ID code: '1VC6' 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 B 101 beta 4 10 7 32 C1' G B 102 beta 27 33 30 55 C1' C B 103 beta 50 56 53 75 C1' C B 104 beta 70 76 73 95 C1' G B 105 beta 90 96 93 118 C1' G B 106 beta 113 119 116 141 C1' C B 107 beta 136 142 139 161 C1' A B 108 beta 156 162 159 183 C1' U B 109 beta 178 184 181 203 C1' G B 110 beta 198 204 201 226 C1' G B 111 beta 221 227 224 249 C1' U B 112 beta 244 250 247 269 C1' C B 113 beta 264 270 267 289 C1' C B 114 beta 284 290 287 309 C1' C B 115 beta 304 310 307 329 C1' A B 116 beta 324 330 327 351 C1' G B 117 beta 346 352 349 374 C1' C B 118 beta 369 375 372 394 C1' C B 119 beta 389 395 392 414 C1' U B 120 beta 409 415 412 434 C1' C B 121 beta 429 435 432 454 C1' C B 122 beta 449 455 452 474 C1' U B 123 beta 469 475 472 494 C1' C B 124 beta 489 495 492 514 C1' G B 125 beta 509 515 512 537 C1' C B 126 beta 532 538 535 557 C1' U B 127 beta 552 558 555 577 C1' G B 128 beta 572 578 575 600 C1' G B 129 beta 595 601 598 623 C1' C B 130 beta 618 624 621 643 C1' G B 131 beta 638 644 641 666 C1' C B 132 beta 661 667 664 686 C1' C B 133 beta 681 687 684 706 C1' G B 134 beta 701 707 704 729 C1' G B 135 beta 724 730 727 752 C1' C B 136 beta 747 753 750 772 C1' U B 137 beta 767 773 770 792 C1' G B 138 beta 787 793 790 815 C1' G B 139 beta 810 816 813 838 C1' G B 140 beta 833 839 836 861 C1' C B 141 beta 856 862 859 881 C1' A B 142 beta 876 882 879 903 C1' A B 143 beta 898 904 901 925 C1' C B 144 beta 920 926 923 945 C1' A B 145 beta 940 946 943 967 C1' C B 146 beta 962 968 965 987 C1' C B 147 beta 982 988 985 1007 C1' A B 148 beta 1002 1008 1005 1029 C1' U B 149 beta 1024 1030 1027 1049 C1' U B 150 beta 1044 1050 1047 1069 C1' G B 151 beta 1064 1070 1067 1092 C1' C B 152 beta 1087 1093 1090 1112 C1' A B 153 beta 1107 1113 1110 1134 C1' C B 154 beta 1129 1135 1132 1154 C1' U B 155 beta 1149 1155 1152 1174 C1' C B 156 beta 1169 1175 1172 1194 C1' C B 157 beta 1189 1195 1192 1214 C1' G B 158 beta 1209 1215 1212 1237 C1' G B 159 beta 1232 1238 1235 1260 C1' U B 160 beta 1255 1261 1258 1280 C1' G B 161 beta 1275 1281 1278 1303 C1' G B 162 beta 1298 1304 1301 1326 C1' U B 163 beta 1321 1327 1324 1346 C1' G B 164 beta 1341 1347 1344 1369 C1' A B 165 beta 1364 1370 1367 1391 C1' A B 166 beta 1386 1392 1389 1413 C1' U B 167 beta 1408 1414 1411 1433 C1' G B 168 beta 1428 1434 1431 1456 C1' G B 169 beta 1451 1457 1454 1479 C1' G B 170 beta 1474 1480 1477 1502 C1' A B 171 beta 1497 1503 1500 1524 C1' C B 172 beta 1519 1525 1522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 101 OK 9 5 8 30 C2' G B 102 OK 32 28 31 53 C2' C B 103 OK 55 51 54 73 C2' C B 104 OK 75 71 74 93 C2' G B 105 OK 95 91 94 116 C2' G B 106 OK 118 114 117 139 C2' C B 107 OK 141 137 140 159 C2' A B 108 OK 161 157 160 181 C2' U B 109 OK 183 179 182 201 C2' G B 110 OK 203 199 202 224 C2' G B 111 OK 226 222 225 247 C2' U B 112 OK 249 245 248 267 C2' C B 113 OK 269 265 268 287 C2' C B 114 OK 289 285 288 307 C2' C B 115 OK 309 305 308 327 C2' A B 116 OK 329 325 328 349 C2' G B 117 OK 351 347 350 372 C2' C B 118 OK 374 370 373 392 C2' C B 119 OK 394 390 393 412 C2' U B 120 OK 414 410 413 432 C2' C