ID code: '1A4D' 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 68 alpha beta 4 27 10 7 44 C1' G A 69 alpha beta 39 62 45 42 78 C1' C A 70 alpha beta 73 93 79 76 109 C1' C A 71 alpha beta 104 124 110 107 140 C1' G A 72 alpha beta 135 158 141 138 174 C1' A A 73 alpha beta 169 191 175 172 207 C1' U A 74 alpha beta 202 222 208 205 237 C1' G A 75 alpha beta 232 255 238 235 271 C1' G A 76 alpha beta 266 289 272 269 305 C1' U A 77 alpha beta 300 320 306 303 335 C1' A A 78 alpha beta 330 352 336 333 368 C1' G A 79 alpha beta 363 386 369 366 402 C1' U A 80 alpha beta 397 417 403 400 432 C1' G A 81 alpha beta 427 450 433 430 466 C1' U A 82 alpha beta 461 481 467 464 496 C1' G A 83 alpha beta 491 514 497 494 530 C1' G A 84 alpha beta 525 548 531 528 564 C1' G A 85 alpha beta 559 582 565 562 598 C1' G A 86 alpha beta 593 616 599 596 632 C1' U A 87 alpha beta 627 647 633 630 662 C1' C A 88 alpha beta 657 677 663 660 694 C1' U B 89 alpha beta 689 709 695 692 724 C1' C B 90 alpha beta 719 739 725 722 755 C1' C B 91 alpha beta 750 770 756 753 786 C1' C B 92 alpha beta 781 801 787 784 817 C1' C B 93 alpha beta 812 832 818 815 848 C1' A B 94 alpha beta 843 865 849 846 881 C1' U B 95 alpha beta 876 896 882 879 911 C1' G B 96 alpha beta 906 929 912 909 945 C1' C B 97 alpha beta 940 960 946 943 976 C1' G B 98 alpha beta 971 994 977 974 1010 C1' A B 99 alpha beta 1005 1027 1011 1008 1043 C1' G B 100 alpha beta 1038 1061 1044 1041 1077 C1' A B 101 alpha beta 1072 1094 1078 1075 1110 C1' G B 102 alpha beta 1105 1128 1111 1108 1144 C1' U B 103 alpha beta 1139 1159 1145 1142 1174 C1' A B 104 alpha beta 1169 1191 1175 1172 1207 C1' G B 105 alpha beta 1202 1225 1208 1205 1241 C1' G B 106 alpha beta 1236 1259 1242 1239 1275 C1' C B 107 alpha beta 1270 1290 1276 1273 1306 C1' C B 108 alpha beta 1301 1322 1307 1304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 68 OK OK 9 5 25 8 42 C2' G A 69 OK OK 44 40 60 43 76 C2' C A 70 OK OK 78 74 91 77 107 C2' C A 71 OK OK 109 105 122 108 138 C2' G A 72 OK OK 140 136 156 139 172 C2' A A 73 OK OK 174 170 189 173 205 C2' U A 74 OK OK 207 203 220 206 235 C2' G A 75 OK OK 237 233 253 236 269 C2' G A 76 OK OK 271 267 287 270 303 C2' U A 77 OK OK 305 301 318 304 333 C2' A A 78 OK OK 335 331 350 334 366 C2' G A 79 OK OK 368 364 384 367 400 C2' U A 80 OK OK 402 398 415 401 430 C2' G A 81 OK OK 432 428 448 431 464 C2' U A 82 OK OK 466 462 479 465 494 C2' G A 83 OK OK 496 492 512 495 528 C2' G A 84 OK OK 530 526 546 529 562 C2' G A 85 OK OK 564 560 580 563 596 C2' G A 86 OK OK 598 594 614 597 630 C2' U A 87 OK OK 632 628 645 631 660 C2' C A 88 OK OK 662 658 675 661 692 C2' U B 89 OK OK 694 690 707 693 722 C2' C B 90 OK OK 724 720 737 723 753 C2' C B 91 OK OK 755 751 768 754 784 C2' C B 92 OK OK 786 782 799 785 815 C2' C B 93 OK OK 817 813 830 816 846 C2' A B 94 OK OK 848 844 863 847 879 C2' U B 95 OK OK 881 877 894 880 909 C2' G B 96 OK OK 911 907 927 910 943 C2' C B 97 OK OK 945 941 958 944 974 C2' G B 98 OK OK 976 972 992 975 1008 C2' A B 99 OK OK 1010 1006 1025 1009 1041 C2' G B 100 OK OK 1043 1039 1059 1042 1075 C2' A B 101 OK OK 1077 1073 1092 1076 1108 C2' G B 102 OK OK 1110 1106 1126 1109 1142 C2' U B 103 OK OK 1144 1140 1157 1143 1172 C2' A B 104 OK OK 1174 1170 1189 1173 1205 C2' G B 105 OK OK 1207 1203 1223 1206 1239 C2' G B 106 OK OK 1241 1237 1257 1240 1273 C2' C B 107 OK OK 1275 1271 1288 1274 1304 C2' C B 108 OK OK 1306 1302 1320 1305 