ID code: '2TPK' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 alpha beta 8 31 14 11 48 C1' C A 2 alpha beta 43 63 49 46 79 C1' U A 3 alpha beta 74 94 80 77 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' C A 7 alpha beta 202 222 208 205 238 C1' A A 8 alpha beta 233 255 239 236 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' C A 10 alpha beta 300 320 306 303 336 C1' U A 11 alpha beta 331 351 337 334 366 C1' A A 12 alpha beta 361 383 367 364 399 C1' U A 13 alpha beta 394 414 400 397 429 C1' G A 14 alpha beta 424 447 430 427 463 C1' A A 15 alpha beta 458 480 464 461 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' G A 17 alpha beta 525 548 531 528 564 C1' U A 18 alpha beta 559 579 565 562 594 C1' C A 19 alpha beta 589 609 595 592 625 C1' A A 20 alpha beta 620 642 626 623 658 C1' U A 21 alpha beta 653 673 659 656 688 C1' A A 22 alpha beta 683 705 689 686 721 C1' C A 23 alpha beta 716 736 722 719 752 C1' A A 24 alpha beta 747 769 753 750 785 C1' U A 25 alpha beta 780 800 786 783 815 C1' C A 26 alpha beta 810 830 816 813 846 C1' G A 27 alpha beta 841 864 847 844 880 C1' U A 28 alpha beta 875 895 881 878 910 C1' C A 29 alpha beta 905 925 911 908 941 C1' A A 30 alpha beta 936 958 942 939 974 C1' U A 31 alpha beta 969 989 975 972 1004 C1' A A 32 alpha beta 999 1021 1005 1002 1037 C1' G A 33 alpha beta 1032 1055 1038 1035 1071 C1' C A 34 alpha beta 1066 1086 1072 1069 1102 C1' A A 35 alpha beta 1097 1119 1103 1100 1135 C1' C A 36 alpha beta 1130 1151 1136 1133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' C A 2 OK OK 48 44 61 47 77 C2' U A 3 OK OK 79 75 92 78 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 174 C2' C A 6 OK OK 176 172 189 175 205 C2' C A 7 OK OK 207 203 220 206 236 C2' A A 8 OK OK 238 234 253 237 269 C2' G A 9 OK OK 271 267 287 270 303 C2' C A 10 OK OK 305 301 318 304 334 C2' U A 11 OK OK 336 332 349 335 364 C2' A A 12 OK OK 366 362 381 365 397 C2' U A 13 OK OK 399 395 412 398 427 C2' G A 14 OK OK 429 425 445 428 461 C2' A A 15 OK OK 463 459 478 462 494 C2' G A 16 OK OK 496 492 512 495 528 C2' G A 17 OK OK 530 526 546 529 562 C2' U A 18 OK OK 564 560 577 563 592 C2' C A 19 OK OK 594 590 607 593 623 C2' A A 20 OK OK 625 621 640 624 656 C2' U A 21 OK OK 658 654 671 657 686 C2' A A 22 OK OK 688 684 703 687 719 C2' C A 23 OK OK 721 717 734 720 750 C2' A A 24 OK OK 752 748 767 751 783 C2' U A 25 OK OK 785 781 798 784 813 C2' C A 26 OK OK 815 811 828 814 844 C2' G A 27 OK OK 846 842 862 845 878 C2' U A 28 OK OK 880 876 893 879 908 C2' C A 29 OK OK 910 906 923 909 939 C2' A A 30 OK OK 941 937 956 940 972 C2' U A 31 OK OK 974 970 987 973 1002 C2' A A 32 OK OK 1004 1000 1019 1003 1035 C2' G A 33 OK OK 1037 1033 1053 1036 1069 C2' C A 34 OK OK 1071 1067 1084 1070 1100 C2' A A 35 OK OK 1102 1098 1117 1101 1133 C2' C A 36 OK OK 1135 1131 1149 1134 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' C