ID code: '2M57' 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' G A 4 alpha beta 106 129 112 109 145 C1' C A 5 alpha beta 140 160 146 143 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' U A 8 alpha beta 236 256 242 239 271 C1' A A 9 alpha beta 266 288 272 269 304 C1' U A 10 alpha beta 299 319 305 302 334 C1' G A 11 alpha beta 329 352 335 332 368 C1' C A 12 alpha beta 363 383 369 366 399 C1' G A 13 alpha beta 394 417 400 397 433 C1' G A 14 alpha beta 428 451 434 431 467 C1' U A 15 alpha beta 462 482 468 465 497 C1' A A 16 alpha beta 492 514 498 495 530 C1' G A 17 alpha beta 525 548 531 528 564 C1' U A 18 alpha beta 559 579 565 562 594 C1' U A 19 alpha beta 589 609 595 592 624 C1' C A 20 alpha beta 619 639 625 622 655 C1' C A 21 alpha beta 650 670 656 653 686 C1' G A 22 alpha beta 681 704 687 684 720 C1' C A 23 alpha beta 715 735 721 718 751 C1' A A 24 alpha beta 746 768 752 749 784 C1' C A 25 alpha beta 779 799 785 782 815 C1' G A 26 alpha beta 810 833 816 813 849 C1' U A 27 alpha beta 844 864 850 847 879 C1' A A 28 alpha beta 874 896 880 877 912 C1' C A 29 alpha beta 907 927 913 910 943 C1' G A 30 alpha beta 938 961 944 941 977 C1' G A 31 alpha beta 972 995 978 975 1011 C1' A A 32 alpha beta 1006 1028 1012 1009 1044 C1' U A 33 alpha beta 1039 1059 1045 1042 1074 C1' C A 34 alpha beta 1069 1089 1075 1072 1105 C1' U A 35 alpha beta 1100 1120 1106 1103 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 111 107 127 110 143 C2' C A 5 OK OK 145 141 158 144 174 C2' C A 6 OK OK 176 172 189 175 205 C2' G A 7 OK OK 207 203 223 206 239 C2' U A 8 OK OK 241 237 254 240 269 C2' A A 9 OK OK 271 267 286 270 302 C2' U A 10 OK OK 304 300 317 303 332 C2' G A 11 OK OK 334 330 350 333 366 C2' C A 12 OK OK 368 364 381 367 397 C2' G A 13 OK OK 399 395 415 398 431 C2' G A 14 OK OK 433 429 449 432 465 C2' U A 15 OK OK 467 463 480 466 495 C2' A A 16 OK OK 497 493 512 496 528 C2' G A 17 OK OK 530 526 546 529 562 C2' U A 18 OK OK 564 560 577 563 592 C2' U A 19 OK OK 594 590 607 593 622 C2' C A 20 OK OK 624 620 637 623 653 C2' C A 21 OK OK 655 651 668 654 684 C2' G A 22 OK OK 686 682 702 685 718 C2' C A 23 OK OK 720 716 733 719 749 C2' A A 24 OK OK 751 747 766 750 782 C2' C A 25 OK OK 784 780 797 783 813 C2' G A 26 OK OK 815 811 831 814 847 C2' U A 27 OK OK 849 845 862 848 877 C2' A A 28 OK OK 879 875 894 878 910 C2' C A 29 OK OK 912 908 925 911 941 C2' G A 30 OK OK 943 939 959 942 975 C2' G A 31 OK OK 977 973 993 976 1009 C2' A A 32 OK OK 1011 1007 1026 1010 1042 C2' U A 33 OK OK 1044 1040 1057 1043 1072 C2' C A 34 OK OK 1074 1070 1087 1073 1103 C2' U A 35 OK OK 1105 1101 1118 1104 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 105 126 108 109 141 C3' C A 5 OK OK 139 157 142 143 172 C3' C A 6 OK OK 170 188 173 174 203 C3' G A 7 OK OK 201 222 204 205 237 C3' U A 8 OK OK 235 253 238 239 267 C3' A A 9 OK OK 265 285 268 269 300 C3' U A 10 OK OK 298 316 301 302 330 C3' G A 11 OK OK 328 349 331 332 364 C3' C A 12 OK OK 362 380 365 366 395 C3' G A 13 OK OK 393 414 396 397 429 C3' G A 14 OK OK 427 448 430 431 463 C3' U A 15 OK OK 461 479 464 465 493 C3' A A 16 OK OK 491 511 494 495 526 C3' G A 17 OK OK 524 545 527 528 560 C3' U A 18 OK OK 558 576 561 562 590 C3' U A 19 OK OK 588 606 591 592 620 C3' C A 20 OK OK 618 636 621 622 651 C3' C A 21 OK OK 649 667 652 653 682 C3' G A 22 OK OK 680 701 683 684 716 C3' C A 23 OK OK 714 732 717 718 747 C3' A A 24 OK OK 745 765 748 749 780 C3' C A 25 OK OK 778 796 781 782 811 C3' G A 26 OK OK 809 830 812 813 845 C3' U A 27 OK OK 843 861 846 847 875 C3' A A 28 OK OK 873 893 876 877 908 C3' C A 29 OK OK 906 924 909 910 939 C3' G A 30 OK OK 937 958 940 941 973 C3' G A 31 OK OK 971 992 974 975 1007 C3' A A 32 OK OK 1005 1025 1008 1009 1040 C3' U A 33 OK OK 1038 1056 1041 1042 1070 C3' C A 34 OK OK 1068 1086 1071 1072 1101 C3' U A 35 OK OK 1099 1117 1102 1103 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 107 125 104 106 139 C4' C A 5 OK OK 141 156 138 140 170 C4' C A 6 OK OK 172 187 169 171 201 