ID code: '1ETG' 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 41 alpha beta 7 30 13 10 46 C1' G A 42 alpha beta 41 64 47 44 80 C1' U A 43 alpha beta 75 95 81 78 110 C1' C A 44 alpha beta 105 125 111 108 141 C1' U A 45 alpha beta 136 156 142 139 171 C1' G A 46 alpha beta 166 189 172 169 205 C1' G A 47 alpha beta 200 223 206 203 239 C1' G A 48 alpha beta 234 257 240 237 273 C1' C A 49 alpha beta 268 288 274 271 304 C1' G A 50 alpha beta 299 322 305 302 338 C1' C A 51 alpha beta 333 353 339 336 369 C1' A A 52 alpha beta 364 386 370 367 402 C1' G A 53 alpha beta 397 420 403 400 436 C1' C A 54 alpha beta 431 451 437 434 467 C1' G A 55 alpha beta 462 485 468 465 501 C1' C A 56 alpha beta 496 516 502 499 532 C1' A A 57 alpha beta 527 549 533 530 565 C1' A A 58 alpha beta 560 582 566 563 598 C1' G A 64 alpha beta 593 616 599 596 632 C1' C A 65 alpha beta 627 647 633 630 663 C1' U A 66 alpha beta 658 678 664 661 693 C1' G A 67 alpha beta 688 711 694 691 727 C1' A A 68 alpha beta 722 744 728 725 760 C1' C A 69 alpha beta 755 775 761 758 791 C1' G A 70 alpha beta 786 809 792 789 825 C1' G A 71 alpha beta 820 843 826 823 859 C1' U A 72 alpha beta 854 874 860 857 889 C1' A A 73 alpha beta 884 906 890 887 922 C1' C A 74 alpha beta 917 937 923 920 953 C1' A A 75 alpha beta 948 970 954 951 986 C1' G A 76 alpha beta 981 1004 987 984 1020 C1' G A 77 alpha beta 1015 1038 1021 1018 1054 C1' C A 78 alpha beta 1049 1069 1055 1052 1085 C1' C A 79 alpha beta 1080 1100 1086 1083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 41 OK OK 12 8 28 11 44 C2' G A 42 OK OK 46 42 62 45 78 C2' U A 43 OK OK 80 76 93 79 108 C2' C A 44 OK OK 110 106 123 109 139 C2' U A 45 OK OK 141 137 154 140 169 C2' G A 46 OK OK 171 167 187 170 203 C2' G A 47 OK OK 205 201 221 204 237 C2' G A 48 OK OK 239 235 255 238 271 C2' C A 49 OK OK 273 269 286 272 302 C2' G A 50 OK OK 304 300 320 303 336 C2' C A 51 OK OK 338 334 351 337 367 C2' A A 52 OK OK 369 365 384 368 400 C2' G A 53 OK OK 402 398 418 401 434 C2' C A 54 OK OK 436 432 449 435 465 C2' G A 55 OK OK 467 463 483 466 499 C2' C A 56 OK OK 501 497 514 500 530 C2' A A 57 OK OK 532 528 547 531 563 C2' A A 58 OK OK 565 561 580 564 596 C2' G A 64 OK OK 598 594 614 597 630 C2' C A 65 OK OK 632 628 645 631 661 C2' U A 66 OK OK 663 659 676 662 691 C2' G A 67 OK OK 693 689 709 692 725 C2' A A 68 OK OK 727 723 742 726 758 C2' C A 69 OK OK 760 756 773 759 789 C2' G A 70 OK OK 791 787 807 790 823 C2' G A 71 OK OK 825 821 841 824 857 C2' U A 72 OK OK 859 855 872 858 887 C2' A A 73 OK OK 889 885 904 888 920 C2' C A 74 OK OK 922 918 935 921 951 C2' A A 75 OK OK 953 949 968 952 984 C2' G A 76 OK OK 986 982 1002 985 1018 C2' G A 77 OK OK 1020 1016 1036 1019 1052 C2' C A 78 OK OK 1054 1050 1067 1053 1083 C2' C A 79 OK OK 1085 1081 1098 1084 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 