ID code: '2LUB' 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' G A 2 alpha beta 43 66 49 46 82 C1' G A 3 alpha beta 77 100 83 80 116 C1' U A 4 alpha beta 111 131 117 114 146 C1' G A 5 alpha beta 141 164 147 144 180 C1' A A 6 alpha beta 175 197 181 178 213 C1' A A 7 alpha beta 208 230 214 211 246 C1' A A 8 alpha beta 241 263 247 244 279 C1' C A 9 alpha beta 274 294 280 277 310 C1' G A 10 alpha beta 305 328 311 308 344 C1' G A 11 alpha beta 339 362 345 342 378 C1' A A 12 alpha beta 373 395 379 376 411 C1' G A 13 alpha beta 406 429 412 409 445 C1' G A 14 alpha beta 440 463 446 443 479 C1' A A 15 alpha beta 474 496 480 477 512 C1' C A 16 alpha beta 507 527 513 510 543 C1' U A 17 alpha beta 538 558 544 541 573 C1' U A 18 alpha beta 568 588 574 571 603 C1' C A 19 alpha beta 598 618 604 601 634 C1' G A 20 alpha beta 629 652 635 632 668 C1' G A 21 alpha beta 663 686 669 666 702 C1' U A 22 alpha beta 697 717 703 700 732 C1' C A 23 alpha beta 727 747 733 730 763 C1' C A 24 alpha beta 758 778 764 761 794 C1' U A 25 alpha beta 789 809 795 792 824 C1' C A 26 alpha beta 819 839 825 822 855 C1' A A 27 alpha beta 850 872 856 853 888 C1' A A 28 alpha beta 883 905 889 886 921 C1' G A 29 alpha beta 916 939 922 919 955 C1' U A 30 alpha beta 950 970 956 953 985 C1' U A 31 alpha beta 980 1000 986 983 1015 C1' U A 32 alpha beta 1010 1030 1016 1013 1045 C1' C A 33 alpha beta 1040 1060 1046 1043 1076 C1' A A 34 alpha beta 1071 1093 1077 1074 1109 C1' C A 35 alpha beta 1104 1124 1110 1107 1140 C1' C A 36 alpha beta 1135 1155 1141 1138 1171 C1' C A 37 alpha beta 1166 1187 1172 1169 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 48 44 64 47 80 C2' G A 3 OK OK 82 78 98 81 114 C2' U A 4 OK OK 116 112 129 115 144 C2' G A 5 OK OK 146 142 162 145 178 C2' A A 6 OK OK 180 176 195 179 211 C2' A A 7 OK OK 213 209 228 212 244 C2' A A 8 OK OK 246 242 261 245 277 C2' C A 9 OK OK 279 275 292 278 308 C2' G A 10 OK OK 310 306 326 309 342 C2' G A 11 OK OK 344 340 360 343 376 C2' A A 12 OK OK 378 374 393 377 409 C2' G A 13 OK OK 411 407 427 410 443 C2' G A 14 OK OK 445 441 461 444 477 C2' A A 15 OK OK 479 475 494 478 510 C2' C A 16 OK OK 512 508 525 511 541 C2' U A 17 OK OK 543 539 556 542 571 C2' U A 18 OK OK 573 569 586 572 601 C2' C A 19 OK OK 603 599 616 602 632 C2' G A 20 OK OK 634 630 650 633 666 C2' G A 21 OK OK 668 664 684 667 700 C2' U A 22 OK OK 702 698 715 701 730 C2' C A 23 OK OK 732 728 745 731 761 C2' C A 24 OK OK 763 759 776 762 792 C2' U A 25 OK OK 794 790 807 793 822 C2' C A 26 OK OK 824 820 837 823 853 C2' A A 27 OK OK 855 851 870 854 886 C2' A A 28 OK OK 888 884 903 887 919 C2' G A 29 OK OK 921 917 937 920 953 C2' U A 30 OK OK 955 951 968 954 983 C2' U A 31 OK OK 985 981 998 984 1013 C2' U A 32 OK OK 1015 1011 1028 1014 1043 C2' C A 33 OK OK 1045 1041 1058 1044 1074 C2' A A 34 OK OK 1076 1072 1091 1075 1107 C2' C A 35 OK OK 1109 1105 1122 1108 1138 C2' C A 36 OK OK 1140 1136 1153 1139 1169 C2' C A 37 OK OK 1171 1167 1185 1170 