ID code: '1P5N' 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 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' A A 4 alpha beta 103 125 109 106 141 C1' G A 5 alpha beta 136 159 142 139 175 C1' A A 6 alpha beta 170 192 176 173 208 C1' A A 7 alpha beta 203 225 209 206 241 C1' A A 8 alpha beta 236 258 242 239 274 C1' G A 9 alpha beta 269 292 275 272 308 C1' C A 10 alpha beta 303 323 309 306 339 C1' G A 11 alpha beta 334 357 340 337 373 C1' U A 12 alpha beta 368 388 374 371 403 C1' C A 13 alpha beta 398 418 404 401 434 C1' U A 14 alpha beta 429 449 435 432 464 C1' A A 15 alpha beta 459 481 465 462 497 C1' G A 16 alpha beta 492 515 498 495 531 C1' C A 17 alpha beta 526 546 532 529 562 C1' C A 18 alpha beta 557 577 563 560 593 C1' A A 19 alpha beta 588 610 594 591 626 C1' U A 20 alpha beta 621 641 627 624 656 C1' G A 21 alpha beta 651 674 657 654 690 C1' G A 22 alpha beta 685 708 691 688 724 C1' C A 23 alpha beta 719 739 725 722 755 C1' G A 24 alpha beta 750 773 756 753 789 C1' U A 25 alpha beta 784 804 790 787 819 C1' U A 26 alpha beta 814 834 820 817 849 C1' A A 27 alpha beta 844 866 850 847 882 C1' G A 28 alpha beta 877 900 883 880 916 C1' U A 29 alpha beta 911 931 917 914 946 C1' A A 30 alpha beta 941 963 947 944 979 C1' U A 31 alpha beta 974 994 980 977 1009 C1' G A 32 alpha beta 1004 1027 1010 1007 1043 C1' C A 33 alpha beta 1038 1058 1044 1041 1074 C1' C A 34 alpha beta 1069 1090 1075 1072 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' G A 2 OK OK 43 39 59 42 75 C2' C A 3 OK OK 77 73 90 76 106 C2' A A 4 OK OK 108 104 123 107 139 C2' G A 5 OK OK 141 137 157 140 173 C2' A A 6 OK OK 175 171 190 174 206 C2' A A 7 OK OK 208 204 223 207 239 C2' A A 8 OK OK 241 237 256 240 272 C2' G A 9 OK OK 274 270 290 273 306 C2' C A 10 OK OK 308 304 321 307 337 C2' G A 11 OK OK 339 335 355 338 371 C2' U A 12 OK OK 373 369 386 372 401 C2' C A 13 OK OK 403 399 416 402 432 C2' U A 14 OK OK 434 430 447 433 462 C2' A A 15 OK OK 464 460 479 463 495 C2' G A 16 OK OK 497 493 513 496 529 C2' C A 17 OK OK 531 527 544 530 560 C2' C A 18 OK OK 562 558 575 561 591 C2' A A 19 OK OK 593 589 608 592 624 C2' U A 20 OK OK 626 622 639 625 654 C2' G A 21 OK OK 656 652 672 655 688 C2' G A 22 OK OK 690 686 706 689 722 C2' C A 23 OK OK 724 720 737 723 753 C2' G A 24 OK OK 755 751 771 754 787 C2' U A 25 OK OK 789 785 802 788 817 C2' U A 26 OK OK 819 815 832 818 847 C2' A A 27 OK OK 849 845 864 848 880 C2' G A 28 OK OK 882 878 898 881 914 C2' U A 29 OK OK 916 912 929 915 944 C2' A A 30 OK OK 946 942 961 945 977 C2' U A 31 OK OK 979 975 992 978 1007 C2' G A 32 OK OK 1009 1005 1025 1008 1041 C2' C A 33 OK OK 1043 1039 1056 1042 1072 C2' C A 34 OK OK 1074 1070 1088 1073 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' C A 3 OK OK 71 89 74 75 104 C3' A A 4 OK OK 102 122 105 106 137 C3' G A 5 OK OK 135 156 138 139 171 C3' A A 6 OK OK 169 189 172 173 204 C3' A A 7 OK OK 202 222 205 206 237 C3' A A 8 OK OK 235 255 238 239 270 C3' G A 9 OK OK 268 289 271 272 304 C3' C A 10 OK OK 302 320 305 306 335 C3' G A 11 OK OK 333 354 336 337 369 C3' U A 12 OK OK 367 385 370 371 399 C3' C A 13 OK OK 397 415 400 401 430 C3' U A 14 OK OK 428 446 431 432 460 C3' A A 15 OK OK 458 478 461 462 493 C3' G A 16 OK OK 491 512 494 495 527 C3' C A 17 OK OK 525 543 528 529 558 C3' C A 18 OK OK 556 574 559 560 589 C3' A A 19 OK OK 587 607 590 591 622 C3' U A 20 OK OK 620 638 623 624 652 C3' G A 21 OK OK 650 671 653 654 686 C3' G A 22 OK OK 684 705 687 688 720 C3' C A 23 OK OK 718 736 721 722 751 C3' G A 24 OK OK 749 770 752 753 785 C3' U A 25 OK OK 783 801 786 787 815 C3' U A 26 OK OK 813 831 816 817 845 C3' A A 27 OK OK 843 863 846 847 878 C3' G A 28 OK OK 876 897 879 880 912 C3' U A 29 OK OK 910 928 913 914 942 C3' A A 30 OK OK 940 960 943 944 975 C3' U A 31 OK OK 973 991 976 977 1005 C3' G A 32 OK OK 1003 1024 1006 1007 1039 C3' C A 33 OK OK 1037 1055 1040 1041 1070 C3' C A 34 OK OK 1068 1086 1071 1072 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' C A 3 OK OK 73 88 70 72 102 C4' A A 4 OK OK 104 121 101 103 135 C4' G A 5 OK