ID code: '1I9F' 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' U A 3 alpha beta 73 93 79 76 108 C1' C A 4 alpha beta 103 123 109 106 139 C1' U A 5 alpha beta 134 154 140 137 169 C1' G A 6 alpha beta 164 187 170 167 203 C1' G A 7 alpha beta 198 221 204 201 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' C A 9 alpha beta 266 286 272 269 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' C A 11 alpha beta 331 351 337 334 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' C A 14 alpha beta 429 449 435 432 465 C1' G A 15 alpha beta 460 483 466 463 499 C1' C A 16 alpha beta 494 514 500 497 530 C1' A A 17 alpha beta 525 547 531 528 563 C1' A A 18 alpha beta 558 580 564 561 596 C1' G A 19 alpha beta 591 614 597 594 630 C1' C A 20 alpha beta 625 645 631 628 661 C1' U A 21 alpha beta 656 676 662 659 691 C1' G A 22 alpha beta 686 709 692 689 725 C1' A A 23 alpha beta 720 742 726 723 758 C1' C A 24 alpha beta 753 773 759 756 789 C1' G A 25 alpha beta 784 807 790 787 823 C1' G A 26 alpha beta 818 841 824 821 857 C1' U A 27 alpha beta 852 872 858 855 887 C1' A A 28 alpha beta 882 904 888 885 920 C1' C A 29 alpha beta 915 935 921 918 951 C1' A A 30 alpha beta 946 968 952 949 984 C1' G A 31 alpha beta 979 1002 985 982 1018 C1' G A 32 alpha beta 1013 1036 1019 1016 1052 C1' C A 33 alpha beta 1047 1067 1053 1050 1083 C1' C A 34 alpha beta 1078 1099 1084 1081 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' C A 4 OK OK 108 104 121 107 137 C2' U A 5 OK OK 139 135 152 138 167 C2' G A 6 OK OK 169 165 185 168 201 C2' G A 7 OK OK 203 199 219 202 235 C2' G A 8 OK OK 237 233 253 236 269 C2' C A 9 OK OK 271 267 284 270 300 C2' G A 10 OK OK 302 298 318 301 334 C2' C A 11 OK OK 336 332 349 335 365 C2' A A 12 OK OK 367 363 382 366 398 C2' G A 13 OK OK 400 396 416 399 432 C2' C A 14 OK OK 434 430 447 433 463 C2' G A 15 OK OK 465 461 481 464 497 C2' C A 16 OK OK 499 495 512 498 528 C2' A A 17 OK OK 530 526 545 529 561 C2' A A 18 OK OK 563 559 578 562 594 C2' G A 19 OK OK 596 592 612 595 628 C2' C A 20 OK OK 630 626 643 629 659 C2' U A 21 OK OK 661 657 674 660 689 C2' G A 22 OK OK 691 687 707 690 723 C2' A A 23 OK OK 725 721 740 724 756 C2' C A 24 OK OK 758 754 771 757 787 C2' G A 25 OK OK 789 785 805 788 821 C2' G A 26 OK OK 823 819 839 822 855 C2' U A 27 OK OK 857 853 870 856 885 C2' A A 28 OK OK 887 883 902 886 918 C2' C A 29 OK OK 920 916 933 919 949 C2' A A 30 OK OK 951 947 966 950 982 C2' G A 31 OK OK 984 980 1000 983 1016 C2' G A 32 OK OK 1018 1014 1034 1017 1050 C2' C A 33 OK OK 1052 1048 1065 1051 1081 C2' C A 34 OK OK 1083 1079 1097 1082 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' C A 4 OK OK 102 120 105 106 135 C3' U A 5 OK OK 133 151 136 137 165 C3' G A 6 OK OK 163 184 166 167 199 C3' G A 7 OK OK 197 218 200 201 233 C3' G A 8 OK OK 231 252 234 235 267 C3' C A 9 OK OK 265 283 268 269 298 C3' G A 10 OK OK 296 317 299 300 332 C3' C A 11 OK OK 330 348 333 334 363 C3' A A 12 OK OK 361 381 364 365 396 C3' G A 13 OK OK 394 415 397 398 430 C3' C A 14 OK OK 428 446 431 432 461 C3' G A 15 OK OK 459 480 462 463 495 C3' C A 16 OK OK 493 511 496 497 526 C3' A A 17 OK OK 524 544 527 528 559 C3' A A 18 OK OK 557 577 560 561 592 C3' G A 19 OK OK 590 611 593 594 626 C3' C A 20 OK OK 624 642 627 628 657 C3' U A 21 OK OK 655 673 658 659 687 C3' G A 22 OK OK 685 706 688 689 721 C3' A A 23 OK OK 719 739 722 723 754 C3' C A 24 OK OK 752 770 755 756 785 C3' G A 25 OK OK 783 804 786 787 819 C3' G A 26 OK OK 817 838 820 821 853 C3' U A 27 OK OK 851 869 854 855 883 C3' A A 28 OK OK 881 901 884 885 916 C3' C A 29 OK OK 914 932 917 918 947 C3' A A 30 OK OK 945 965 948 949 980 C3' G A 31 OK OK 978 999 981 982 1014 C3' G A 32 OK OK 1012 1033 1015 1016 1048 C3' C A 33 OK OK 1046 1064 1049 1050 1079 C3' C A 34 OK OK 1077 1095 1080 1081 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' C A 4 OK OK 104 119 101 103 133 C4' U A 5 OK OK 135 150 132 134 163 C4' G A 6 