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 68 OK OK 3 24 6 7 40 C3' G A 69 OK OK 38 59 41 42 74 C3' C A 70 OK OK 72 90 75 76 105 C3' C A 71 OK OK 103 121 106 107 136 C3' G A 72 OK OK 134 155 137 138 170 C3' A A 73 OK OK 168 188 171 172 203 C3' U A 74 OK OK 201 219 204 205 233 C3' G A 75 OK OK 231 252 234 235 267 C3' G A 76 OK OK 265 286 268 269 301 C3' U A 77 OK OK 299 317 302 303 331 C3' A A 78 OK OK 329 349 332 333 364 C3' G A 79 OK OK 362 383 365 366 398 C3' U A 80 OK OK 396 414 399 400 428 C3' G A 81 OK OK 426 447 429 430 462 C3' U A 82 OK OK 460 478 463 464 492 C3' G A 83 OK OK 490 511 493 494 526 C3' G A 84 OK OK 524 545 527 528 560 C3' G A 85 OK OK 558 579 561 562 594 C3' G A 86 OK OK 592 613 595 596 628 C3' U A 87 OK OK 626 644 629 630 658 C3' C A 88 OK OK 656 674 659 660 690 C3' U B 89 OK OK 688 706 691 692 720 C3' C B 90 OK OK 718 736 721 722 751 C3' C B 91 OK OK 749 767 752 753 782 C3' C B 92 OK OK 780 798 783 784 813 C3' C B 93 OK OK 811 829 814 815 844 C3' A B 94 OK OK 842 862 845 846 877 C3' U B 95 OK OK 875 893 878 879 907 C3' G B 96 OK OK 905 926 908 909 941 C3' C B 97 OK OK 939 957 942 943 972 C3' G B 98 OK OK 970 991 973 974 1006 C3' A B 99 OK OK 1004 1024 1007 1008 1039 C3' G B 100 OK OK 1037 1058 1040 1041 1073 C3' A B 101 OK OK 1071 1091 1074 1075 1106 C3' G B 102 OK OK 1104 1125 1107 1108 1140 C3' U B 103 OK OK 1138 1156 1141 1142 1170 C3' A B 104 OK OK 1168 1188 1171 1172 1203 C3' G B 105 OK OK 1201 1222 1204 1205 1237 C3' G B 106 OK OK 1235 1256 1238 1239 1271 C3' C B 107 OK OK 1269 1287 1272 1273 1302 C3' C B 108 OK OK 1300 1318 1303 1304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 68 OK OK 5 23 2 4 38 C4' G A 69 OK OK 40 58 37 39 72 C4' C A 70 OK OK 74 89 71 73 103 C4' C A 71 OK OK 105 120 102 104 134 C4' G A 72 OK OK 136 154 133 135 168 C4' A A 73 OK OK 170 187 167 169 201 C4' U A 74 OK OK 203 218 200 202 231 C4' G A 75 OK OK 233 251 230 232 265 C4' G A 76 OK OK 267 285 264 266 299 C4' U A 77 OK OK 301 316 298 300 329 C4' A A 78 OK OK 331 348 328 330 362 C4' G A 79 OK OK 364 382 361 363 396 C4' U A 80 OK OK 398 413 395 397 426 C4' G A 81 OK OK 428 446 425 427 460 C4' U A 82 OK OK 462 477 459 461 490 C4' G A 83 OK OK 492 510 489 491 524 C4' G A 84 OK OK 526 544 523 525 558 C4' G A 85 OK OK 560 578 557 559 592 C4' G A 86 OK OK 594 612 591 593 626 C4' U A 87 OK OK 628 643 625 627 656 C4' C A 88 OK OK 658 673 655 657 688 C4' U B 89 OK OK 690 705 687 689 718 C4' C B 90 OK OK 720 735 717 719 749 C4' C B 91 OK OK 751 766 748 750 780 C4' C B 92 OK OK 782 797 779 781 811 C4' C B 93 OK OK 813 828 810 812 842 C4' A B 94 OK OK 844 861 841 843 875 C4' U B 95 OK OK 877 892 874 876 905 C4' G B 96 OK OK 907 925 904 906 939 C4' C B 97 OK OK 941 956 938 940 970 C4' G B 98 OK OK 972 990 969 971 1004 C4' A B 99 OK OK 1006 1023 1003 1005 1037 C4' G B 100 OK OK 1039 1057 1036 1038 1071 C4' A B 101 OK OK 1073 1090 1070 1072 1104 C4' G B 102 OK OK 1106 1124 1103 1105 1138 C4' U B 103 OK OK 1140 1155 1137 1139 1168 C4' A B 104 OK OK 1170 1187 1167 1169 1201 C4' G B 105 OK OK 1203 1221 1200 1202 1235 C4' G B 106 OK OK 1237 1255 1234 1236 1269 C4' C B 107 OK OK 1271 1286 1268 1270 1300 C4' C B 108 OK OK 1302 1317 1299 1301 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 68 OK OK 1 21 22 3 37 C5' G A 69 OK OK 36 56 57 38 71 C5' C A 70 OK OK 70 87 88 72 102 C5' C A 71 OK OK 101 118 119 103 133 C5' G A 72 OK OK 132 152 153 134 167 C5' A A 73 OK OK 166 185 186 168 200 C5' U A 74 OK OK 