ID code: '1P66' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 beta 7 13 10 35 C1' A A 2 beta 30 36 33 57 C1' G A 3 beta 52 58 55 80 C1' U A 4 beta 75 81 78 100 C1' C A 5 beta 95 101 98 120 C1' A A 6 beta 115 121 118 142 C1' C A 7 beta 137 143 140 162 C1' C A 8 beta 157 163 160 182 C1' A A 9 beta 177 183 180 204 C1' C A 10 beta 199 205 202 224 C1' A A 11 beta 219 225 222 246 C1' U A 12 beta 241 247 244 266 C1' G A 13 beta 261 267 264 289 C1' U A 14 beta 284 290 287 309 C1' G A 15 beta 304 310 307 332 C1' C A 16 beta 327 333 330 352 C1' U A 17 beta 347 353 350 372 C1' U A 18 beta 367 373 370 392 C1' U A 19 beta 387 393 390 412 C1' G A 20 beta 407 413 410 435 C1' U A 21 beta 430 436 433 455 C1' G A 22 beta 450 456 453 478 C1' G A 23 beta 473 479 476 501 C1' U A 24 beta 496 502 499 521 C1' C A 25 beta 516 522 519 541 C1' U A 26 beta 536 542 539 561 C1' G A 27 beta 556 562 559 584 C1' A A 28 beta 579 585 582 606 C1' U A 29 beta 601 607 604 626 C1' G A 30 beta 621 627 624 649 C1' A A 31 beta 644 650 647 671 C1' G A 32 beta 666 672 669 694 C1' G A 33 beta 689 695 692 717 C1' C A 34 beta 712 718 715 737 C1' C A 35 beta 732 738 735 757 C1' G A 36 beta 752 758 755 780 C1' U A 37 beta 775 781 778 800 C1' G A 38 beta 795 801 798 823 C1' A A 39 beta 818 824 821 845 C1' G A 40 beta 840 846 843 868 C1' G A 41 beta 863 869 866 891 C1' C A 42 beta 886 892 889 911 C1' C A 43 beta 906 912 909 931 C1' G A 44 beta 926 932 929 954 C1' A A 45 beta 949 955 952 976 C1' A A 46 beta 971 977 974 998 C1' A A 47 beta 993 999 996 1020 C1' C A 48 beta 1015 1021 1018 1040 C1' U A 49 beta 1035 1041 1038 1060 C1' C A 50 beta 1055 1061 1058 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK 12 8 11 33 C2' A A 2 OK 35 31 34 55 C2' G A 3 OK 57 53 56 78 C2' U A 4 OK 80 76 79 98 C2' C A 5 OK 100 96 99 118 C2' A A 6 OK 120 116 119 140 C2' C A 7 OK 142 138 141 160 C2' C A 8 OK 162 158 161 180 C2' A A 9 OK 182 178 181 202 C2' C A 10 OK 204 200 203 222 C2' A A 11 OK 224 220 223 244 C2' U A 12 OK 246 242 245 264 C2' G A 13 OK 266 262 265 287 C2' U A 14 OK 289 285 288 307 C2' G A 15 OK 309 305 308 330 C2' C A 16 OK 332 328 331 350 C2' U A 17 OK 352 348 351 370 C2' U A 18 OK 372 368 371 390 C2' U A 19 OK 392 388 391 410 C2' G A 20 OK 412 408 411 433 C2' U A 21 OK 435 431 434 453 C2' G A 22 OK 455 451 454 476 C2' G A 23 OK 478 474 477 499 C2' U A 24 OK 501 497 500 519 C2' C A 25 OK 521 517 520 539 C2' U A 26 OK 541 537 540 559 C2' G A 27 OK 561 557 560 582 C2' A A 28 OK 584 580 583 604 C2' U A 29 OK 606 602 605 624 C2' G A 30 OK 626 622 625 647 C2' A A 31 OK 649 645 648 669 C2' G A 32 OK 671 667 670 692 C2' G A 33 OK 694 690 693 715 C2' C A 34 OK 717 713 716 735 C2' C A 35 OK 737 733 736 755 C2' G A 36 OK 757 753 756 778 C2' U A 37 OK 780 776 779 798 C2' G A 38 OK 800 796 799 821 C2' A A 39 OK 823 819 822 843 C2' G A 40 OK 845 841 844 866 C2' G A 41 OK 868 864 867 889 C2' C A 42 OK 891 887 890 909 C2' C A 43 OK 911 907 910 929 C2' G A 44 OK 931 927 930 952 C2' A A 45 OK 954 950 953 974 C2' A A 46 OK 976 972 975 996 C2' A A 47 OK 998 994 997 1018 C2' C A 48 OK 1020 1016 1019 1038 C2' U A 49 OK 1040 1036 1039 1058 C2' C A 50 OK 1060 1056 1059 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 31 C3' A A 2 OK 29 32 33 53 C3' G A 3 OK 51 54 55 76 C3' U A 4 OK 74 77 78 