OK OK 165 183 162 164 197 C4' G A 7 OK OK 199 217 196 198 231 C4' G A 8 OK OK 233 251 230 232 265 C4' C A 9 OK OK 267 282 264 266 296 C4' G A 10 OK OK 298 316 295 297 330 C4' C A 11 OK OK 332 347 329 331 361 C4' A A 12 OK OK 363 380 360 362 394 C4' G A 13 OK OK 396 414 393 395 428 C4' C A 14 OK OK 430 445 427 429 459 C4' G A 15 OK OK 461 479 458 460 493 C4' C A 16 OK OK 495 510 492 494 524 C4' A A 17 OK OK 526 543 523 525 557 C4' A A 18 OK OK 559 576 556 558 590 C4' G A 19 OK OK 592 610 589 591 624 C4' C A 20 OK OK 626 641 623 625 655 C4' U A 21 OK OK 657 672 654 656 685 C4' G A 22 OK OK 687 705 684 686 719 C4' A A 23 OK OK 721 738 718 720 752 C4' C A 24 OK OK 754 769 751 753 783 C4' G A 25 OK OK 785 803 782 784 817 C4' G A 26 OK OK 819 837 816 818 851 C4' U A 27 OK OK 853 868 850 852 881 C4' A A 28 OK OK 883 900 880 882 914 C4' C A 29 OK OK 916 931 913 915 945 C4' A A 30 OK OK 947 964 944 946 978 C4' G A 31 OK OK 980 998 977 979 1012 C4' G A 32 OK OK 1014 1032 1011 1013 1046 C4' C A 33 OK OK 1048 1063 1045 1047 1077 C4' C A 34 OK OK 1079 1094 1076 1078 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' C A 4 OK OK 100 117 118 102 132 C5' U A 5 OK OK 131 148 149 133 162 C5' G A 6 OK OK 161 181 182 163 196 C5' G A 7 OK OK 195 215 216 197 230 C5' G A 8 OK OK 229 249 250 231 264 C5' C A 9 OK OK 263 280 281 265 295 C5' G A 10 OK OK 294 314 315 296 329 C5' C A 11 OK OK 328 345 346 330 360 C5' A A 12 OK OK 359 378 379 361 393 C5' G A 13 OK OK 392 412 413 394 427 C5' C A 14 OK OK 426 443 444 428 458 C5' G A 15 OK OK 457 477 478 459 492 C5' C A 16 OK OK 491 508 509 493 523 C5' A A 17 OK OK 522 541 542 524 556 C5' A A 18 OK OK 555 574 575 557 589 C5' G A 19 OK OK 588 608 609 590 623 C5' C A 20 OK OK 622 639 640 624 654 C5' U A 21 OK OK 653 670 671 655 684 C5' G A 22 OK OK 683 703 704 685 718 C5' A A 23 OK OK 717 736 737 719 751 C5' C A 24 OK OK 750 767 768 752 782 C5' G A 25 OK OK 781 801 802 783 816 C5' G A 26 OK OK 815 835 836 817 850 C5' U A 27 OK OK 849 866 867 851 880 C5' A A 28 OK OK 879 898 899 881 913 C5' C A 29 OK OK 912 929 930 914 944 C5' A A 30 OK OK 943 962 963 945 977 C5' G A 31 OK OK 976 996 997 978 1011 C5' G A 32 OK OK 1010 1030 1031 1012 1045 C5' C A 33 OK OK 1044 1061 1062 1046 1076 C5' C A 34 OK OK 1075 1092 1093 1077 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P C A 4 distorted distorted 75 98 99 100 128 P U A 5 distorted distorted 105 129 130 131 158 P G A 6 distorted distorted 136 159 160 161 192 P G A 7 distorted distorted 166 193 194 195 226 P G A 8 distorted distorted 200 227 228 229 260 P C A 9 distorted distorted 234 261 262 263 291 P G A 10 distorted distorted 268 292 293 294 325 P C A 11 distorted distorted 299 326 327 328 356 P A A 12 distorted distorted 333 357 358 359 389 P G A 13 distorted distorted 364 390 391 392 423 P C A 14 distorted distorted 397 424 425 426 454 P G A 15 distorted distorted 431 455 456 457 488 P C A 16 distorted distorted 462 489 490 491 519 P A A 17 distorted distorted 496 520 521 522 552 P A A 18 distorted distorted 527 553 554 555 585 P G A 19 distorted distorted 560 586 587 588 619 P C A 20 distorted distorted 593 620 621 622 650 P U A 21 distorted distorted 627 651 652 653 680 P G A 22 distorted distorted 658 681 682 683 714 P A A 23 distorted distorted 688 715 716 717 747 P C A 24 distorted distorted 722 748 749 750 778 P G A 25 distorted distorted 755 779 780 781 812 P G A 26 distorted distorted 786 813 814 815 846 P U A 27 distorted distorted 820 847 848 849 876 P A A 28 distorted distorted 854 877 878 879 909 P C A 29 distorted distorted 884 910 911 912 940 P A A 30 distorted distorted 917 941 942 943 973 P G A 31 distorted distorted 948 974 975 976 1007 P G A 32 distorted distorted 981 1008 1009 1010 1041 P C A 33 distorted distorted 1015 1042 1043 1044 1072 P C A 34 distorted distorted 1049 1073 1074 1075 ---------------------------------------------------------------------------------