OK 137 155 134 136 169 C4' A A 6 OK OK 171 188 168 170 202 C4' A A 7 OK OK 204 221 201 203 235 C4' A A 8 OK OK 237 254 234 236 268 C4' G A 9 OK OK 270 288 267 269 302 C4' C A 10 OK OK 304 319 301 303 333 C4' G A 11 OK OK 335 353 332 334 367 C4' U A 12 OK OK 369 384 366 368 397 C4' C A 13 OK OK 399 414 396 398 428 C4' U A 14 OK OK 430 445 427 429 458 C4' A A 15 OK OK 460 477 457 459 491 C4' G A 16 OK OK 493 511 490 492 525 C4' C A 17 OK OK 527 542 524 526 556 C4' C A 18 OK OK 558 573 555 557 587 C4' A A 19 OK OK 589 606 586 588 620 C4' U A 20 OK OK 622 637 619 621 650 C4' G A 21 OK OK 652 670 649 651 684 C4' G A 22 OK OK 686 704 683 685 718 C4' C A 23 OK OK 720 735 717 719 749 C4' G A 24 OK OK 751 769 748 750 783 C4' U A 25 OK OK 785 800 782 784 813 C4' U A 26 OK OK 815 830 812 814 843 C4' A A 27 OK OK 845 862 842 844 876 C4' G A 28 OK OK 878 896 875 877 910 C4' U A 29 OK OK 912 927 909 911 940 C4' A A 30 OK OK 942 959 939 941 973 C4' U A 31 OK OK 975 990 972 974 1003 C4' G A 32 OK OK 1005 1023 1002 1004 1037 C4' C A 33 OK OK 1039 1054 1036 1038 1068 C4' C A 34 OK OK 1070 1085 1067 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' G A 2 OK OK 35 55 56 37 70 C5' C A 3 OK OK 69 86 87 71 101 C5' A A 4 OK OK 100 119 120 102 134 C5' G A 5 OK OK 133 153 154 135 168 C5' A A 6 OK OK 167 186 187 169 201 C5' A A 7 OK OK 200 219 220 202 234 C5' A A 8 OK OK 233 252 253 235 267 C5' G A 9 OK OK 266 286 287 268 301 C5' C A 10 OK OK 300 317 318 302 332 C5' G A 11 OK OK 331 351 352 333 366 C5' U A 12 OK OK 365 382 383 367 396 C5' C A 13 OK OK 395 412 413 397 427 C5' U A 14 OK OK 426 443 444 428 457 C5' A A 15 OK OK 456 475 476 458 490 C5' G A 16 OK OK 489 509 510 491 524 C5' C A 17 OK OK 523 540 541 525 555 C5' C A 18 OK OK 554 571 572 556 586 C5' A A 19 OK OK 585 604 605 587 619 C5' U A 20 OK OK 618 635 636 620 649 C5' G A 21 OK OK 648 668 669 650 683 C5' G A 22 OK OK 682 702 703 684 717 C5' C A 23 OK OK 716 733 734 718 748 C5' G A 24 OK OK 747 767 768 749 782 C5' U A 25 OK OK 781 798 799 783 812 C5' U A 26 OK OK 811 828 829 813 842 C5' A A 27 OK OK 841 860 861 843 875 C5' G A 28 OK OK 874 894 895 876 909 C5' U A 29 OK OK 908 925 926 910 939 C5' A A 30 OK OK 938 957 958 940 972 C5' U A 31 OK OK 971 988 989 973 1002 C5' G A 32 OK OK 1001 1021 1022 1003 1036 C5' C A 33 OK OK 1035 1052 1053 1037 1067 C5' C A 34 OK OK 1066 1083 1084 1068 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P C A 3 distorted distorted 40 67 68 69 97 P A A 4 distorted distorted 74 98 99 100 130 P G A 5 distorted distorted 105 131 132 133 164 P A A 6 distorted distorted 138 165 166 167 197 P A A 7 distorted distorted 172 198 199 200 230 P A A 8 distorted distorted 205 231 232 233 263 P G A 9 distorted distorted 238 264 265 266 297 P C A 10 distorted distorted 271 298 299 300 328 P G A 11 distorted distorted 305 329 330 331 362 P U A 12 distorted distorted 336 363 364 365 392 P C A 13 distorted distorted 370 393 394 395 423 P U A 14 distorted distorted 400 424 425 426 453 P A A 15 distorted distorted 431 454 455 456 486 P G A 16 distorted distorted 461 487 488 489 520 P C A 17 distorted distorted 494 521 522 523 551 P C A 18 distorted distorted 528 552 553 554 582 P A A 19 distorted distorted 559 583 584 585 615 P U A 20 distorted distorted 590 616 617 618 645 P G A 21 distorted distorted 623 646 647 648 679 P G A 22 distorted distorted 653 680 681 682 713 P C A 23 distorted distorted 687 714 715 716 744 P G A 24 distorted distorted 721 745 746 747 778 P U A 25 distorted distorted 752 779 780 781 808 P U A 26 distorted distorted 786 809 810 811 838 P A A 27 distorted distorted 816 839 840 841 871 P G A 28 distorted distorted 846 872 873 874 905 P U A 29 distorted distorted 879 906 907 908 935 P A A 30 distorted distorted 913 936 937 938 968 P U A 31 distorted distorted 943 969 970 971 998 P G A 32 distorted distorted 976 999 1000 1001 1032 P C A 33 distorted distorted 1006 1033 1034 1035 1063 P C A 34 distorted distorted 1040 1064 1065 1066 ---------------------------------------------------------------------------------