C4' G A 7 OK OK 203 221 200 202 235 C4' U A 8 OK OK 237 252 234 236 265 C4' A A 9 OK OK 267 284 264 266 298 C4' U A 10 OK OK 300 315 297 299 328 C4' G A 11 OK OK 330 348 327 329 362 C4' C A 12 OK OK 364 379 361 363 393 C4' G A 13 OK OK 395 413 392 394 427 C4' G A 14 OK OK 429 447 426 428 461 C4' U A 15 OK OK 463 478 460 462 491 C4' A A 16 OK OK 493 510 490 492 524 C4' G A 17 OK OK 526 544 523 525 558 C4' U A 18 OK OK 560 575 557 559 588 C4' U A 19 OK OK 590 605 587 589 618 C4' C A 20 OK OK 620 635 617 619 649 C4' C A 21 OK OK 651 666 648 650 680 C4' G A 22 OK OK 682 700 679 681 714 C4' C A 23 OK OK 716 731 713 715 745 C4' A A 24 OK OK 747 764 744 746 778 C4' C A 25 OK OK 780 795 777 779 809 C4' G A 26 OK OK 811 829 808 810 843 C4' U A 27 OK OK 845 860 842 844 873 C4' A A 28 OK OK 875 892 872 874 906 C4' C A 29 OK OK 908 923 905 907 937 C4' G A 30 OK OK 939 957 936 938 971 C4' G A 31 OK OK 973 991 970 972 1005 C4' A A 32 OK OK 1007 1024 1004 1006 1038 C4' U A 33 OK OK 1040 1055 1037 1039 1068 C4' C A 34 OK OK 1070 1085 1067 1069 1099 C4' U A 35 OK OK 1101 1116 1098 1100 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 103 123 124 105 138 C5' C A 5 OK OK 137 154 155 139 169 C5' C A 6 OK OK 168 185 186 170 200 C5' G A 7 OK OK 199 219 220 201 234 C5' U A 8 OK OK 233 250 251 235 264 C5' A A 9 OK OK 263 282 283 265 297 C5' U A 10 OK OK 296 313 314 298 327 C5' G A 11 OK OK 326 346 347 328 361 C5' C A 12 OK OK 360 377 378 362 392 C5' G A 13 OK OK 391 411 412 393 426 C5' G A 14 OK OK 425 445 446 427 460 C5' U A 15 OK OK 459 476 477 461 490 C5' A A 16 OK OK 489 508 509 491 523 C5' G A 17 OK OK 522 542 543 524 557 C5' U A 18 OK OK 556 573 574 558 587 C5' U A 19 OK OK 586 603 604 588 617 C5' C A 20 OK OK 616 633 634 618 648 C5' C A 21 OK OK 647 664 665 649 679 C5' G A 22 OK OK 678 698 699 680 713 C5' C A 23 OK OK 712 729 730 714 744 C5' A A 24 OK OK 743 762 763 745 777 C5' C A 25 OK OK 776 793 794 778 808 C5' G A 26 OK OK 807 827 828 809 842 C5' U A 27 OK OK 841 858 859 843 872 C5' A A 28 OK OK 871 890 891 873 905 C5' C A 29 OK OK 904 921 922 906 936 C5' G A 30 OK OK 935 955 956 937 970 C5' G A 31 OK OK 969 989 990 971 1004 C5' A A 32 OK OK 1003 1022 1023 1005 1037 C5' U A 33 OK OK 1036 1053 1054 1038 1067 C5' C A 34 OK OK 1066 1083 1084 1068 1098 C5' U A 35 OK OK 1097 1114 1115 1099 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 101 102 103 134 P C A 5 distorted distorted 108 135 136 137 165 P C A 6 distorted distorted 142 166 167 168 196 P G A 7 distorted distorted 173 197 198 199 230 P U A 8 distorted distorted 204 231 232 233 260 P A A 9 distorted distorted 238 261 262 263 293 P U A 10 distorted distorted 268 294 295 296 323 P G A 11 distorted distorted 301 324 325 326 357 P C A 12 distorted distorted 331 358 359 360 388 P G A 13 distorted distorted 365 389 390 391 422 P G A 14 distorted distorted 396 423 424 425 456 P U A 15 distorted distorted 430 457 458 459 486 P A A 16 distorted distorted 464 487 488 489 519 P G A 17 distorted distorted 494 520 521 522 553 P U A 18 distorted distorted 527 554 555 556 583 P U A 19 distorted distorted 561 584 585 586 613 P C A 20 distorted distorted 591 614 615 616 644 P C A 21 distorted distorted 621 645 646 647 675 P G A 22 distorted distorted 652 676 677 678 709 P C A 23 distorted distorted 683 710 711 712 740 P A A 24 distorted distorted 717 741 742 743 773 P C A 25 distorted distorted 748 774 775 776 804 P G A 26 distorted distorted 781 805 806 807 838 P U A 27 distorted distorted 812 839 840 841 868 P A A 28 distorted distorted 846 869 870 871 901 P C A 29 distorted distorted 876 902 903 904 932 P G A 30 distorted distorted 909 933 934 935 966 P G A 31 distorted distorted 940 967 968 969 1000 P A A 32 distorted distorted 974 1001 1002 1003 1033 P U A 33 distorted distorted 1008 1034 1035 1036 1063 P C A 34 distorted distorted 1041 1064 1065 1066 1094 P U A 35 distorted distorted 1071 1095 1096 1097 ---------------------------------------------------------------------------------