A 2 OK OK 42 60 45 46 75 C3' U A 3 OK OK 73 91 76 77 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' C A 6 OK OK 170 188 173 174 203 C3' C A 7 OK OK 201 219 204 205 234 C3' A A 8 OK OK 232 252 235 236 267 C3' G A 9 OK OK 265 286 268 269 301 C3' C A 10 OK OK 299 317 302 303 332 C3' U A 11 OK OK 330 348 333 334 362 C3' A A 12 OK OK 360 380 363 364 395 C3' U A 13 OK OK 393 411 396 397 425 C3' G A 14 OK OK 423 444 426 427 459 C3' A A 15 OK OK 457 477 460 461 492 C3' G A 16 OK OK 490 511 493 494 526 C3' G A 17 OK OK 524 545 527 528 560 C3' U A 18 OK OK 558 576 561 562 590 C3' C A 19 OK OK 588 606 591 592 621 C3' A A 20 OK OK 619 639 622 623 654 C3' U A 21 OK OK 652 670 655 656 684 C3' A A 22 OK OK 682 702 685 686 717 C3' C A 23 OK OK 715 733 718 719 748 C3' A A 24 OK OK 746 766 749 750 781 C3' U A 25 OK OK 779 797 782 783 811 C3' C A 26 OK OK 809 827 812 813 842 C3' G A 27 OK OK 840 861 843 844 876 C3' U A 28 OK OK 874 892 877 878 906 C3' C A 29 OK OK 904 922 907 908 937 C3' A A 30 OK OK 935 955 938 939 970 C3' U A 31 OK OK 968 986 971 972 1000 C3' A A 32 OK OK 998 1018 1001 1002 1033 C3' G A 33 OK OK 1031 1052 1034 1035 1067 C3' C A 34 OK OK 1065 1083 1068 1069 1098 C3' A A 35 OK OK 1096 1116 1099 1100 1131 C3' C A 36 OK OK 1129 1147 1132 1133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' C A 2 OK OK 44 59 41 43 73 C4' U A 3 OK OK 75 90 72 74 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 170 C4' C A 6 OK OK 172 187 169 171 201 C4' C A 7 OK OK 203 218 200 202 232 C4' A A 8 OK OK 234 251 231 233 265 C4' G A 9 OK OK 267 285 264 266 299 C4' C A 10 OK OK 301 316 298 300 330 C4' U A 11 OK OK 332 347 329 331 360 C4' A A 12 OK OK 362 379 359 361 393 C4' U A 13 OK OK 395 410 392 394 423 C4' G A 14 OK OK 425 443 422 424 457 C4' A A 15 OK OK 459 476 456 458 490 C4' G A 16 OK OK 492 510 489 491 524 C4' G A 17 OK OK 526 544 523 525 558 C4' U A 18 OK OK 560 575 557 559 588 C4' C A 19 OK OK 590 605 587 589 619 C4' A A 20 OK OK 621 638 618 620 652 C4' U A 21 OK OK 654 669 651 653 682 C4' A A 22 OK OK 684 701 681 683 715 C4' C A 23 OK OK 717 732 714 716 746 C4' A A 24 OK OK 748 765 745 747 779 C4' U A 25 OK OK 781 796 778 780 809 C4' C A 26 OK OK 811 826 808 810 840 C4' G A 27 OK OK 842 860 839 841 874 C4' U A 28 OK OK 876 891 873 875 904 C4' C A 29 OK OK 906 921 903 905 935 C4' A A 30 OK OK 937 954 934 936 968 C4' U A 31 OK OK 970 985 967 969 998 C4' A A 32 OK OK 1000 1017 997 999 1031 C4' G A 33 OK OK 1033 1051 1030 1032 1065 C4' C A 34 OK OK 1067 1082 1064 1066 1096 C4' A A 35 OK OK 1098 1115 1095 1097 1129 C4' C A 36 OK OK 1131 1146 1128 1130 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' C A 2 OK OK 40 57 58 42 72 C5' U A 3 OK OK 71 88 89 73 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 169 C5' C A 6 OK OK 168 185 186 170 200 C5' C A 7 OK OK 199 216 217 201 231 C5' A A 8 OK OK 230 249 250 232 264 C5' G A 