ID code: '4OJI' 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' --------------------------------------------------------------------------------- 46 C1' C A 2 beta 41 47 44 66 C1' G A 3 beta 61 67 64 89 C1' C A 4 beta 84 90 87 109 C1' C A 5 beta 104 110 107 128 C1' DU A 6 beta 124 129 127 192 C1' A A 8 beta 187 193 190 214 C1' C A 9 beta 209 215 212 234 C1' A A 10 beta 229 235 232 256 C1' C A 11 beta 251 257 254 276 C1' U A 12 beta 271 277 274 296 C1' G A 13 beta 291 297 294 319 C1' C A 14 beta 314 320 317 339 C1' C A 15 beta 334 340 337 359 C1' A A 16 beta 354 360 357 381 C1' G A 19 beta 376 382 379 404 C1' C A 20 beta 399 405 402 424 C1' C A 21 beta 419 425 422 444 C1' G A 22 beta 439 445 442 467 C1' G A 23 beta 462 468 465 490 C1' U A 24 beta 485 491 488 510 C1' C A 25 beta 505 511 508 530 C1' C A 26 beta 525 531 528 550 C1' C A 27 beta 545 551 548 570 C1' A A 28 beta 565 571 568 592 C1' A A 29 beta 587 593 590 614 C1' G A 30 beta 609 615 612 637 C1' C A 31 beta 632 638 635 657 C1' C A 32 beta 652 658 655 677 C1' C A 33 beta 672 678 675 697 C1' G A 34 beta 692 698 695 720 C1' G A 35 beta 715 721 718 743 C1' A A 36 beta 738 744 741 765 C1' U A 37 beta 760 766 763 785 C1' A A 38 beta 780 786 783 807 C1' A A 39 beta 802 808 805 829 C1' A A 40 beta 824 830 827 851 C1' A A 41 beta 846 852 849 873 C1' G A 42 beta 868 874 871 896 C1' U A 43 beta 891 897 894 916 C1' G A 44 beta 911 917 914 939 C1' G A 45 beta 934 940 937 962 C1' A A 46 beta 957 963 960 984 C1' G A 47 beta 979 985 982 1007 C1' G A 48 beta 1002 1008 1005 1030 C1' G A 49 beta 1025 1031 1028 1053 C1' G A 50 beta 1048 1054 1051 1076 C1' G A 51 beta 1071 1077 1074 1099 C1' C A 52 beta 1094 1100 1097 1119 C1' G A 53 beta 1114 1120 1117 1142 C1' G A 54 beta 1137 1143 1140 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 44 C2' C A 2 OK 46 42 45 64 C2' G A 3 OK 66 62 65 87 C2' C A 4 OK 89 85 88 107 C2' C A 5 OK 109 105 108 127 C2' DU A 6 128 125 190 C2' A A 8 OK 192 188 191 212 C2' C A 9 OK 214 210 213 232 C2' A A 10 OK 234 230 233 254 C2' C A 11 OK 256 252 255 274 C2' U A 12 OK 276 272 275 294 C2' G A 13 OK 296 292 295 317 C2' C A 14 OK 319 315 318 337 C2' C A 15 OK 339 335 338 357 C2' A A 16 OK 359 355 358 379 C2' G A 19 OK 381 377 380 402 C2' C A 20 OK 404 400 403 422 C2' C A 21 OK 424 420 423 442 C2' G A 22 OK 444 440 443 465 C2' G A 23 OK 467 463 466 488 C2' U A 24 OK 490 486 489 508 C2' C A 25 OK 510 506 509 528 C2' C A 26 OK 530 526 529 548 C2' C A 27 OK 550 546 549 568 C2' A A 28 OK 570 566 569 590 C2' A A 29 OK 592 588 591 612 C2' G A 30 OK 614 610 613 635 C2' C A 31 OK 637 633 636 655 C2' C A 32 OK 657 653 656 675 C2' C A 33 OK 677 673 676 695 C2' G A 34 OK 697 693 696 718 C2' G A 35 OK 720 716 719 741 C2' A A 36 OK 743 739 742 763 C2' U A 37 OK 765 761 764 783 C2' A A 38 OK 785 781 784 805 C2' A A 39 OK 807 803 806 827 C2' A A 40 OK 829 825 828 849 C2' A A 41 OK 851 847 850 871 C2' G A 42 OK 873 869 872 894 C2' U A 43 OK 896 892 895 914 C2' G A 44 OK 916 912 915 937 C2' G A 45 OK 939 935 938 960 C2' A A 46 OK 962 958 961 982 C2' G A 47 OK 984 980 983 1005 C2' G A 48 OK 1007 1003 1006 1028 C2' G A 49 OK 1030 1026 1029 1051 C2' G A 50 OK 1053 1049 1052 1074 C2' G A 51 OK 1076 1072 1075 1097 C2' C A 52 OK 1099 1095 1098 1117 C2' G A 53 OK 1119 1115 1118 1140 C2' G A 54 OK 1142 1138 1141 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 42 C3' C A 2 OK 40 43 44 62 C3' G A 3 OK 60 63 64 