96 C3' C A 5 OK 94 97 98 116 C3' A A 6 OK 114 117 118 138 C3' C A 7 OK 136 139 140 158 C3' C A 8 OK 156 159 160 178 C3' A A 9 OK 176 179 180 200 C3' C A 10 OK 198 201 202 220 C3' A A 11 OK 218 221 222 242 C3' U A 12 OK 240 243 244 262 C3' G A 13 OK 260 263 264 285 C3' U A 14 OK 283 286 287 305 C3' G A 15 OK 303 306 307 328 C3' C A 16 OK 326 329 330 348 C3' U A 17 OK 346 349 350 368 C3' U A 18 OK 366 369 370 388 C3' U A 19 OK 386 389 390 408 C3' G A 20 OK 406 409 410 431 C3' U A 21 OK 429 432 433 451 C3' G A 22 OK 449 452 453 474 C3' G A 23 OK 472 475 476 497 C3' U A 24 OK 495 498 499 517 C3' C A 25 OK 515 518 519 537 C3' U A 26 OK 535 538 539 557 C3' G A 27 OK 555 558 559 580 C3' A A 28 OK 578 581 582 602 C3' U A 29 OK 600 603 604 622 C3' G A 30 OK 620 623 624 645 C3' A A 31 OK 643 646 647 667 C3' G A 32 OK 665 668 669 690 C3' G A 33 OK 688 691 692 713 C3' C A 34 OK 711 714 715 733 C3' C A 35 OK 731 734 735 753 C3' G A 36 OK 751 754 755 776 C3' U A 37 OK 774 777 778 796 C3' G A 38 OK 794 797 798 819 C3' A A 39 OK 817 820 821 841 C3' G A 40 OK 839 842 843 864 C3' G A 41 OK 862 865 866 887 C3' C A 42 OK 885 888 889 907 C3' C A 43 OK 905 908 909 927 C3' G A 44 OK 925 928 929 950 C3' A A 45 OK 948 951 952 972 C3' A A 46 OK 970 973 974 994 C3' A A 47 OK 992 995 996 1016 C3' C A 48 OK 1014 1017 1018 1036 C3' U A 49 OK 1034 1037 1038 1056 C3' C A 50 OK 1054 1057 1058 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 29 C4' A A 2 OK 31 28 30 51 C4' G A 3 OK 53 50 52 74 C4' U A 4 OK 76 73 75 94 C4' C A 5 OK 96 93 95 114 C4' A A 6 OK 116 113 115 136 C4' C A 7 OK 138 135 137 156 C4' C A 8 OK 158 155 157 176 C4' A A 9 OK 178 175 177 198 C4' C A 10 OK 200 197 199 218 C4' A A 11 OK 220 217 219 240 C4' U A 12 OK 242 239 241 260 C4' G A 13 OK 262 259 261 283 C4' U A 14 OK 285 282 284 303 C4' G A 15 OK 305 302 304 326 C4' C A 16 OK 328 325 327 346 C4' U A 17 OK 348 345 347 366 C4' U A 18 OK 368 365 367 386 C4' U A 19 OK 388 385 387 406 C4' G A 20 OK 408 405 407 429 C4' U A 21 OK 431 428 430 449 C4' G A 22 OK 451 448 450 472 C4' G A 23 OK 474 471 473 495 C4' U A 24 OK 497 494 496 515 C4' C A 25 OK 517 514 516 535 C4' U A 26 OK 537 534 536 555 C4' G A 27 OK 557 554 556 578 C4' A A 28 OK 580 577 579 600 C4' U A 29 OK 602 599 601 620 C4' G A 30 OK 622 619 621 643 C4' A A 31 OK 645 642 644 665 C4' G A 32 OK 667 664 666 688 C4' G A 33 OK 690 687 689 711 C4' C A 34 OK 713 710 712 731 C4' C A 35 OK 733 730 732 751 C4' G A 36 OK 753 750 752 774 C4' U A 37 OK 776 773 775 794 C4' G A 38 OK 796 793 795 817 C4' A A 39 OK 819 816 818 839 C4' G A 40 OK 841 838 840 862 C4' G A 41 OK 864 861 863 885 C4' C A 42 OK 887 884 886 905 C4' C A 43 OK 907 904 906 925 C4' G A 44 OK 927 924 926 948 C4' A A 45 OK 950 947 949 970 C4' A A 46 OK 972 969 971 992 C4' A A 47 OK 994 991 993 1014 C4' C A 48 OK 1016 1013 1015 1034 C4' U A 49 OK 1036 1033 1035 1054 C4' C A 50 OK 1056 1053 1055 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 28 C5' A A 2 27 29 50 C5' G A 3 49 51 73 C5' U A 4 72 74 93 C5' C A 5 92 94 113 C5' A A 6 112 114 135 C5' C A 7 134 136 155 C5' C A 8 154 156 175 C5' A A 9 174 176 197 C5' C A 10 196 198 217 C5' A A 11 216 218 239 C5' U A 12 238 240 259 C5' G A 13 258 260 282 C5' U A 14 281 283 302 C5' G A 15 301 303 325 C5' C A 16 324 326 345 C5' U A 17 344 