199 216 217 201 230 C5' G A 75 OK OK 229 249 250 231 264 C5' G A 76 OK OK 263 283 284 265 298 C5' U A 77 OK OK 297 314 315 299 328 C5' A A 78 OK OK 327 346 347 329 361 C5' G A 79 OK OK 360 380 381 362 395 C5' U A 80 OK OK 394 411 412 396 425 C5' G A 81 OK OK 424 444 445 426 459 C5' U A 82 OK OK 458 475 476 460 489 C5' G A 83 OK OK 488 508 509 490 523 C5' G A 84 OK OK 522 542 543 524 557 C5' G A 85 OK OK 556 576 577 558 591 C5' G A 86 OK OK 590 610 611 592 625 C5' U A 87 OK OK 624 641 642 626 655 C5' C A 88 OK OK 654 671 672 656 687 C5' U B 89 OK OK 686 703 704 688 717 C5' C B 90 OK OK 716 733 734 718 748 C5' C B 91 OK OK 747 764 765 749 779 C5' C B 92 OK OK 778 795 796 780 810 C5' C B 93 OK OK 809 826 827 811 841 C5' A B 94 OK OK 840 859 860 842 874 C5' U B 95 OK OK 873 890 891 875 904 C5' G B 96 OK OK 903 923 924 905 938 C5' C B 97 OK OK 937 954 955 939 969 C5' G B 98 OK OK 968 988 989 970 1003 C5' A B 99 OK OK 1002 1021 1022 1004 1036 C5' G B 100 OK OK 1035 1055 1056 1037 1070 C5' A B 101 OK OK 1069 1088 1089 1071 1103 C5' G B 102 OK OK 1102 1122 1123 1104 1137 C5' U B 103 OK OK 1136 1153 1154 1138 1167 C5' A B 104 OK OK 1166 1185 1186 1168 1200 C5' G B 105 OK OK 1199 1219 1220 1201 1234 C5' G B 106 OK OK 1233 1253 1254 1235 1268 C5' C B 107 OK OK 1267 1284 1285 1269 1299 C5' C B 108 OK OK 1298 1315 1316 1300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 69 distorted distorted 6 34 35 36 67 P C A 70 distorted distorted 41 68 69 70 98 P C A 71 distorted distorted 75 99 100 101 129 P G A 72 distorted distorted 106 130 131 132 163 P A A 73 distorted distorted 137 164 165 166 196 P U A 74 distorted distorted 171 197 198 199 226 P G A 75 distorted distorted 204 227 228 229 260 P G A 76 distorted distorted 234 261 262 263 294 P U A 77 distorted distorted 268 295 296 297 324 P A A 78 distorted distorted 302 325 326 327 357 P G A 79 distorted distorted 332 358 359 360 391 P U A 80 distorted distorted 365 392 393 394 421 P G A 81 distorted distorted 399 422 423 424 455 P U A 82 distorted distorted 429 456 457 458 485 P G A 83 distorted distorted 463 486 487 488 519 P G A 84 distorted distorted 493 520 521 522 553 P G A 85 distorted distorted 527 554 555 556 587 P G A 86 distorted distorted 561 588 589 590 621 P U A 87 distorted distorted 595 622 623 624 651 P C A 88 distorted distorted 629 652 653 654 683 P U B 89 OK OK 659 684 685 686 713 P C B 90 distorted distorted 691 714 715 716 744 P C B 91 distorted distorted 721 745 746 747 775 P C B 92 distorted distorted 752 776 777 778 806 P C B 93 distorted distorted 783 807 808 809 837 P A B 94 distorted distorted 814 838 839 840 870 P U B 95 distorted distorted 845 871 872 873 900 P G B 96 distorted distorted 878 901 902 903 934 P C B 97 distorted distorted 908 935 936 937 965 P G B 98 distorted distorted 942 966 967 968 999 P A B 99 distorted distorted 973 1000 1001 1002 1032 P G B 100 distorted distorted 1007 1033 1034 1035 1066 P A B 101 distorted distorted 1040 1067 1068 1069 1099 P G B 102 distorted distorted 1074 1100 1101 1102 1133 P U B 103 distorted distorted 1107 1134 1135 1136 1163 P A B 104 distorted distorted 1141 1164 1165 1166 1196 P G B 105 distorted distorted 1171 1197 1198 1199 1230 P G B 106 distorted distorted 1204 1231 1232 1233 1264 P C B 107 distorted distorted 1238 1265 1266 1267 1295 P C B 108 distorted distorted 1272 1296 1297 1298 ---------------------------------------------------------------------------------