85 C3' C A 4 OK 83 86 87 105 C3' C A 5 OK 103 106 107 125 C3' DU A 6 OK 123 126 127 188 C3' A A 8 OK 186 189 190 210 C3' C A 9 OK 208 211 212 230 C3' A A 10 OK 228 231 232 252 C3' C A 11 OK 250 253 254 272 C3' U A 12 OK 270 273 274 292 C3' G A 13 OK 290 293 294 315 C3' C A 14 OK 313 316 317 335 C3' C A 15 OK 333 336 337 355 C3' A A 16 OK 353 356 357 377 C3' G A 19 OK 375 378 379 400 C3' C A 20 OK 398 401 402 420 C3' C A 21 OK 418 421 422 440 C3' G A 22 OK 438 441 442 463 C3' G A 23 OK 461 464 465 486 C3' U A 24 OK 484 487 488 506 C3' C A 25 OK 504 507 508 526 C3' C A 26 OK 524 527 528 546 C3' C A 27 OK 544 547 548 566 C3' A A 28 OK 564 567 568 588 C3' A A 29 OK 586 589 590 610 C3' G A 30 OK 608 611 612 633 C3' C A 31 OK 631 634 635 653 C3' C A 32 OK 651 654 655 673 C3' C A 33 OK 671 674 675 693 C3' G A 34 OK 691 694 695 716 C3' G A 35 OK 714 717 718 739 C3' A A 36 OK 737 740 741 761 C3' U A 37 OK 759 762 763 781 C3' A A 38 OK 779 782 783 803 C3' A A 39 OK 801 804 805 825 C3' A A 40 OK 823 826 827 847 C3' A A 41 OK 845 848 849 869 C3' G A 42 OK 867 870 871 892 C3' U A 43 OK 890 893 894 912 C3' G A 44 OK 910 913 914 935 C3' G A 45 OK 933 936 937 958 C3' A A 46 OK 956 959 960 980 C3' G A 47 OK 978 981 982 1003 C3' G A 48 OK 1001 1004 1005 1026 C3' G A 49 OK 1024 1027 1028 1049 C3' G A 50 OK 1047 1050 1051 1072 C3' G A 51 OK 1070 1073 1074 1095 C3' C A 52 OK 1093 1096 1097 1115 C3' G A 53 OK 1113 1116 1117 1138 C3' G A 54 OK 1136 1139 1140 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 40 C4' C A 2 OK 42 39 41 60 C4' G A 3 OK 62 59 61 83 C4' C A 4 OK 85 82 84 103 C4' C A 5 OK 105 102 104 123 C4' DU A 6 OK 125 122 124 186 C4' A A 8 OK 188 185 187 208 C4' C A 9 OK 210 207 209 228 C4' A A 10 OK 230 227 229 250 C4' C A 11 OK 252 249 251 270 C4' U A 12 OK 272 269 271 290 C4' G A 13 OK 292 289 291 313 C4' C A 14 OK 315 312 314 333 C4' C A 15 OK 335 332 334 353 C4' A A 16 OK 355 352 354 375 C4' G A 19 OK 377 374 376 398 C4' C A 20 OK 400 397 399 418 C4' C A 21 OK 420 417 419 438 C4' G A 22 OK 440 437 439 461 C4' G A 23 OK 463 460 462 484 C4' U A 24 OK 486 483 485 504 C4' C A 25 OK 506 503 505 524 C4' C A 26 OK 526 523 525 544 C4' C A 27 OK 546 543 545 564 C4' A A 28 OK 566 563 565 586 C4' A A 29 OK 588 585 587 608 C4' G A 30 OK 610 607 609 631 C4' C A 31 OK 633 630 632 651 C4' C A 32 OK 653 650 652 671 C4' C A 33 OK 673 670 672 691 C4' G A 34 OK 693 690 692 714 C4' G A 35 OK 716 713 715 737 C4' A A 36 OK 739 736 738 759 C4' U A 37 OK 761 758 760 779 C4' A A 38 OK 781 778 780 801 C4' A A 39 OK 803 800 802 823 C4' A A 40 OK 825 822 824 845 C4' A A 41 OK 847 844 846 867 C4' G A 42 OK 869 866 868 890 C4' U A 43 OK 892 889 891 910 C4' G A 44 OK 912 909 911 933 C4' G A 45 OK 935 932 934 956 C4' A A 46 OK 958 955 957 978 C4' G A 47 OK 980 977 979 1001 C4' G A 48 OK 1003 1000 1002 1024 C4' G A 49 OK 1026 1023 1025 1047 C4' G A 50 OK 1049 1046 1048 1070 C4' G A 51 OK 1072 1069 1071 1093 C4' C A 52 OK 1095 1092 1094 1113 C4' G A 53 OK 1115 1112 1114 1136 C4' G A 54 OK 1138 1135 1137 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 39 C5' C A 2 38 40 59 C5' G A 3 58 60 82 C5' C A 4 81 83 102 C5' C A 5 101 103 122 C5' DU A 6 121 123 185 C5' A A 8 184 186 207 C5' C A 9 206 208 227 C5' A A 10 226 228 249 C5' C A 11 248 250 269 C5' U A 12 268 270 289 C5' G A 13 288 290 312 C5' C A 14 311 313 332 C5' C A 15 331 333 352 C5' A A 16 351 353 374 C5' G A 19 373 375 397 C5' C A 20 