ID code: '2JTP' 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 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' U A 4 alpha beta 106 126 112 109 141 C1' G A 5 alpha beta 136 159 142 139 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' G A 7 alpha beta 204 227 210 207 243 C1' G A 8 alpha beta 238 261 244 241 277 C1' A A 9 alpha beta 272 294 278 275 310 C1' A A 10 alpha beta 305 327 311 308 343 C1' A A 11 alpha beta 338 360 344 341 376 C1' G A 12 alpha beta 371 394 377 374 410 C1' A A 13 alpha beta 405 427 411 408 443 C1' A A 14 alpha beta 438 460 444 441 476 C1' G A 15 alpha beta 471 494 477 474 510 C1' C A 16 alpha beta 505 525 511 508 541 C1' C A 17 alpha beta 536 556 542 539 572 C1' C A 18 alpha beta 567 587 573 570 603 C1' C A 19 alpha beta 598 618 604 601 634 C1' G A 20 alpha beta 629 652 635 632 668 C1' C A 21 alpha beta 663 683 669 666 699 C1' A A 22 alpha beta 694 716 700 697 732 C1' A A 23 alpha beta 727 749 733 730 765 C1' U A 24 alpha beta 760 780 766 763 795 C1' U A 25 alpha beta 790 810 796 793 825 C1' U A 26 alpha beta 820 840 826 823 855 C1' C A 27 alpha beta 850 870 856 853 886 C1' C A 28 alpha beta 881 901 887 884 917 C1' C A 29 alpha beta 912 932 918 915 948 C1' C A 30 alpha beta 943 963 949 946 979 C1' A A 31 alpha beta 974 996 980 977 1012 C1' U A 32 alpha beta 1007 1027 1013 1010 1042 C1' C A 33 alpha beta 1037 1057 1043 1040 1073 C1' C A 34 alpha beta 1068 1089 1074 1071 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' U A 4 OK OK 111 107 124 110 139 C2' G A 5 OK OK 141 137 157 140 173 C2' G A 6 OK OK 175 171 191 174 207 C2' G A 7 OK OK 209 205 225 208 241 C2' G A 8 OK OK 243 239 259 242 275 C2' A A 9 OK OK 277 273 292 276 308 C2' A A 10 OK OK 310 306 325 309 341 C2' A A 11 OK OK 343 339 358 342 374 C2' G A 12 OK OK 376 372 392 375 408 C2' A A 13 OK OK 410 406 425 409 441 C2' A A 14 OK OK 443 439 458 442 474 C2' G A 15 OK OK 476 472 492 475 508 C2' C A 16 OK OK 510 506 523 509 539 C2' C A 17 OK OK 541 537 554 540 570 C2' C A 18 OK OK 572 568 585 571 601 C2' C A 19 OK OK 603 599 616 602 632 C2' G A 20 OK OK 634 630 650 633 666 C2' C A 21 OK OK 668 664 681 667 697 C2' A A 22 OK OK 699 695 714 698 730 C2' A A 23 OK OK 732 728 747 731 763 C2' U A 24 OK OK 765 761 778 764 793 C2' U A 25 OK OK 795 791 808 794 823 C2' U A 26 OK OK 825 821 838 824 853 C2' C A 27 OK OK 855 851 868 854 884 C2' C A 28 OK OK 886 882 899 885 915 C2' C A 29 OK OK 917 913 930 916 946 C2' C A 30 OK OK 948 944 961 947 977 C2' A A 31 OK OK 979 975 994 978 1010 C2' U A 32 OK OK 1012 1008 1025 1011 1040 C2' C A 33 OK OK 1042 1038 1055 1041 1071 C2' C A 34 OK OK 1073 1069 1087 1072 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' U A 4 OK OK 105 123 108 109 137 C3' G A 5 OK OK 135 156 138 139 171 C3' G A 6 OK OK 169 190 172 173 205 C3' G A 7 OK OK 203 224 206 207 239 C3' G A 8 OK OK 237 258 240 241 273 C3' A A 9 OK OK 271 291 274 275 306 C3' A A 10 OK OK 304 324 307 308 339 C3' A A 11 OK OK 337 357 340 341 372 C3' G A 12 OK OK 370 391 373 374 406 C3' A A 13 OK OK 404 424 407 408 439 C3' A A 14 OK OK 437 457 440 441 472 C3' G A 15 OK OK 470 491 473 474 506 C3' C A 16 OK OK 504 522 507 508 537 C3' C A 17 OK OK 535 553 538 539 568 C3' C A 18 OK OK 566 584 569 570 599 C3' C A 19 OK OK 597 615 600 601 630 C3' G A 20 OK OK 628 649 631 632 664 C3' C A 21 OK OK 662 680 665 666 695 C3' A A 22 OK OK 693 713 696 697 728 C3' A A 23 OK OK 726 746 729 730 761 C3' U A 24 OK OK 759 777 762 763 791 C3' U A 25 OK OK 789 807 792 793 821 C3' U A 26 OK OK 819 837 822 823 851 C3' C A 27 OK OK 849 867 852 853 882 C3' C A 28 OK OK 880 898 883 884 913 C3' C A 29 OK OK 911 929 914 915 944 C3' C A 30 OK OK 942 960 945 946 975 C3' A A 31 OK OK 973 993 976 977 1008 C3' U A 32 OK OK 1006 1024 1009 1010 1038 C3' C A 33 OK OK 1036 1054 1039 1040 1069 C3' C A 34 OK OK 1067 1085 1070 1071 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' U A 4 OK OK 107 122 104 106 135 C4' G A 5 OK OK 137 155 