ID code: '1TXS' 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' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' C A 8 alpha beta 235 255 241 238 271 C1' A A 9 alpha beta 266 288 272 269 304 C1' C A 10 alpha beta 299 319 305 302 335 C1' U A 11 alpha beta 330 350 336 333 365 C1' C A 12 alpha beta 360 380 366 363 396 C1' U A 13 alpha beta 391 411 397 394 426 C1' G A 14 alpha beta 421 444 427 424 460 C1' G A 15 alpha beta 455 478 461 458 494 C1' U A 16 alpha beta 489 509 495 492 524 C1' A A 17 alpha beta 519 541 525 522 557 C1' U A 18 alpha beta 552 572 558 555 587 C1' U A 19 alpha beta 582 602 588 585 617 C1' A A 20 alpha beta 612 634 618 615 650 C1' C A 21 alpha beta 645 665 651 648 681 C1' G A 22 alpha beta 676 699 682 679 715 C1' G A 23 alpha beta 710 733 716 713 749 C1' U A 24 alpha beta 744 764 750 747 779 C1' A A 25 alpha beta 774 796 780 777 812 C1' C A 26 alpha beta 807 827 813 810 843 C1' C A 27 alpha beta 838 858 844 841 874 C1' U A 28 alpha beta 869 889 875 872 904 C1' U A 29 alpha beta 899 919 905 902 934 C1' U A 30 alpha beta 929 949 935 932 964 C1' G A 31 alpha beta 959 982 965 962 998 C1' U A 32 alpha beta 993 1013 999 996 1028 C1' G A 33 alpha beta 1023 1046 1029 1026 1062 C1' C A 34 alpha beta 1057 1077 1063 1060 1093 C1' G A 35 alpha beta 1088 1111 1094 1091 1127 C1' C A 36 alpha beta 1122 1142 1128 1125 1158 C1' C A 37 alpha beta 1153 1173 1159 1156 1189 C1' C A 38 alpha beta 1184 1205 1190 1187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' U A 5 OK OK 143 139 156 142 171 C2' A A 6 OK OK 173 169 188 172 204 C2' G A 7 OK OK 206 202 222 205 238 C2' C A 8 OK OK 240 236 253 239 269 C2' A A 9 OK OK 271 267 286 270 302 C2' C A 10 OK OK 304 300 317 303 333 C2' U A 11 OK OK 335 331 348 334 363 C2' C A 12 OK OK 365 361 378 364 394 C2' U A 13 OK OK 396 392 409 395 424 C2' G A 14 OK OK 426 422 442 425 458 C2' G A 15 OK OK 460 456 476 459 492 C2' U A 16 OK OK 494 490 507 493 522 C2' A A 17 OK OK 524 520 539 523 555 C2' U A 18 OK OK 557 553 570 556 585 C2' U A 19 OK OK 587 583 600 586 615 C2' A A 20 OK OK 617 613 632 616 648 C2' C A 21 OK OK 650 646 663 649 679 C2' G A 22 OK OK 681 677 697 680 713 C2' G A 23 OK OK 715 711 731 714 747 C2' U A 24 OK OK 749 745 762 748 777 C2' A A 25 OK OK 779 775 794 778 810 C2' C A 26 OK OK 812 808 825 811 841 C2' C A 27 OK OK 843 839 856 842 872 C2' U A 28 OK OK 874 870 887 873 902 C2' U A 29 OK OK 904 900 917 903 932 C2' U A 30 OK OK 934 930 947 933 962 C2' G A 31 OK OK 964 960 980 963 996 C2' U A 32 OK OK 998 994 1011 997 1026 C2' G A 33 OK OK 1028 1024 1044 1027 1060 C2' C A 34 OK OK 1062 1058 1075 1061 1091 C2' G A 35 OK OK 1093 1089 1109 1092 1125 C2' C A 36 OK OK 1127 1123 1140 1126 1156 C2' C A 37 OK OK 1158 1154 1171 1157 1187 C2' C A 38 OK OK 1189 1185 1203 1188 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' U A 5 OK OK 137 155 140 141 169 