ID code: '2EUY' 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' C A 4 alpha beta 104 124 110 107 140 C1' U A 5 alpha beta 135 155 141 138 170 C1' U A 6 alpha beta 165 185 171 168 200 C1' A A 7 alpha beta 195 217 201 198 233 C1' G A 8 alpha beta 228 251 234 231 267 C1' G A 9 alpha beta 262 285 268 265 301 C1' A A 10 alpha beta 296 318 302 299 334 C1' A A 11 alpha beta 329 351 335 332 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' C A 13 alpha beta 395 415 401 398 431 C1' A A 14 alpha beta 426 448 432 429 464 C1' G A 15 alpha beta 459 482 465 462 498 C1' U A 16 alpha beta 493 513 499 496 528 C1' U A 17 alpha beta 523 543 529 526 558 C1' C A 18 alpha beta 553 573 559 556 589 C1' G A 19 alpha beta 584 607 590 587 623 C1' C A 20 alpha beta 618 638 624 621 654 C1' U A 21 alpha beta 649 669 655 652 684 C1' G A 22 alpha beta 679 702 685 682 718 C1' U A 23 alpha beta 713 733 719 716 748 C1' G A 24 alpha beta 743 766 749 746 782 C1' C A 25 alpha beta 777 797 783 780 813 C1' C A 26 alpha beta 808 828 814 811 844 C1' G A 27 alpha beta 839 862 845 842 878 C1' A A 28 alpha beta 873 895 879 876 911 C1' A A 29 alpha beta 906 928 912 909 944 C1' A A 30 alpha beta 939 961 945 942 977 C1' G A 31 alpha beta 972 995 978 975 1011 C1' G A 32 alpha beta 1006 1029 1012 1009 1045 C1' U A 33 alpha beta 1040 1060 1046 1043 1075 C1' C A 34 alpha beta 1070 1091 1076 1073 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 4 OK OK 109 105 122 108 138 C2' U A 5 OK OK 140 136 153 139 168 C2' U A 6 OK OK 170 166 183 169 198 C2' A A 7 OK OK 200 196 215 199 231 C2' G A 8 OK OK 233 229 249 232 265 C2' G A 9 OK OK 267 263 283 266 299 C2' A A 10 OK OK 301 297 316 300 332 C2' A A 11 OK OK 334 330 349 333 365 C2' A A 12 OK OK 367 363 382 366 398 C2' C A 13 OK OK 400 396 413 399 429 C2' A A 14 OK OK 431 427 446 430 462 C2' G A 15 OK OK 464 460 480 463 496 C2' U A 16 OK OK 498 494 511 497 526 C2' U A 17 OK OK 528 524 541 527 556 C2' C A 18 OK OK 558 554 571 557 587 C2' G A 19 OK OK 589 585 605 588 621 C2' C A 20 OK OK 623 619 636 622 652 C2' U A 21 OK OK 654 650 667 653 682 C2' G A 22 OK OK 684 680 700 683 716 C2' U A 23 OK OK 718 714 731 717 746 C2' G A 24 OK OK 748 744 764 747 780 C2' C A 25 OK OK 782 778 795 781 811 C2' C A 26 OK OK 813 809 826 812 842 C2' G A 27 OK OK 844 840 860 843 876 C2' A A 28 OK OK 878 874 893 877 909 C2' A A 29 OK OK 911 907 926 910 942 C2' A A 30 OK OK 944 940 959 943 975 C2' G A 31 OK OK 977 973 993 976 1009 C2' G A 32 OK OK 1011 1007 1027 1010 1043 C2' U A 33 OK OK 1045 1041 1058 1044 1073 C2' C A 34 OK OK 1075 1071 1089 1074 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 103 121 106 107 136 C3' U A 5 OK OK 134 152 137 138 166 C3' U A 6 OK OK 164 182 167 168 196 C3' A A 7 OK OK 194 214 197 198 229 C3' G A 8 OK OK 227 248 230 231 263 C3' G A 9 OK OK 261 282 264 265 297 C3' A A 10 OK OK 295 315 298 299 330 C3' A A 11 OK OK 328 348 331 332 363 C3' A A 12 OK OK 361 381 364 365 396 C3' C A 13 OK OK 394 412 397 398 427 C3' A A 14 OK OK 425 445 428 429 460 C3' G A 15 OK OK 458 479 461 462 494 C3' U A 16 OK OK 492 510 495 496 524 C3' U A 17 OK OK 522 540 525 526 554 C3' C A 18 OK OK 552 570 555 556 585 C3' G A 19 OK OK 583 604 586 587 619 C3' C A 20 OK OK 617 635 620 621 650 C3' U A 21 OK OK 648 666 651 652 680 C3' G A 22 OK OK 678 699 681 682 714 C3' U A 23 OK OK 712 730 715 716 744 C3' G A 24 OK OK 742 763 745 746 778 C3' C A 25 OK OK 776 794 779 780 809 C3' C A 26 OK OK 807 825 810 811 840 C3' G A 27 OK OK 838 859 841 842 874 C3' A A 28 OK OK 872 892 875 876 907 C3' A A 29 OK OK 905 925 908 909 940 C3' A A 30 OK OK 938 958 941 942 973 C3' G A 31 OK OK 971 992 974 975 1007 C3' G A 32 OK OK 1005 1026 1008 1009 1041 C3' U A 33 OK OK 1039 1057 1042 1043 1071 C3' C A 34 OK OK 1069 1087 1072 1073 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 105 120 102 104 134 C4' U A 5 OK OK 136 151 133 135 164 C4' U A 6 OK OK 166 