9 OK OK 263 283 284 265 298 C5' C A 10 OK OK 297 314 315 299 329 C5' U A 11 OK OK 328 345 346 330 359 C5' A A 12 OK OK 358 377 378 360 392 C5' U A 13 OK OK 391 408 409 393 422 C5' G A 14 OK OK 421 441 442 423 456 C5' A A 15 OK OK 455 474 475 457 489 C5' G A 16 OK OK 488 508 509 490 523 C5' G A 17 OK OK 522 542 543 524 557 C5' U A 18 OK OK 556 573 574 558 587 C5' C A 19 OK OK 586 603 604 588 618 C5' A A 20 OK OK 617 636 637 619 651 C5' U A 21 OK OK 650 667 668 652 681 C5' A A 22 OK OK 680 699 700 682 714 C5' C A 23 OK OK 713 730 731 715 745 C5' A A 24 OK OK 744 763 764 746 778 C5' U A 25 OK OK 777 794 795 779 808 C5' C A 26 OK OK 807 824 825 809 839 C5' G A 27 OK OK 838 858 859 840 873 C5' U A 28 OK OK 872 889 890 874 903 C5' C A 29 OK OK 902 919 920 904 934 C5' A A 30 OK OK 933 952 953 935 967 C5' U A 31 OK OK 966 983 984 968 997 C5' A A 32 OK OK 996 1015 1016 998 1030 C5' G A 33 OK OK 1029 1049 1050 1031 1064 C5' C A 34 OK OK 1063 1080 1081 1065 1095 C5' A A 35 OK OK 1094 1113 1114 1096 1128 C5' C A 36 OK OK 1127 1144 1145 1129 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 37 P C A 2 distorted distorted 10 38 39 40 68 P U A 3 distorted distorted 45 69 70 71 98 P G A 4 distorted distorted 76 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P C A 6 distorted distorted 140 166 167 168 196 P C A 7 distorted distorted 173 197 198 199 227 P A A 8 distorted distorted 204 228 229 230 260 P G A 9 distorted distorted 235 261 262 263 294 P C A 10 distorted distorted 268 295 296 297 325 P U A 11 distorted distorted 302 326 327 328 355 P A A 12 distorted distorted 333 356 357 358 388 P U A 13 distorted distorted 363 389 390 391 418 P G A 14 distorted distorted 396 419 420 421 452 P A A 15 distorted distorted 426 453 454 455 485 P G A 16 distorted distorted 460 486 487 488 519 P G A 17 distorted distorted 493 520 521 522 553 P U A 18 distorted distorted 527 554 555 556 583 P C A 19 distorted distorted 561 584 585 586 614 P A A 20 distorted distorted 591 615 616 617 647 P U A 21 distorted distorted 622 648 649 650 677 P A A 22 distorted distorted 655 678 679 680 710 P C A 23 distorted distorted 685 711 712 713 741 P A A 24 distorted distorted 718 742 743 744 774 P U A 25 distorted distorted 749 775 776 777 804 P C A 26 distorted distorted 782 805 806 807 835 P G A 27 distorted distorted 812 836 837 838 869 P U A 28 distorted distorted 843 870 871 872 899 P C A 29 distorted distorted 877 900 901 902 930 P A A 30 distorted distorted 907 931 932 933 963 P U A 31 distorted distorted 938 964 965 966 993 P A A 32 distorted distorted 971 994 995 996 1026 P G A 33 distorted distorted 1001 1027 1028 1029 1060 P C A 34 distorted distorted 1034 1061 1062 1063 1091 P A A 35 distorted distorted 1068 1092 1093 1094 1124 P C A 36 distorted distorted 1099 1125 1126 1127 ---------------------------------------------------------------------------------