ID code: '2LPT' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' C A 11 alpha beta 330 350 336 333 366 C1' G A 12 alpha beta 361 384 367 364 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' U A 14 alpha beta 428 448 434 431 463 C1' G A 15 alpha beta 458 481 464 461 497 C1' A A 16 alpha beta 492 514 498 495 530 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' U A 20 alpha beta 625 645 631 628 660 C1' C A 21 alpha beta 655 675 661 658 691 C1' G A 22 alpha beta 686 709 692 689 725 C1' C A 23 alpha beta 720 740 726 723 756 C1' A A 24 alpha beta 751 773 757 754 789 C1' A A 25 alpha beta 784 806 790 787 822 C1' G A 26 alpha beta 817 840 823 820 856 C1' C A 27 alpha beta 851 871 857 854 887 C1' A A 28 alpha beta 882 904 888 885 920 C1' C A 29 alpha beta 915 935 921 918 951 C1' G A 30 alpha beta 946 969 952 949 985 C1' G A 31 alpha beta 980 1003 986 983 1019 C1' U A 32 alpha beta 1014 1034 1020 1017 1049 C1' U A 33 alpha beta 1044 1064 1050 1047 1079 C1' C A 34 alpha beta 1074 1095 1080 1077 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' C A 4 OK OK 111 107 124 110 140 C2' C A 5 OK OK 142 138 155 141 171 C2' G A 6 OK OK 173 169 189 172 205 C2' U A 7 OK OK 207 203 220 206 235 C2' G A 8 OK OK 237 233 253 236 269 C2' U A 9 OK OK 271 267 284 270 299 C2' G A 10 OK OK 301 297 317 300 333 C2' C A 11 OK OK 335 331 348 334 364 C2' G A 12 OK OK 366 362 382 365 398 C2' A A 13 OK OK 400 396 415 399 431 C2' U A 14 OK OK 433 429 446 432 461 C2' G A 15 OK OK 463 459 479 462 495 C2' A A 16 OK OK 497 493 512 496 528 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' U A 20 OK OK 630 626 643 629 658 C2' C A 21 OK OK 660 656 673 659 689 C2' G A 22 OK OK 691 687 707 690 723 C2' C A 23 OK OK 725 721 738 724 754 C2' A A 24 OK OK 756 752 771 755 787 C2' A A 25 OK OK 789 785 804 788 820 C2' G A 26 OK OK 822 818 838 821 854 C2' C A 27 OK OK 856 852 869 855 885 C2' A A 28 OK OK 887 883 902 886 918 C2' C A 29 OK OK 920 916 933 919 949 C2' G A 30 OK OK 951 947 967 950 983 C2' G A 31 OK OK 985 981 1001 984 1017 C2' U A 32 OK OK 1019 1015 1032 1018 1047 C2' U A 33 OK OK 1049 1045 1062 1048 1077 C2' C A 34 OK OK 1079 1075 1093 1078 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' C A 4 OK OK 105 123 108 109 138 C3' C A 5 OK OK 136 154 139 140 169 C3' G A 6 OK OK 167 188 170 171 203 C3' U A 7 OK OK 201 219 204 205 233 C3' G A 8 OK OK 231 252 234 235 267 C3' U A 9 OK OK 265 283 268 269 297 C3' G A 10 OK OK 295 316 298 299 331 C3' C A 11 OK OK 329 347 332 333 362 C3' G A 12 OK OK 360 381 363 364 396 C3' A A 13 OK OK 394 414 397 398 429 C3' U A 14 OK OK 427 445 430 431 459 C3' G A 15 OK OK 457 478 460 461 493 C3' A A 16 OK OK 491 511 494 495 526 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' U A 20 OK OK 624 642 627 628 656 C3' C A 21 OK OK 654 672 657 658 687 C3' G A 22 OK OK 685 706 688 689 721 C3' C A 23 OK OK 719 737 722 723 752 C3' A A 24 OK OK 750 770 753 754 785 C3' A A 25 OK OK 783 803 786 787 818 C3' G A 26 OK OK 816 837 819 820 852 C3' C A 27 OK OK 850 868 853 854 883 C3' A A 28 OK OK 881 901 884 885 916 C3' C A 29 OK OK 914 932 917 918 947 C3' G A 30 OK OK 945 966 948 949 981 C3' G A 31 OK OK 979 1000 982 983 1015 C3' U A 32 OK OK 1013 1031 1016 1017 1045 C3' U A 33 OK OK 1043 1061 1046 1047 1075 C3' C A 34 OK OK 1073 1091 1076 1077 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' C A 4 OK OK 107 122 104 106 136 C4' C A 5 OK OK 138 153 135 137 167 C4' G A 6 OK OK 169 187 166 168 201 C4' U A 7 OK OK 203 218 200 202 231 C4' G A 8 OK OK 233 251 230 232 265 C4' U A 9 OK OK 267 282 264 266 295 C4' G A 10 OK OK 297 315 294 296 329 C4' C A 11 OK