396 398 417 C5' C A 21 416 418 437 C5' G A 22 436 438 460 C5' G A 23 459 461 483 C5' U A 24 482 484 503 C5' C A 25 502 504 523 C5' C A 26 522 524 543 C5' C A 27 542 544 563 C5' A A 28 562 564 585 C5' A A 29 584 586 607 C5' G A 30 606 608 630 C5' C A 31 629 631 650 C5' C A 32 649 651 670 C5' C A 33 669 671 690 C5' G A 34 689 691 713 C5' G A 35 712 714 736 C5' A A 36 735 737 758 C5' U A 37 757 759 778 C5' A A 38 777 779 800 C5' A A 39 799 801 822 C5' A A 40 821 823 844 C5' A A 41 843 845 866 C5' G A 42 865 867 889 C5' U A 43 888 890 909 C5' G A 44 908 910 932 C5' G A 45 931 933 955 C5' A A 46 954 956 977 C5' G A 47 976 978 1000 C5' G A 48 999 1001 1023 C5' G A 49 1022 1024 1046 C5' G A 50 1045 1047 1069 C5' G A 51 1068 1070 1092 C5' C A 52 1091 1093 1112 C5' G A 53 1111 1113 1135 C5' G A 54 1134 1136 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 35 P C A 2 distorted distorted 36 37 38 55 P G A 3 distorted distorted 43 56 57 58 78 P C A 4 distorted distorted 63 79 80 81 98 P C A 5 distorted distorted 86 99 100 101 118 P DU A 6 distorted distorted 106 119 120 121 137 P A A 7 126 138 P A A 7 126 181 P A A 8 distorted distorted 182 183 184 203 P C A 9 distorted distorted 189 204 205 206 223 P A A 10 distorted distorted 211 224 225 226 245 P C A 11 distorted distorted 231 246 247 248 265 P U A 12 distorted distorted 253 266 267 268 285 P G A 13 distorted distorted 273 286 287 288 308 P C A 14 distorted distorted 293 309 310 311 328 P C A 15 distorted distorted 316 329 330 331 348 P A A 16 distorted distorted 336 349 350 351 370 P G A 19 distorted distorted 371 372 373 393 P C A 20 distorted distorted 378 394 395 396 413 P C A 21 distorted distorted 401 414 415 416 433 P G A 22 distorted distorted 421 434 435 436 456 P G A 23 distorted distorted 441 457 458 459 479 P U A 24 distorted distorted 464 480 481 482 499 P C A 25 distorted distorted 487 500 501 502 519 P C A 26 distorted distorted 507 520 521 522 539 P C A 27 distorted distorted 527 540 541 542 559 P A A 28 distorted distorted 547 560 561 562 581 P A A 29 distorted distorted 567 582 583 584 603 P G A 30 distorted distorted 589 604 605 606 626 P C A 31 distorted distorted 611 627 628 629 646 P C A 32 distorted distorted 634 647 648 649 666 P C A 33 distorted distorted 654 667 668 669 686 P G A 34 distorted distorted 674 687 688 689 709 P G A 35 distorted distorted 694 710 711 712 732 P A A 36 distorted distorted 717 733 734 735 754 P U A 37 distorted distorted 740 755 756 757 774 P A A 38 distorted distorted 762 775 776 777 796 P A A 39 distorted distorted 782 797 798 799 818 P A A 40 distorted distorted 804 819 820 821 840 P A A 41 distorted distorted 826 841 842 843 862 P G A 42 distorted distorted 848 863 864 865 885 P U A 43 distorted distorted 870 886 887 888 905 P G A 44 distorted distorted 893 906 907 908 928 P G A 45 distorted distorted 913 929 930 931 951 P A A 46 distorted distorted 936 952 953 954 973 P G A 47 distorted distorted 959 974 975 976 996 P G A 48 distorted distorted 981 997 998 999 1019 P G A 49 distorted distorted 1004 1020 1021 1022 1042 P G A 50 distorted distorted 1027 1043 1044 1045 1065 P G A 51 distorted distorted 1050 1066 1067 1068 1088 P C A 52 distorted distorted 1073 1089 1090 1091 1108 P G A 53 distorted distorted 1096 1109 1110 1111 1131 P G A 54 distorted distorted 1116 1132 1133 1134 ---------------------------------------------------------------------------------