ID code: '1EXY' 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' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' G A 5 alpha beta 138 161 144 141 177 C1' C A 6 alpha beta 172 192 178 175 208 C1' C A 7 alpha beta 203 223 209 206 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' U A 10 alpha beta 302 322 308 305 337 C1' A A 11 alpha beta 332 354 338 335 370 C1' C A 12 alpha beta 365 385 371 368 401 C1' G A 13 alpha beta 396 419 402 399 435 C1' C A 14 alpha beta 430 450 436 433 466 C1' A A 15 alpha beta 461 483 467 464 499 C1' A A 16 alpha beta 494 516 500 497 532 C1' G A 17 alpha beta 527 550 533 530 566 C1' U A 18 alpha beta 561 581 567 564 596 C1' A A 19 alpha beta 591 613 597 594 629 C1' C A 20 alpha beta 624 644 630 627 660 C1' G A 21 alpha beta 655 678 661 658 694 C1' A A 22 alpha beta 689 711 695 692 727 C1' C A 23 alpha beta 722 742 728 725 758 C1' G A 24 alpha beta 753 776 759 756 792 C1' G A 25 alpha beta 787 810 793 790 826 C1' U A 26 alpha beta 821 841 827 824 856 C1' A A 27 alpha beta 851 873 857 854 889 C1' C A 28 alpha beta 884 904 890 887 920 C1' G A 29 alpha beta 915 938 921 918 954 C1' C A 30 alpha beta 949 969 955 952 985 C1' U A 31 alpha beta 980 1000 986 983 1015 C1' C A 32 alpha beta 1010 1030 1016 1013 1046 C1' C A 33 alpha beta 1041 1062 1047 1044 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' G A 5 OK OK 143 139 159 142 175 C2' C A 6 OK OK 177 173 190 176 206 C2' C A 7 OK OK 208 204 221 207 237 C2' G A 8 OK OK 239 235 255 238 271 C2' G A 9 OK OK 273 269 289 272 305 C2' U A 10 OK OK 307 303 320 306 335 C2' A A 11 OK OK 337 333 352 336 368 C2' C A 12 OK OK 370 366 383 369 399 C2' G A 13 OK OK 401 397 417 400 433 C2' C A 14 OK OK 435 431 448 434 464 C2' A A 15 OK OK 466 462 481 465 497 C2' A A 16 OK OK 499 495 514 498 530 C2' G A 17 OK OK 532 528 548 531 564 C2' U A 18 OK OK 566 562 579 565 594 C2' A A 19 OK OK 596 592 611 595 627 C2' C A 20 OK OK 629 625 642 628 658 C2' G A 21 OK OK 660 656 676 659 692 C2' A A 22 OK OK 694 690 709 693 725 C2' C A 23 OK OK 727 723 740 726 756 C2' G A 24 OK OK 758 754 774 757 790 C2' G A 25 OK OK 792 788 808 791 824 C2' U A 26 OK OK 826 822 839 825 854 C2' A A 27 OK OK 856 852 871 855 887 C2' C A 28 OK OK 889 885 902 888 918 C2' G A 29 OK OK 920 916 936 919 952 C2' C A 30 OK OK 954 950 967 953 983 C2' U A 31 OK OK 985 981 998 984 1013 C2' C A 32 OK OK 1015 1011 1028 1014 1044 C2' C A 33 OK OK 1046 1042 1060 1045 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' G A 5 OK OK 137 158 140 141 173 C3' C A 6 OK OK 171 189 174 175 204 C3' C A 7 OK OK 202 220 205 206 235 C3' G A 8 OK OK 233 254 236 237 269 C3' G A 9 OK OK 267 288 270 271 303 C3' U A 10 OK OK 301 319 304 305 333 C3' A A 11 OK OK 331 351 334 335 366 C3' C A 12 OK OK 364 382 367 368 397 C3' G A 13 OK OK 395 416 398 399 431 C3' C A 14 OK OK 429 447 432 433 462 C3' A A 15 OK OK 460 480 463 464 495 C3' A A 16 OK OK 493 513 496 497 528 C3' G A 17 OK OK 526 547 529 530 562 C3' U A 18 OK OK 560 578 563 564 592 C3' A A 19 OK OK 590 610 593 594 625 C3' C A 20 OK OK 623 641 626 627 656 C3' G A 21 OK OK 654 675 657 658 690 C3' A A 22 OK OK 688 708 691 692 723 C3' C A 23 OK OK 721 739 724 725 754 C3' G A 24 OK OK 752 773 755 756 788 C3' G A 25 OK OK 786 807 789 790 822 C3' U A 26 OK OK 820 838 823 824 852 C3' A A 27 OK OK 850 870 853 854 885 C3' C A 28 OK OK 883 901 886 887 916 C3' G A 29 OK OK 914 935 917 918 950 C3' C A 30 OK OK 948 966 951 952 981 C3' U A 31 OK OK 979 997 982 983 1011 C3' C A 32 OK OK 1009 1027 1012 1013 1042 C3' C A 33 OK OK 1040 1058 1043 1044 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' G A 5 OK OK 139 157 136 138 171 C4' C A 6 OK OK 173 188 170 172 202 