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' G A 3 OK OK 76 97 79 80 112 C3' U A 4 OK OK 110 128 113 114 142 C3' G A 5 OK OK 140 161 143 144 176 C3' A A 6 OK OK 174 194 177 178 209 C3' A A 7 OK OK 207 227 210 211 242 C3' A A 8 OK OK 240 260 243 244 275 C3' C A 9 OK OK 273 291 276 277 306 C3' G A 10 OK OK 304 325 307 308 340 C3' G A 11 OK OK 338 359 341 342 374 C3' A A 12 OK OK 372 392 375 376 407 C3' G A 13 OK OK 405 426 408 409 441 C3' G A 14 OK OK 439 460 442 443 475 C3' A A 15 OK OK 473 493 476 477 508 C3' C A 16 OK OK 506 524 509 510 539 C3' U A 17 OK OK 537 555 540 541 569 C3' U A 18 OK OK 567 585 570 571 599 C3' C A 19 OK OK 597 615 600 601 630 C3' G A 20 OK OK 628 649 631 632 664 C3' G A 21 OK OK 662 683 665 666 698 C3' U A 22 OK OK 696 714 699 700 728 C3' C A 23 OK OK 726 744 729 730 759 C3' C A 24 OK OK 757 775 760 761 790 C3' U A 25 OK OK 788 806 791 792 820 C3' C A 26 OK OK 818 836 821 822 851 C3' A A 27 OK OK 849 869 852 853 884 C3' A A 28 OK OK 882 902 885 886 917 C3' G A 29 OK OK 915 936 918 919 951 C3' U A 30 OK OK 949 967 952 953 981 C3' U A 31 OK OK 979 997 982 983 1011 C3' U A 32 OK OK 1009 1027 1012 1013 1041 C3' C A 33 OK OK 1039 1057 1042 1043 1072 C3' A A 34 OK OK 1070 1090 1073 1074 1105 C3' C A 35 OK OK 1103 1121 1106 1107 1136 C3' C A 36 OK OK 1134 1152 1137 1138 1167 C3' C A 37 OK OK 1165 1183 1168 1169 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' G A 3 OK OK 78 96 75 77 110 C4' U A 4 OK OK 112 127 109 111 140 C4' G A 5 OK OK 142 160 139 141 174 C4' A A 6 OK OK 176 193 173 175 207 C4' A A 7 OK OK 209 226 206 208 240 C4' A A 8 OK OK 242 259 239 241 273 C4' C A 9 OK OK 275 290 272 274 304 C4' G A 10 OK OK 306 324 303 305 338 C4' G A 11 OK OK 340 358 337 339 372 C4' A A 12 OK OK 374 391 371 373 405 C4' G A 13 OK OK 407 425 404 406 439 C4' G A 14 OK OK 441 459 438 440 473 C4' A A 15 OK OK 475 492 472 474 506 C4' C A 16 OK OK 508 523 505 507 537 C4' U A 17 OK OK 539 554 536 538 567 C4' U A 18 OK OK 569 584 566 568 597 C4' C A 19 OK OK 599 614 596 598 628 C4' G A 20 OK OK 630 648 627 629 662 C4' G A 21 OK OK 664 682 661 663 696 C4' U A 22 OK OK 698 713 695 697 726 C4' C A 23 OK OK 728 743 725 727 757 C4' C A 24 OK OK 759 774 756 758 788 C4' U A 25 OK OK 790 805 787 789 818 C4' C A 26 OK OK 820 835 817 819 849 C4' A A 27 OK OK 851 868 848 850 882 C4' A A 28 OK OK 884 901 881 883 915 C4' G A 29 OK OK 917 935 914 916 949 C4' U A 30 OK OK 951 966 948 950 979 C4' U A 31 OK OK 981 996 978 980 1009 C4' U A 32 OK OK 1011 1026 1008 1010 1039 C4' C A 33 OK OK 1041 1056 1038 1040 1070 C4' A A 34 OK OK 1072 1089 1069 1071 1103 C4' C A 35 OK OK 1105 1120 1102 1104 1134 C4' C A 36 OK OK 1136 1151 1133 1135 1165 C4' C A 37 OK OK 1167 1182 1164 1166 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 40 60 61 42 75 C5' G A 3 OK OK 74 94 95 76 109 C5' U A 4 OK OK 108 125 126 110 139 C5' G A 5 OK OK 138 158 159 140 173 C5' A A 6 OK OK 172 191 192 174 206 C5' A A 7 OK OK 205 224 225 207 239 C5' A A 8 OK OK 238 