181 163 165 194 C4' A A 7 OK OK 196 213 193 195 227 C4' G A 8 OK OK 229 247 226 228 261 C4' G A 9 OK OK 263 281 260 262 295 C4' A A 10 OK OK 297 314 294 296 328 C4' A A 11 OK OK 330 347 327 329 361 C4' A A 12 OK OK 363 380 360 362 394 C4' C A 13 OK OK 396 411 393 395 425 C4' A A 14 OK OK 427 444 424 426 458 C4' G A 15 OK OK 460 478 457 459 492 C4' U A 16 OK OK 494 509 491 493 522 C4' U A 17 OK OK 524 539 521 523 552 C4' C A 18 OK OK 554 569 551 553 583 C4' G A 19 OK OK 585 603 582 584 617 C4' C A 20 OK OK 619 634 616 618 648 C4' U A 21 OK OK 650 665 647 649 678 C4' G A 22 OK OK 680 698 677 679 712 C4' U A 23 OK OK 714 729 711 713 742 C4' G A 24 OK OK 744 762 741 743 776 C4' C A 25 OK OK 778 793 775 777 807 C4' C A 26 OK OK 809 824 806 808 838 C4' G A 27 OK OK 840 858 837 839 872 C4' A A 28 OK OK 874 891 871 873 905 C4' A A 29 OK OK 907 924 904 906 938 C4' A A 30 OK OK 940 957 937 939 971 C4' G A 31 OK OK 973 991 970 972 1005 C4' G A 32 OK OK 1007 1025 1004 1006 1039 C4' U A 33 OK OK 1041 1056 1038 1040 1069 C4' C A 34 OK OK 1071 1086 1068 1070 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 101 118 119 103 133 C5' U A 5 OK OK 132 149 150 134 163 C5' U A 6 OK OK 162 179 180 164 193 C5' A A 7 OK OK 192 211 212 194 226 C5' G A 8 OK OK 225 245 246 227 260 C5' G A 9 OK OK 259 279 280 261 294 C5' A A 10 OK OK 293 312 313 295 327 C5' A A 11 OK OK 326 345 346 328 360 C5' A A 12 OK OK 359 378 379 361 393 C5' C A 13 OK OK 392 409 410 394 424 C5' A A 14 OK OK 423 442 443 425 457 C5' G A 15 OK OK 456 476 477 458 491 C5' U A 16 OK OK 490 507 508 492 521 C5' U A 17 OK OK 520 537 538 522 551 C5' C A 18 OK OK 550 567 568 552 582 C5' G A 19 OK OK 581 601 602 583 616 C5' C A 20 OK OK 615 632 633 617 647 C5' U A 21 OK OK 646 663 664 648 677 C5' G A 22 OK OK 676 696 697 678 711 C5' U A 23 OK OK 710 727 728 712 741 C5' G A 24 OK OK 740 760 761 742 775 C5' C A 25 OK OK 774 791 792 776 806 C5' C A 26 OK OK 805 822 823 807 837 C5' G A 27 OK OK 836 856 857 838 871 C5' A A 28 OK OK 870 889 890 872 904 C5' A A 29 OK OK 903 922 923 905 937 C5' A A 30 OK OK 936 955 956 938 970 C5' G A 31 OK OK 969 989 990 971 1004 C5' G A 32 OK OK 1003 1023 1024 1005 1038 C5' U A 33 OK OK 1037 1054 1055 1039 1068 C5' C A 34 OK OK 1067 1084 1085 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C A 4 distorted distorted 75 99 100 101 129 P U A 5 distorted distorted 106 130 131 132 159 P U A 6 distorted distorted 137 160 161 162 189 P A A 7 distorted distorted 167 190 191 192 222 P G A 8 distorted distorted 197 223 224 225 256 P G A 9 distorted distorted 230 257 258 259 290 P A A 10 distorted distorted 264 291 292 293 323 P A A 11 distorted distorted 298 324 325 326 356 P A A 12 distorted distorted 331 357 358 359 389 P C A 13 distorted distorted 364 390 391 392 420 P A A 14 distorted distorted 397 421 422 423 453 P G A 15 distorted distorted 428 454 455 456 487 P U A 16 distorted distorted 461 488 489 490 517 P U A 17 distorted distorted 495 518 519 520 547 P C A 18 distorted distorted 525 548 549 550 578 P G A 19 distorted distorted 555 579 580 581 612 P C A 20 distorted distorted 586 613 614 615 643 P U A 21 distorted distorted 620 644 645 646 673 P G A 22 distorted distorted 651 674 675 676 707 P U A 23 distorted distorted 681 708 709 710 737 P G A 24 distorted distorted 715 738 739 740 771 P C A 25 distorted distorted 745 772 773 774 802 P C A 26 distorted distorted 779 803 804 805 833 P G A 27 distorted distorted 810 834 835 836 867 P A A 28 distorted distorted 841 868 869 870 900 P A A 29 distorted distorted 875 901 902 903 933 P A A 30 distorted distorted 908 934 935 936 966 P G A 31 distorted distorted 941 967 968 969 1000 P G A 32 distorted distorted 974 1001 1002 1003 1034 P U A 33 distorted distorted 1008 1035 1036 1037 1064 P C A 34 distorted distorted 1042 1065 1066 1067 ---------------------------------------------------------------------------------