OK 331 346 328 330 360 C4' G A 12 OK OK 362 380 359 361 394 C4' A A 13 OK OK 396 413 393 395 427 C4' U A 14 OK OK 429 444 426 428 457 C4' G A 15 OK OK 459 477 456 458 491 C4' A A 16 OK OK 493 510 490 492 524 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' U A 20 OK OK 626 641 623 625 654 C4' C A 21 OK OK 656 671 653 655 685 C4' G A 22 OK OK 687 705 684 686 719 C4' C A 23 OK OK 721 736 718 720 750 C4' A A 24 OK OK 752 769 749 751 783 C4' A A 25 OK OK 785 802 782 784 816 C4' G A 26 OK OK 818 836 815 817 850 C4' C A 27 OK OK 852 867 849 851 881 C4' A A 28 OK OK 883 900 880 882 914 C4' C A 29 OK OK 916 931 913 915 945 C4' G A 30 OK OK 947 965 944 946 979 C4' G A 31 OK OK 981 999 978 980 1013 C4' U A 32 OK OK 1015 1030 1012 1014 1043 C4' U A 33 OK OK 1045 1060 1042 1044 1073 C4' C A 34 OK OK 1075 1090 1072 1074 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' C A 4 OK OK 103 120 121 105 135 C5' C A 5 OK OK 134 151 152 136 166 C5' G A 6 OK OK 165 185 186 167 200 C5' U A 7 OK OK 199 216 217 201 230 C5' G A 8 OK OK 229 249 250 231 264 C5' U A 9 OK OK 263 280 281 265 294 C5' G A 10 OK OK 293 313 314 295 328 C5' C A 11 OK OK 327 344 345 329 359 C5' G A 12 OK OK 358 378 379 360 393 C5' A A 13 OK OK 392 411 412 394 426 C5' U A 14 OK OK 425 442 443 427 456 C5' G A 15 OK OK 455 475 476 457 490 C5' A A 16 OK OK 489 508 509 491 523 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' U A 20 OK OK 622 639 640 624 653 C5' C A 21 OK OK 652 669 670 654 684 C5' G A 22 OK OK 683 703 704 685 718 C5' C A 23 OK OK 717 734 735 719 749 C5' A A 24 OK OK 748 767 768 750 782 C5' A A 25 OK OK 781 800 801 783 815 C5' G A 26 OK OK 814 834 835 816 849 C5' C A 27 OK OK 848 865 866 850 880 C5' A A 28 OK OK 879 898 899 881 913 C5' C A 29 OK OK 912 929 930 914 944 C5' G A 30 OK OK 943 963 964 945 978 C5' G A 31 OK OK 977 997 998 979 1012 C5' U A 32 OK OK 1011 1028 1029 1013 1042 C5' U A 33 OK OK 1041 1058 1059 1043 1072 C5' C A 34 OK OK 1071 1088 1089 1073 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P C A 4 distorted distorted 74 101 102 103 131 P C A 5 distorted distorted 108 132 133 134 162 P G A 6 distorted distorted 139 163 164 165 196 P U A 7 distorted distorted 170 197 198 199 226 P G A 8 distorted distorted 204 227 228 229 260 P U A 9 distorted distorted 234 261 262 263 290 P G A 10 distorted distorted 268 291 292 293 324 P C A 11 distorted distorted 298 325 326 327 355 P G A 12 distorted distorted 332 356 357 358 389 P A A 13 distorted distorted 363 390 391 392 422 P U A 14 distorted distorted 397 423 424 425 452 P G A 15 distorted distorted 430 453 454 455 486 P A A 16 distorted distorted 460 487 488 489 519 P A A 17 distorted distorted 494 520 521 522 552 P A A 18 distorted distorted 527 553 554 555 585 P G A 19 distorted distorted 560 586 587 588 619 P U A 20 distorted distorted 593 620 621 622 649 P C A 21 distorted distorted 627 650 651 652 680 P G A 22 distorted distorted 657 681 682 683 714 P C A 23 distorted distorted 688 715 716 717 745 P A A 24 distorted distorted 722 746 747 748 778 P A A 25 distorted distorted 753 779 780 781 811 P G A 26 distorted distorted 786 812 813 814 845 P C A 27 distorted distorted 819 846 847 848 876 P A A 28 distorted distorted 853 877 878 879 909 P C A 29 distorted distorted 884 910 911 912 940 P G A 30 distorted distorted 917 941 942 943 974 P G A 31 distorted distorted 948 975 976 977 1008 P U A 32 distorted distorted 982 1009 1010 1011 1038 P U A 33 distorted distorted 1016 1039 1040 1041 1068 P C A 34 distorted distorted 1046 1069 1070 1071 ---------------------------------------------------------------------------------