distorted distorted 89 102 103 104 123 P U A 7 distorted distorted 109 124 125 126 143 P G A 8 distorted distorted 131 144 145 146 166 P U A 9 distorted distorted 151 167 168 169 186 P G A 10 distorted distorted 174 187 188 189 209 P U A 11 distorted distorted 194 210 211 212 229 P A A 12 distorted distorted 217 230 231 232 251 P U A 13 distorted distorted 237 252 253 254 271 P G A 14 distorted distorted 259 272 273 274 294 P U A 15 distorted distorted 279 295 296 297 314 P G A 16 distorted distorted 302 315 316 317 337 P G A 17 distorted distorted 322 338 339 340 360 P G A 18 distorted distorted 345 361 362 363 401 P C B 2 distorted distorted 389 402 403 404 421 P C B 3 distorted distorted 409 422 423 424 441 P A B 4 distorted distorted 429 442 443 444 463 P C B 5 distorted distorted 449 464 465 466 483 P A B 6 distorted distorted 471 484 485 486 505 P U B 7 distorted distorted 491 506 507 508 525 P A B 8 distorted distorted 513 526 527 528 547 P C B 9 distorted distorted 533 548 549 550 567 P U B 10 distorted distorted 555 568 569 570 587 P U B 11 distorted distorted 575 588 589 590 607 P U B 12 distorted distorted 595 608 609 610 627 P G B 13 distorted distorted 615 628 629 630 650 P U B 14 distorted distorted 635 651 652 653 670 P U B 15 distorted distorted 658 671 672 673 690 P G B 16 distorted distorted 678 691 692 693 713 P A B 17 distorted distorted 698 714 715 716 735 P U B 18 distorted distorted 721 736 737 738 755 P C B 19 distorted distorted 743 756 757 758 775 P C B 20 distorted distorted 763 776 777 778 816 P G C 2 distorted distorted 801 817 818 819 839 P A C 3 distorted distorted 824 840 841 842 861 P U C 4 distorted distorted 847 862 863 864 881 P C C 5 distorted distorted 869 882 883 884 901 P A C 6 distorted distorted 889 902 903 904 923 P A C 7 distorted distorted 909 924 925 926 945 P U C 8 distorted distorted 931 946 947 948 965 P C C 9 distorted distorted 953 966 967 968 985 P A C 10 distorted distorted 973 986 987 988 1007 P U C 11 distorted distorted 993 1008 1009 1010 1027 P G C 12 distorted distorted 1015 1028 1029 1030 1050 P G C 13 distorted distorted 1035 1051 1052 1053 1073 P C C 14 distorted distorted 1058 1074 1075 1076 1093 P A C 15 distorted distorted 1081 1094 1095 1096 1115 P A C 16 distorted distorted 1101 1116 1117 1118 ---------------------------------------------------------------------------------