41 OK OK 6 27 9 10 42 C3' G A 42 OK OK 40 61 43 44 76 C3' U A 43 OK OK 74 92 77 78 106 C3' C A 44 OK OK 104 122 107 108 137 C3' U A 45 OK OK 135 153 138 139 167 C3' G A 46 OK OK 165 186 168 169 201 C3' G A 47 OK OK 199 220 202 203 235 C3' G A 48 OK OK 233 254 236 237 269 C3' C A 49 OK OK 267 285 270 271 300 C3' G A 50 OK OK 298 319 301 302 334 C3' C A 51 OK OK 332 350 335 336 365 C3' A A 52 OK OK 363 383 366 367 398 C3' G A 53 OK OK 396 417 399 400 432 C3' C A 54 OK OK 430 448 433 434 463 C3' G A 55 OK OK 461 482 464 465 497 C3' C A 56 OK OK 495 513 498 499 528 C3' A A 57 OK OK 526 546 529 530 561 C3' A A 58 OK OK 559 579 562 563 594 C3' G A 64 OK OK 592 613 595 596 628 C3' C A 65 OK OK 626 644 629 630 659 C3' U A 66 OK OK 657 675 660 661 689 C3' G A 67 OK OK 687 708 690 691 723 C3' A A 68 OK OK 721 741 724 725 756 C3' C A 69 OK OK 754 772 757 758 787 C3' G A 70 OK OK 785 806 788 789 821 C3' G A 71 OK OK 819 840 822 823 855 C3' U A 72 OK OK 853 871 856 857 885 C3' A A 73 OK OK 883 903 886 887 918 C3' C A 74 OK OK 916 934 919 920 949 C3' A A 75 OK OK 947 967 950 951 982 C3' G A 76 OK OK 980 1001 983 984 1016 C3' G A 77 OK OK 1014 1035 1017 1018 1050 C3' C A 78 OK OK 1048 1066 1051 1052 1081 C3' C A 79 OK OK 1079 1097 1082 1083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 41 OK OK 8 26 5 7 40 C4' G A 42 OK OK 42 60 39 41 74 C4' U A 43 OK OK 76 91 73 75 104 C4' C A 44 OK OK 106 121 103 105 135 C4' U A 45 OK OK 137 152 134 136 165 C4' G A 46 OK OK 167 185 164 166 199 C4' G A 47 OK OK 201 219 198 200 233 C4' G A 48 OK OK 235 253 232 234 267 C4' C A 49 OK OK 269 284 266 268 298 C4' G A 50 OK OK 300 318 297 299 332 C4' C A 51 OK OK 334 349 331 333 363 C4' A A 52 OK OK 365 382 362 364 396 C4' G A 53 OK OK 398 416 395 397 430 C4' C A 54 OK OK 432 447 429 431 461 C4' G A 55 OK OK 463 481 460 462 495 C4' C A 56 OK OK 497 512 494 496 526 C4' A A 57 OK OK 528 545 525 527 559 C4' A A 58 OK OK 561 578 558 560 592 C4' G A 64 OK OK 594 612 591 593 626 C4' C A 65 OK OK 628 643 625 627 657 C4' U A 66 OK OK 659 674 656 658 687 C4' G A 67 OK OK 689 707 686 688 721 C4' A A 68 OK OK 723 740 720 722 754 C4' C A 69 OK OK 756 771 753 755 785 C4' G A 70 OK OK 787 805 784 786 819 C4' G A 71 OK OK 821 839 818 820 853 C4' U A 72 OK OK 855 870 852 854 883 C4' A A 73 OK OK 885 902 882 884 916 C4' C A 74 OK OK 918 933 915 917 947 C4' A A 75 OK OK 949 966 946 948 980 C4' G A 76 OK OK 982 1000 979 981 1014 C4' G A 77 OK OK 1016 1034 1013 1015 1048 C4' C A 78 OK OK 1050 1065 1047 1049 1079 C4' C A 79 OK OK 1081 1096 1078 1080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 41 OK OK 4 24 25 6 39 C5' G A 42 OK OK 38 58 59 40 73 C5' U A 43 OK OK 72 89 90 74 103 C5' C A 44 OK OK 102 119 120 104 134 C5' U A 45 OK OK 133 150 151 135 164 C5' G A 46 OK OK 163 183 184 165 