134 136 169 C4' G A 6 OK OK 171 189 168 170 203 C4' G A 7 OK OK 205 223 202 204 237 C4' G A 8 OK OK 239 257 236 238 271 C4' A A 9 OK OK 273 290 270 272 304 C4' A A 10 OK OK 306 323 303 305 337 C4' A A 11 OK OK 339 356 336 338 370 C4' G A 12 OK OK 372 390 369 371 404 C4' A A 13 OK OK 406 423 403 405 437 C4' A A 14 OK OK 439 456 436 438 470 C4' G A 15 OK OK 472 490 469 471 504 C4' C A 16 OK OK 506 521 503 505 535 C4' C A 17 OK OK 537 552 534 536 566 C4' C A 18 OK OK 568 583 565 567 597 C4' C A 19 OK OK 599 614 596 598 628 C4' G A 20 OK OK 630 648 627 629 662 C4' C A 21 OK OK 664 679 661 663 693 C4' A A 22 OK OK 695 712 692 694 726 C4' A A 23 OK OK 728 745 725 727 759 C4' U A 24 OK OK 761 776 758 760 789 C4' U A 25 OK OK 791 806 788 790 819 C4' U A 26 OK OK 821 836 818 820 849 C4' C A 27 OK OK 851 866 848 850 880 C4' C A 28 OK OK 882 897 879 881 911 C4' C A 29 OK OK 913 928 910 912 942 C4' C A 30 OK OK 944 959 941 943 973 C4' A A 31 OK OK 975 992 972 974 1006 C4' U A 32 OK OK 1008 1023 1005 1007 1036 C4' C A 33 OK OK 1038 1053 1035 1037 1067 C4' C A 34 OK OK 1069 1084 1066 1068 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' U A 4 OK OK 103 120 121 105 134 C5' G A 5 OK OK 133 153 154 135 168 C5' G A 6 OK OK 167 187 188 169 202 C5' G A 7 OK OK 201 221 222 203 236 C5' G A 8 OK OK 235 255 256 237 270 C5' A A 9 OK OK 269 288 289 271 303 C5' A A 10 OK OK 302 321 322 304 336 C5' A A 11 OK OK 335 354 355 337 369 C5' G A 12 OK OK 368 388 389 370 403 C5' A A 13 OK OK 402 421 422 404 436 C5' A A 14 OK OK 435 454 455 437 469 C5' G A 15 OK OK 468 488 489 470 503 C5' C A 16 OK OK 502 519 520 504 534 C5' C A 17 OK OK 533 550 551 535 565 C5' C A 18 OK OK 564 581 582 566 596 C5' C A 19 OK OK 595 612 613 597 627 C5' G A 20 OK OK 626 646 647 628 661 C5' C A 21 OK OK 660 677 678 662 692 C5' A A 22 OK OK 691 710 711 693 725 C5' A A 23 OK OK 724 743 744 726 758 C5' U A 24 OK OK 757 774 775 759 788 C5' U A 25 OK OK 787 804 805 789 818 C5' U A 26 OK OK 817 834 835 819 848 C5' C A 27 OK OK 847 864 865 849 879 C5' C A 28 OK OK 878 895 896 880 910 C5' C A 29 OK OK 909 926 927 911 941 C5' C A 30 OK OK 940 957 958 942 972 C5' A A 31 OK OK 971 990 991 973 1005 C5' U A 32 OK OK 1004 1021 1022 1006 1035 C5' C A 33 OK OK 1034 1051 1052 1036 1066 C5' C A 34 OK OK 1065 1082 1083 1067 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P U A 4 distorted distorted 75 101 102 103 130 P G A 5 distorted distorted 108 131 132 133 164 P G A 6 distorted distorted 138 165 166 167 198 P G A 7 distorted distorted 172 199 200 201 232 P G A 8 distorted distorted 206 233 234 235 266 P A A 9 distorted distorted 240 267 268 269 299 P A A 10 distorted distorted 274 300 301 302 332 P A A 11 distorted distorted 307 333 334 335 365 P G A 12 distorted distorted 340 366 367 368 399 P A A 13 distorted distorted 373 400 401 402 432 P A A 14 distorted distorted 407 433 434 435 465 P G A 15 distorted distorted 440 466 467 468 499 P C A 16 distorted distorted 473 500 501 502 530 P C A 17 distorted distorted 507 531 532 533 561 P C A 18 distorted distorted 538 562 563 564 592 P C A 19 distorted distorted 569 593 594 595 623 P G A 20 distorted distorted 600 624 625 626 657 P C A 21 distorted distorted 631 658 659 660 688 P A A 22 distorted distorted 665 689 690 691 721 P A A 23 distorted distorted 696 722 723 724 754 P U A 24 distorted distorted 729 755 756 757 784 P U A 25 distorted distorted 762 785 786 787 814 P U A 26 distorted distorted 792 815 816 817 844 P C A 27 distorted distorted 822 845 846 847 875 P C A 28 distorted distorted 852 876 877 878 906 P C A 29 distorted distorted 883 907 908 909 937 P C A 30 distorted distorted 914 938 939 940 968 P A A 31 distorted distorted 945 969 970 971 1001 P U A 32 distorted distorted 976 1002 1003 1004 1031 P C A 33 distorted distorted 1009 1032 1033 1034 1062 P C A 34 distorted distorted 1039 1063 1064 1065 ---------------------------------------------------------------------------------