ID code: '1O15' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' U A 6 alpha beta 171 191 177 174 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' C A 9 alpha beta 265 285 271 268 301 C1' A A 10 alpha beta 296 318 302 299 334 C1' G A 11 alpha beta 329 352 335 332 368 C1' C A 12 alpha beta 363 383 369 366 399 C1' C A 13 alpha beta 394 414 400 397 430 C1' G A 14 alpha beta 425 448 431 428 464 C1' A A 15 alpha beta 459 481 465 462 497 C1' A A 16 alpha beta 492 514 498 495 530 C1' A A 17 alpha beta 525 547 531 528 563 C1' G A 18 alpha beta 558 581 564 561 597 C1' G A 19 alpha beta 592 615 598 595 631 C1' C A 20 alpha beta 626 646 632 629 662 C1' C A 21 alpha beta 657 677 663 660 693 C1' C A 22 alpha beta 688 708 694 691 724 C1' U A 23 alpha beta 719 739 725 722 754 C1' U A 24 alpha beta 749 769 755 752 784 C1' G A 25 alpha beta 779 802 785 782 818 C1' G A 26 alpha beta 813 836 819 816 852 C1' C A 27 alpha beta 847 867 853 850 883 C1' A A 28 alpha beta 878 900 884 881 916 C1' G A 29 alpha beta 911 934 917 914 950 C1' C A 30 alpha beta 945 965 951 948 981 C1' G A 31 alpha beta 976 999 982 979 1015 C1' U A 32 alpha beta 1010 1030 1016 1013 1045 C1' C A 33 alpha beta 1040 1061 1046 1043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 174 C2' U A 6 OK OK 176 172 189 175 204 C2' A A 7 OK OK 206 202 221 205 237 C2' C A 8 OK OK 239 235 252 238 268 C2' C A 9 OK OK 270 266 283 269 299 C2' A A 10 OK OK 301 297 316 300 332 C2' G A 11 OK OK 334 330 350 333 366 C2' C A 12 OK OK 368 364 381 367 397 C2' C A 13 OK OK 399 395 412 398 428 C2' G A 14 OK OK 430 426 446 429 462 C2' A A 15 OK OK 464 460 479 463 495 C2' A A 16 OK OK 497 493 512 496 528 C2' A A 17 OK OK 530 526 545 529 561 C2' G A 18 OK OK 563 559 579 562 595 C2' G A 19 OK OK 597 593 613 596 629 C2' C A 20 OK OK 631 627 644 630 660 C2' C A 21 OK OK 662 658 675 661 691 C2' C A 22 OK OK 693 689 706 692 722 C2' U A 23 OK OK 724 720 737 723 752 C2' U A 24 OK OK 754 750 767 753 782 C2' G A 25 OK OK 784 780 800 783 816 C2' G A 26 OK OK 818 814 834 817 850 C2' C A 27 OK OK 852 848 865 851 881 C2' A A 28 OK OK 883 879 898 882 914 C2' G A 29 OK OK 916 912 932 915 948 C2' C A 30 OK OK 950 946 963 949 979 C2' G A 31 OK OK 981 977 997 980 1013 C2' U A 32 OK OK 1015 1011 1028 1014 1043 C2' C A 33 OK OK 1045 1041 1059 1044 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' U A 6 OK OK 170 188 173 174 202 C3' A A 7 OK OK 200 220 203 204 235 C3' C A 8 OK OK 233 251 236 237 266 C3' C A 9 OK OK 264 282 267 268 297 C3' A A 10 OK OK 295 315 298 299 330 C3' G A 11 OK OK 328 349 331 332 364 C3' C A 12 OK OK 362 380 365 366 395 C3' C A 13 OK OK 393 411 396 397 426 C3' G A 14 OK OK 424 445 427 428 460 C3' A A 15 OK OK 458 478 461 462 493 C3' A A 16 OK OK 491 511 494 495 526 C3' A A 17 OK OK 524 544 527 528 559 C3' G A 18 OK OK 557 578 560 561 593 C3' G A 19 OK OK 591 612 594 595 627 C3' C A 20 OK OK 625 643 628 629 658 C3' C A 21 OK OK 656 674 659 660 689 C3' C A 22 OK OK 687 705 690 691 720 C3' U A 23 OK OK 718 736 721 722 750 C3' U A 24 OK OK 748 766 751 752 780 C3' G A 25 OK OK 778 799 781 782 814 C3' G A 26 OK OK 812 833 815 816 848 C3' C A 27 OK OK 846 864 849 850 879 C3' A A 28 OK OK 877 897 880 881 912 C3' G A 29 OK OK 910 931 913 914 946 C3' C A 30 OK OK 944 962 947 948 977 C3' G A 31 OK OK 975 996 978 979 1011 C3' U A 32 OK OK 1009 1027 1012 1013 1041 C3' C A 33 OK OK 1039 1057 1042 1043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 170 C4' U A 6 OK OK 172 187 169 171 200 C4' A A 7 OK OK 202 219 199 201 233 C4' C A 8 OK OK 235 250 