C3' A A 6 OK OK 167 187 170 171 202 C3' G A 7 OK OK 200 221 203 204 236 C3' C A 8 OK OK 234 252 237 238 267 C3' A A 9 OK OK 265 285 268 269 300 C3' C A 10 OK OK 298 316 301 302 331 C3' U A 11 OK OK 329 347 332 333 361 C3' C A 12 OK OK 359 377 362 363 392 C3' U A 13 OK OK 390 408 393 394 422 C3' G A 14 OK OK 420 441 423 424 456 C3' G A 15 OK OK 454 475 457 458 490 C3' U A 16 OK OK 488 506 491 492 520 C3' A A 17 OK OK 518 538 521 522 553 C3' U A 18 OK OK 551 569 554 555 583 C3' U A 19 OK OK 581 599 584 585 613 C3' A A 20 OK OK 611 631 614 615 646 C3' C A 21 OK OK 644 662 647 648 677 C3' G A 22 OK OK 675 696 678 679 711 C3' G A 23 OK OK 709 730 712 713 745 C3' U A 24 OK OK 743 761 746 747 775 C3' A A 25 OK OK 773 793 776 777 808 C3' C A 26 OK OK 806 824 809 810 839 C3' C A 27 OK OK 837 855 840 841 870 C3' U A 28 OK OK 868 886 871 872 900 C3' U A 29 OK OK 898 916 901 902 930 C3' U A 30 OK OK 928 946 931 932 960 C3' G A 31 OK OK 958 979 961 962 994 C3' U A 32 OK OK 992 1010 995 996 1024 C3' G A 33 OK OK 1022 1043 1025 1026 1058 C3' C A 34 OK OK 1056 1074 1059 1060 1089 C3' G A 35 OK OK 1087 1108 1090 1091 1123 C3' C A 36 OK OK 1121 1139 1124 1125 1154 C3' C A 37 OK OK 1152 1170 1155 1156 1185 C3' C A 38 OK OK 1183 1201 1186 1187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' U A 5 OK OK 139 154 136 138 167 C4' A A 6 OK OK 169 186 166 168 200 C4' G A 7 OK OK 202 220 199 201 234 C4' C A 8 OK OK 236 251 233 235 265 C4' A A 9 OK OK 267 284 264 266 298 C4' C A 10 OK OK 300 315 297 299 329 C4' U A 11 OK OK 331 346 328 330 359 C4' C A 12 OK OK 361 376 358 360 390 C4' U A 13 OK OK 392 407 389 391 420 C4' G A 14 OK OK 422 440 419 421 454 C4' G A 15 OK OK 456 474 453 455 488 C4' U A 16 OK OK 490 505 487 489 518 C4' A A 17 OK OK 520 537 517 519 551 C4' U A 18 OK OK 553 568 550 552 581 C4' U A 19 OK OK 583 598 580 582 611 C4' A A 20 OK OK 613 630 610 612 644 C4' C A 21 OK OK 646 661 643 645 675 C4' G A 22 OK OK 677 695 674 676 709 C4' G A 23 OK OK 711 729 708 710 743 C4' U A 24 OK OK 745 760 742 744 773 C4' A A 25 OK OK 775 792 772 774 806 C4' C A 26 OK OK 808 823 805 807 837 C4' C A 27 OK OK 839 854 836 838 868 C4' U A 28 OK OK 870 885 867 869 898 C4' U A 29 OK OK 900 915 897 899 928 C4' U A 30 OK OK 930 945 927 929 958 C4' G A 31 OK OK 960 978 957 959 992 C4' U A 32 OK OK 994 1009 991 993 1022 C4' G A 33 OK OK 1024 1042 1021 1023 1056 C4' C A 34 OK OK 1058 1073 1055 1057 1087 C4' G A 35 OK OK 1089 1107 1086 1088 1121 C4' C A 36 OK OK 1123 1138 1120 1122 1152 C4' C A 37 OK OK 1154 1169 1151 1153 1183 C4' C A 38 OK OK 1185 1200 1182 1184 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' U A 5 OK OK 135 152 153 137 166 C5' A A 6 OK OK 165 184 185 167 199 C5' G A 7 OK OK 198 218 219 200 233 C5' C A 8 OK OK 232 249 250 234 264 C5' A A 9 OK OK 263 282 283 265 297 C5' C A 10 OK OK 296 313 314 298 328 C5' U A 11 OK OK 327 