198 C5' G A 47 OK OK 197 217 218 199 232 C5' G A 48 OK OK 231 251 252 233 266 C5' C A 49 OK OK 265 282 283 267 297 C5' G A 50 OK OK 296 316 317 298 331 C5' C A 51 OK OK 330 347 348 332 362 C5' A A 52 OK OK 361 380 381 363 395 C5' G A 53 OK OK 394 414 415 396 429 C5' C A 54 OK OK 428 445 446 430 460 C5' G A 55 OK OK 459 479 480 461 494 C5' C A 56 OK OK 493 510 511 495 525 C5' A A 57 OK OK 524 543 544 526 558 C5' A A 58 OK OK 557 576 577 559 591 C5' G A 64 OK OK 590 610 611 592 625 C5' C A 65 OK OK 624 641 642 626 656 C5' U A 66 OK OK 655 672 673 657 686 C5' G A 67 OK OK 685 705 706 687 720 C5' A A 68 OK OK 719 738 739 721 753 C5' C A 69 OK OK 752 769 770 754 784 C5' G A 70 OK OK 783 803 804 785 818 C5' G A 71 OK OK 817 837 838 819 852 C5' U A 72 OK OK 851 868 869 853 882 C5' A A 73 OK OK 881 900 901 883 915 C5' C A 74 OK OK 914 931 932 916 946 C5' A A 75 OK OK 945 964 965 947 979 C5' G A 76 OK OK 978 998 999 980 1013 C5' G A 77 OK OK 1012 1032 1033 1014 1047 C5' C A 78 OK OK 1046 1063 1064 1048 1078 C5' C A 79 OK OK 1077 1094 1095 1079 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 41 OK OK 2 3 4 35 P G A 42 distorted distorted 9 36 37 38 69 P U A 43 distorted distorted 43 70 71 72 99 P C A 44 distorted distorted 77 100 101 102 130 P U A 45 distorted distorted 107 131 132 133 160 P G A 46 distorted distorted 138 161 162 163 194 P G A 47 distorted distorted 168 195 196 197 228 P G A 48 distorted distorted 202 229 230 231 262 P C A 49 distorted distorted 236 263 264 265 293 P G A 50 distorted distorted 270 294 295 296 327 P C A 51 distorted distorted 301 328 329 330 358 P A A 52 distorted distorted 335 359 360 361 391 P G A 53 distorted distorted 366 392 393 394 425 P C A 54 distorted distorted 399 426 427 428 456 P G A 55 distorted distorted 433 457 458 459 490 P C A 56 distorted distorted 464 491 492 493 521 P A A 57 distorted distorted 498 522 523 524 554 P A A 58 distorted distorted 529 555 556 557 587 P G A 64 distorted distorted 562 588 589 590 621 P C A 65 distorted distorted 595 622 623 624 652 P U A 66 distorted distorted 629 653 654 655 682 P G A 67 distorted distorted 660 683 684 685 716 P A A 68 distorted distorted 690 717 718 719 749 P C A 69 distorted distorted 724 750 751 752 780 P G A 70 distorted distorted 757 781 782 783 814 P G A 71 distorted distorted 788 815 816 817 848 P U A 72 distorted distorted 822 849 850 851 878 P A A 73 distorted distorted 856 879 880 881 911 P C A 74 distorted distorted 886 912 913 914 942 P A A 75 distorted distorted 919 943 944 945 975 P G A 76 distorted distorted 950 976 977 978 1009 P G A 77 distorted distorted 983 1010 1011 1012 1043 P C A 78 distorted distorted 1017 1044 1045 1046 1074 P C A 79 distorted distorted 1051 1075 1076 1077 ---------------------------------------------------------------------------------