232 234 264 C4' C A 9 OK OK 266 281 263 265 295 C4' A A 10 OK OK 297 314 294 296 328 C4' G A 11 OK OK 330 348 327 329 362 C4' C A 12 OK OK 364 379 361 363 393 C4' C A 13 OK OK 395 410 392 394 424 C4' G A 14 OK OK 426 444 423 425 458 C4' A A 15 OK OK 460 477 457 459 491 C4' A A 16 OK OK 493 510 490 492 524 C4' A A 17 OK OK 526 543 523 525 557 C4' G A 18 OK OK 559 577 556 558 591 C4' G A 19 OK OK 593 611 590 592 625 C4' C A 20 OK OK 627 642 624 626 656 C4' C A 21 OK OK 658 673 655 657 687 C4' C A 22 OK OK 689 704 686 688 718 C4' U A 23 OK OK 720 735 717 719 748 C4' U A 24 OK OK 750 765 747 749 778 C4' G A 25 OK OK 780 798 777 779 812 C4' G A 26 OK OK 814 832 811 813 846 C4' C A 27 OK OK 848 863 845 847 877 C4' A A 28 OK OK 879 896 876 878 910 C4' G A 29 OK OK 912 930 909 911 944 C4' C A 30 OK OK 946 961 943 945 975 C4' G A 31 OK OK 977 995 974 976 1009 C4' U A 32 OK OK 1011 1026 1008 1010 1039 C4' C A 33 OK OK 1041 1056 1038 1040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 169 C5' U A 6 OK OK 168 185 186 170 199 C5' A A 7 OK OK 198 217 218 200 232 C5' C A 8 OK OK 231 248 249 233 263 C5' C A 9 OK OK 262 279 280 264 294 C5' A A 10 OK OK 293 312 313 295 327 C5' G A 11 OK OK 326 346 347 328 361 C5' C A 12 OK OK 360 377 378 362 392 C5' C A 13 OK OK 391 408 409 393 423 C5' G A 14 OK OK 422 442 443 424 457 C5' A A 15 OK OK 456 475 476 458 490 C5' A A 16 OK OK 489 508 509 491 523 C5' A A 17 OK OK 522 541 542 524 556 C5' G A 18 OK OK 555 575 576 557 590 C5' G A 19 OK OK 589 609 610 591 624 C5' C A 20 OK OK 623 640 641 625 655 C5' C A 21 OK OK 654 671 672 656 686 C5' C A 22 OK OK 685 702 703 687 717 C5' U A 23 OK OK 716 733 734 718 747 C5' U A 24 OK OK 746 763 764 748 777 C5' G A 25 OK OK 776 796 797 778 811 C5' G A 26 OK OK 810 830 831 812 845 C5' C A 27 OK OK 844 861 862 846 876 C5' A A 28 OK OK 875 894 895 877 909 C5' G A 29 OK OK 908 928 929 910 943 C5' C A 30 OK OK 942 959 960 944 974 C5' G A 31 OK OK 973 993 994 975 1008 C5' U A 32 OK OK 1007 1024 1025 1009 1038 C5' C A 33 OK OK 1037 1054 1055 1039 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P U A 6 distorted distorted 140 166 167 168 195 P A A 7 distorted distorted 173 196 197 198 228 P C A 8 distorted distorted 203 229 230 231 259 P C A 9 distorted distorted 236 260 261 262 290 P A A 10 distorted distorted 267 291 292 293 323 P G A 11 distorted distorted 298 324 325 326 357 P C A 12 distorted distorted 331 358 359 360 388 P C A 13 distorted distorted 365 389 390 391 419 P G A 14 distorted distorted 396 420 421 422 453 P A A 15 distorted distorted 427 454 455 456 486 P A A 16 distorted distorted 461 487 488 489 519 P A A 17 distorted distorted 494 520 521 522 552 P G A 18 distorted distorted 527 553 554 555 586 P G A 19 distorted distorted 560 587 588 589 620 P C A 20 distorted distorted 594 621 622 623 651 P C A 21 distorted distorted 628 652 653 654 682 P C A 22 distorted distorted 659 683 684 685 713 P U A 23 distorted distorted 690 714 715 716 743 P U A 24 distorted distorted 721 744 745 746 773 P G A 25 distorted distorted 751 774 775 776 807 P G A 26 distorted distorted 781 808 809 810 841 P C A 27 distorted distorted 815 842 843 844 872 P A A 28 distorted distorted 849 873 874 875 905 P G A 29 distorted distorted 880 906 907 908 939 P C A 30 distorted distorted 913 940 941 942 970 P G A 31 distorted distorted 947 971 972 973 1004 P U A 32 distorted distorted 978 1005 1006 1007 1034 P C A 33 distorted distorted 1012 1035 1036 1037 ---------------------------------------------------------------------------------