344 345 329 358 C5' C A 12 OK OK 357 374 375 359 389 C5' U A 13 OK OK 388 405 406 390 419 C5' G A 14 OK OK 418 438 439 420 453 C5' G A 15 OK OK 452 472 473 454 487 C5' U A 16 OK OK 486 503 504 488 517 C5' A A 17 OK OK 516 535 536 518 550 C5' U A 18 OK OK 549 566 567 551 580 C5' U A 19 OK OK 579 596 597 581 610 C5' A A 20 OK OK 609 628 629 611 643 C5' C A 21 OK OK 642 659 660 644 674 C5' G A 22 OK OK 673 693 694 675 708 C5' G A 23 OK OK 707 727 728 709 742 C5' U A 24 OK OK 741 758 759 743 772 C5' A A 25 OK OK 771 790 791 773 805 C5' C A 26 OK OK 804 821 822 806 836 C5' C A 27 OK OK 835 852 853 837 867 C5' U A 28 OK OK 866 883 884 868 897 C5' U A 29 OK OK 896 913 914 898 927 C5' U A 30 OK OK 926 943 944 928 957 C5' G A 31 OK OK 956 976 977 958 991 C5' U A 32 OK OK 990 1007 1008 992 1021 C5' G A 33 OK OK 1020 1040 1041 1022 1055 C5' C A 34 OK OK 1054 1071 1072 1056 1086 C5' G A 35 OK OK 1085 1105 1106 1087 1120 C5' C A 36 OK OK 1119 1136 1137 1121 1151 C5' C A 37 OK OK 1150 1167 1168 1152 1182 C5' C A 38 OK OK 1181 1198 1199 1183 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P U A 5 distorted distorted 109 133 134 135 162 P A A 6 distorted distorted 140 163 164 165 195 P G A 7 distorted distorted 170 196 197 198 229 P C A 8 distorted distorted 203 230 231 232 260 P A A 9 distorted distorted 237 261 262 263 293 P C A 10 distorted distorted 268 294 295 296 324 P U A 11 distorted distorted 301 325 326 327 354 P C A 12 distorted distorted 332 355 356 357 385 P U A 13 distorted distorted 362 386 387 388 415 P G A 14 distorted distorted 393 416 417 418 449 P G A 15 distorted distorted 423 450 451 452 483 P U A 16 distorted distorted 457 484 485 486 513 P A A 17 distorted distorted 491 514 515 516 546 P U A 18 distorted distorted 521 547 548 549 576 P U A 19 distorted distorted 554 577 578 579 606 P A A 20 distorted distorted 584 607 608 609 639 P C A 21 distorted distorted 614 640 641 642 670 P G A 22 distorted distorted 647 671 672 673 704 P G A 23 distorted distorted 678 705 706 707 738 P U A 24 distorted distorted 712 739 740 741 768 P A A 25 distorted distorted 746 769 770 771 801 P C A 26 distorted distorted 776 802 803 804 832 P C A 27 distorted distorted 809 833 834 835 863 P U A 28 distorted distorted 840 864 865 866 893 P U A 29 distorted distorted 871 894 895 896 923 P U A 30 distorted distorted 901 924 925 926 953 P G A 31 distorted distorted 931 954 955 956 987 P U A 32 distorted distorted 961 988 989 990 1017 P G A 33 distorted distorted 995 1018 1019 1020 1051 P C A 34 distorted distorted 1025 1052 1053 1054 1082 P G A 35 distorted distorted 1059 1083 1084 1085 1116 P C A 36 distorted distorted 1090 1117 1118 1119 1147 P C A 37 distorted distorted 1124 1148 1149 1150 1178 P C A 38 distorted distorted 1155 1179 1180 1181 ---------------------------------------------------------------------------------