346 365 C5' U A 18 364 366 385 C5' U A 19 384 386 405 C5' G A 20 404 406 428 C5' U A 21 427 429 448 C5' G A 22 447 449 471 C5' G A 23 470 472 494 C5' U A 24 493 495 514 C5' C A 25 513 515 534 C5' U A 26 533 535 554 C5' G A 27 553 555 577 C5' A A 28 576 578 599 C5' U A 29 598 600 619 C5' G A 30 618 620 642 C5' A A 31 641 643 664 C5' G A 32 663 665 687 C5' G A 33 686 688 710 C5' C A 34 709 711 730 C5' C A 35 729 731 750 C5' G A 36 749 751 773 C5' U A 37 772 774 793 C5' G A 38 792 794 816 C5' A A 39 815 817 838 C5' G A 40 837 839 861 C5' G A 41 860 862 884 C5' C A 42 883 885 904 C5' C A 43 903 905 924 C5' G A 44 923 925 947 C5' A A 45 946 948 969 C5' A A 46 968 970 991 C5' A A 47 990 992 1013 C5' C A 48 1012 1014 1033 C5' U A 49 1032 1034 1053 C5' C A 50 1052 1054 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 24 P A A 2 distorted distorted 9 25 26 27 46 P G A 3 distorted distorted 32 47 48 49 69 P U A 4 distorted distorted 54 70 71 72 89 P C A 5 distorted distorted 77 90 91 92 109 P A A 6 distorted distorted 97 110 111 112 131 P C A 7 distorted distorted 117 132 133 134 151 P C A 8 distorted distorted 139 152 153 154 171 P A A 9 distorted distorted 159 172 173 174 193 P C A 10 distorted distorted 179 194 195 196 213 P A A 11 distorted distorted 201 214 215 216 235 P U A 12 distorted distorted 221 236 237 238 255 P G A 13 distorted distorted 243 256 257 258 278 P U A 14 distorted distorted 263 279 280 281 298 P G A 15 distorted distorted 286 299 300 301 321 P C A 16 distorted distorted 306 322 323 324 341 P U A 17 distorted distorted 329 342 343 344 361 P U A 18 distorted distorted 349 362 363 364 381 P U A 19 distorted distorted 369 382 383 384 401 P G A 20 distorted distorted 389 402 403 404 424 P U A 21 distorted distorted 409 425 426 427 444 P G A 22 distorted distorted 432 445 446 447 467 P G A 23 distorted distorted 452 468 469 470 490 P U A 24 distorted distorted 475 491 492 493 510 P C A 25 distorted distorted 498 511 512 513 530 P U A 26 distorted distorted 518 531 532 533 550 P G A 27 distorted distorted 538 551 552 553 573 P A A 28 distorted distorted 558 574 575 576 595 P U A 29 distorted distorted 581 596 597 598 615 P G A 30 distorted distorted 603 616 617 618 638 P A A 31 distorted distorted 623 639 640 641 660 P G A 32 distorted distorted 646 661 662 663 683 P G A 33 distorted distorted 668 684 685 686 706 P C A 34 distorted distorted 691 707 708 709 726 P C A 35 distorted distorted 714 727 728 729 746 P G A 36 distorted distorted 734 747 748 749 769 P U A 37 distorted distorted 754 770 771 772 789 P G A 38 distorted distorted 777 790 791 792 812 P A A 39 distorted distorted 797 813 814 815 834 P G A 40 distorted distorted 820 835 836 837 857 P G A 41 distorted distorted 842 858 859 860 880 P C A 42 distorted distorted 865 881 882 883 900 P C A 43 distorted distorted 888 901 902 903 920 P G A 44 distorted distorted 908 921 922 923 943 P A A 45 distorted distorted 928 944 945 946 965 P A A 46 distorted distorted 951 966 967 968 987 P A A 47 distorted distorted 973 988 989 990 1009 P C A 48 distorted distorted 995 1010 1011 1012 1029 P U A 49 distorted distorted 1017 1030 1031 1032 1049 P C A 50 distorted distorted 1037 1050 1051 1052 ---------------------------------------------------------------------------------