257 258 240 272 C5' C A 9 OK OK 271 288 289 273 303 C5' G A 10 OK OK 302 322 323 304 337 C5' G A 11 OK OK 336 356 357 338 371 C5' A A 12 OK OK 370 389 390 372 404 C5' G A 13 OK OK 403 423 424 405 438 C5' G A 14 OK OK 437 457 458 439 472 C5' A A 15 OK OK 471 490 491 473 505 C5' C A 16 OK OK 504 521 522 506 536 C5' U A 17 OK OK 535 552 553 537 566 C5' U A 18 OK OK 565 582 583 567 596 C5' C A 19 OK OK 595 612 613 597 627 C5' G A 20 OK OK 626 646 647 628 661 C5' G A 21 OK OK 660 680 681 662 695 C5' U A 22 OK OK 694 711 712 696 725 C5' C A 23 OK OK 724 741 742 726 756 C5' C A 24 OK OK 755 772 773 757 787 C5' U A 25 OK OK 786 803 804 788 817 C5' C A 26 OK OK 816 833 834 818 848 C5' A A 27 OK OK 847 866 867 849 881 C5' A A 28 OK OK 880 899 900 882 914 C5' G A 29 OK OK 913 933 934 915 948 C5' U A 30 OK OK 947 964 965 949 978 C5' U A 31 OK OK 977 994 995 979 1008 C5' U A 32 OK OK 1007 1024 1025 1009 1038 C5' C A 33 OK OK 1037 1054 1055 1039 1069 C5' A A 34 OK OK 1068 1087 1088 1070 1102 C5' C A 35 OK OK 1101 1118 1119 1103 1133 C5' C A 36 OK OK 1132 1149 1150 1134 1164 C5' C A 37 OK OK 1163 1180 1181 1165 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P G A 3 distorted distorted 45 72 73 74 105 P U A 4 distorted distorted 79 106 107 108 135 P G A 5 distorted distorted 113 136 137 138 169 P A A 6 distorted distorted 143 170 171 172 202 P A A 7 distorted distorted 177 203 204 205 235 P A A 8 distorted distorted 210 236 237 238 268 P C A 9 distorted distorted 243 269 270 271 299 P G A 10 distorted distorted 276 300 301 302 333 P G A 11 distorted distorted 307 334 335 336 367 P A A 12 distorted distorted 341 368 369 370 400 P G A 13 distorted distorted 375 401 402 403 434 P G A 14 distorted distorted 408 435 436 437 468 P A A 15 distorted distorted 442 469 470 471 501 P C A 16 distorted distorted 476 502 503 504 532 P U A 17 distorted distorted 509 533 534 535 562 P U A 18 distorted distorted 540 563 564 565 592 P C A 19 distorted distorted 570 593 594 595 623 P G A 20 distorted distorted 600 624 625 626 657 P G A 21 distorted distorted 631 658 659 660 691 P U A 22 distorted distorted 665 692 693 694 721 P C A 23 distorted distorted 699 722 723 724 752 P C A 24 distorted distorted 729 753 754 755 783 P U A 25 distorted distorted 760 784 785 786 813 P C A 26 distorted distorted 791 814 815 816 844 P A A 27 distorted distorted 821 845 846 847 877 P A A 28 distorted distorted 852 878 879 880 910 P G A 29 distorted distorted 885 911 912 913 944 P U A 30 distorted distorted 918 945 946 947 974 P U A 31 distorted distorted 952 975 976 977 1004 P U A 32 distorted distorted 982 1005 1006 1007 1034 P C A 33 distorted distorted 1012 1035 1036 1037 1065 P A A 34 distorted distorted 1042 1066 1067 1068 1098 P C A 35 distorted distorted 1073 1099 1100 1101 1129 P C A 36 distorted distorted 1106 1130 1131 1132 1160 P C A 37 distorted distorted 1137 1161 1162 1163 ---------------------------------------------------------------------------------