C4' C A 7 OK OK 204 219 201 203 233 C4' G A 8 OK OK 235 253 232 234 267 C4' G A 9 OK OK 269 287 266 268 301 C4' U A 10 OK OK 303 318 300 302 331 C4' A A 11 OK OK 333 350 330 332 364 C4' C A 12 OK OK 366 381 363 365 395 C4' G A 13 OK OK 397 415 394 396 429 C4' C A 14 OK OK 431 446 428 430 460 C4' A A 15 OK OK 462 479 459 461 493 C4' A A 16 OK OK 495 512 492 494 526 C4' G A 17 OK OK 528 546 525 527 560 C4' U A 18 OK OK 562 577 559 561 590 C4' A A 19 OK OK 592 609 589 591 623 C4' C A 20 OK OK 625 640 622 624 654 C4' G A 21 OK OK 656 674 653 655 688 C4' A A 22 OK OK 690 707 687 689 721 C4' C A 23 OK OK 723 738 720 722 752 C4' G A 24 OK OK 754 772 751 753 786 C4' G A 25 OK OK 788 806 785 787 820 C4' U A 26 OK OK 822 837 819 821 850 C4' A A 27 OK OK 852 869 849 851 883 C4' C A 28 OK OK 885 900 882 884 914 C4' G A 29 OK OK 916 934 913 915 948 C4' C A 30 OK OK 950 965 947 949 979 C4' U A 31 OK OK 981 996 978 980 1009 C4' C A 32 OK OK 1011 1026 1008 1010 1040 C4' C A 33 OK OK 1042 1057 1039 1041 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' G A 5 OK OK 135 155 156 137 170 C5' C A 6 OK OK 169 186 187 171 201 C5' C A 7 OK OK 200 217 218 202 232 C5' G A 8 OK OK 231 251 252 233 266 C5' G A 9 OK OK 265 285 286 267 300 C5' U A 10 OK OK 299 316 317 301 330 C5' A A 11 OK OK 329 348 349 331 363 C5' C A 12 OK OK 362 379 380 364 394 C5' G A 13 OK OK 393 413 414 395 428 C5' C A 14 OK OK 427 444 445 429 459 C5' A A 15 OK OK 458 477 478 460 492 C5' A A 16 OK OK 491 510 511 493 525 C5' G A 17 OK OK 524 544 545 526 559 C5' U A 18 OK OK 558 575 576 560 589 C5' A A 19 OK OK 588 607 608 590 622 C5' C A 20 OK OK 621 638 639 623 653 C5' G A 21 OK OK 652 672 673 654 687 C5' A A 22 OK OK 686 705 706 688 720 C5' C A 23 OK OK 719 736 737 721 751 C5' G A 24 OK OK 750 770 771 752 785 C5' G A 25 OK OK 784 804 805 786 819 C5' U A 26 OK OK 818 835 836 820 849 C5' A A 27 OK OK 848 867 868 850 882 C5' C A 28 OK OK 881 898 899 883 913 C5' G A 29 OK OK 912 932 933 914 947 C5' C A 30 OK OK 946 963 964 948 978 C5' U A 31 OK OK 977 994 995 979 1008 C5' C A 32 OK OK 1007 1024 1025 1009 1039 C5' C A 33 OK OK 1038 1055 1056 1040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P G A 5 distorted distorted 109 133 134 135 166 P C A 6 distorted distorted 140 167 168 169 197 P C A 7 distorted distorted 174 198 199 200 228 P G A 8 distorted distorted 205 229 230 231 262 P G A 9 distorted distorted 236 263 264 265 296 P U A 10 distorted distorted 270 297 298 299 326 P A A 11 distorted distorted 304 327 328 329 359 P C A 12 distorted distorted 334 360 361 362 390 P G A 13 distorted distorted 367 391 392 393 424 P C A 14 distorted distorted 398 425 426 427 455 P A A 15 distorted distorted 432 456 457 458 488 P A A 16 distorted distorted 463 489 490 491 521 P G A 17 distorted distorted 496 522 523 524 555 P U A 18 distorted distorted 529 556 557 558 585 P A A 19 distorted distorted 563 586 587 588 618 P C A 20 distorted distorted 593 619 620 621 649 P G A 21 distorted distorted 626 650 651 652 683 P A A 22 distorted distorted 657 684 685 686 716 P C A 23 distorted distorted 691 717 718 719 747 P G A 24 distorted distorted 724 748 749 750 781 P G A 25 distorted distorted 755 782 783 784 815 P U A 26 distorted distorted 789 816 817 818 845 P A A 27 distorted distorted 823 846 847 848 878 P C A 28 distorted distorted 853 879 880 881 909 P G A 29 distorted distorted 886 910 911 912 943 P C A 30 distorted distorted 917 944 945 946 974 P U A 31 distorted distorted 951 975 976 977 1004 P C A 32 distorted distorted 982 1005 1006 1007 1035 P C A 33 distorted distorted 1012 1036 1037 1038 ---------------------------------------------------------------------------------