B 121 OK 434 430 433 452 C2' C B 122 OK 454 450 453 472 C2' U B 123 OK 474 470 473 492 C2' C B 124 OK 494 490 493 512 C2' G B 125 OK 514 510 513 535 C2' C B 126 OK 537 533 536 555 C2' U B 127 OK 557 553 556 575 C2' G B 128 OK 577 573 576 598 C2' G B 129 OK 600 596 599 621 C2' C B 130 OK 623 619 622 641 C2' G B 131 OK 643 639 642 664 C2' C B 132 OK 666 662 665 684 C2' C B 133 OK 686 682 685 704 C2' G B 134 OK 706 702 705 727 C2' G B 135 OK 729 725 728 750 C2' C B 136 OK 752 748 751 770 C2' U B 137 OK 772 768 771 790 C2' G B 138 OK 792 788 791 813 C2' G B 139 OK 815 811 814 836 C2' G B 140 OK 838 834 837 859 C2' C B 141 OK 861 857 860 879 C2' A B 142 OK 881 877 880 901 C2' A B 143 OK 903 899 902 923 C2' C B 144 OK 925 921 924 943 C2' A B 145 OK 945 941 944 965 C2' C B 146 OK 967 963 966 985 C2' C B 147 OK 987 983 986 1005 C2' A B 148 OK 1007 1003 1006 1027 C2' U B 149 OK 1029 1025 1028 1047 C2' U B 150 OK 1049 1045 1048 1067 C2' G B 151 OK 1069 1065 1068 1090 C2' C B 152 OK 1092 1088 1091 1110 C2' A B 153 OK 1112 1108 1111 1132 C2' C B 154 OK 1134 1130 1133 1152 C2' U B 155 OK 1154 1150 1153 1172 C2' C B 156 OK 1174 1170 1173 1192 C2' C B 157 OK 1194 1190 1193 1212 C2' G B 158 OK 1214 1210 1213 1235 C2' G B 159 OK 1237 1233 1236 1258 C2' U B 160 OK 1260 1256 1259 1278 C2' G B 161 OK 1280 1276 1279 1301 C2' G B 162 OK 1303 1299 1302 1324 C2' U B 163 OK 1326 1322 1325 1344 C2' G B 164 OK 1346 1342 1345 1367 C2' A B 165 OK 1369 1365 1368 1389 C2' A B 166 OK 1391 1387 1390 1411 C2' U B 167 OK 1413 1409 1412 1431 C2' G B 168 OK 1433 1429 1432 1454 C2' G B 169 OK 1456 1452 1455 1477 C2' G B 170 OK 1479 1475 1478 1500 C2' A B 171 OK 1502 1498 1501 1522 C2' C B 172 OK 1524 1520 1523 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 101 OK 3 6 7 28 C3' G B 102 OK 26 29 30 51 C3' C B 103 OK 49 52 53 71 C3' C B 104 OK 69 72 73 91 C3' G B 105 OK 89 92 93 114 C3' G B 106 OK 112 115 116 137 C3' C B 107 OK 135 138 139 157 C3' A B 108 OK 155 158 159 179 C3' U B 109 OK 177 180 181 199 C3' G B 110 OK 197 200 201 222 C3' G B 111 OK 220 223 224 245 C3' U B 112 OK 243 246 247 265 C3' C B 113 OK 263 266 267 285 C3' C B 114 OK 283 286 287 305 C3' C B 115 OK 303 306 307 325 C3' A B 116 OK 323 326 327 347 C3' G B 117 OK 345 348 349 370 C3' C B 118 OK 368 371 372 390 C3' C B 119 OK 388 391 392 410 C3' U B 120 OK 408 411 412 430 C3' C B 121 OK 428 431 432 450 C3' C B 122 OK 448 451 452 470 C3' U B 123 OK 468 471 472 490 C3' C B 124 OK 488 491 492 510 C3' G B 125 OK 508 511 512 533 C3' C B 126 OK 531 534 535 553 C3' U B 127 OK 551 554 555 573 C3' G B 128 OK 571 574 575 596 C3' G B 129 OK 594 597 598 619 C3' C B 130 OK 617 620 621 639 C3' G B 131 OK 637 640 641 662 C3' C B 132 OK 660 663 664 682 C3' C B 133 OK 680 683 684 702 C3' G B 134 OK 700 703 704 725 C3' G B 135 OK 723 726 727 748 C3' C B 136 OK 746 749 750 768 C3' U B 137 OK 766 769 770 788 C3' G B 138 OK 786 789 790 811 C3' G B 139 OK 809 812 813 834 C3' G B 140 OK 832 835 836 857 C3' C B 141 OK 855 858 859 877 C3' A B 142 OK 875 878 879 899 C3' A B 143 OK 897 900 901 921 C3' C B 144 OK 919 922 923 941 C3' A B 145 OK 939 942 943 963 C3' C B 146 OK 961 964 965 983 C3' C B 147 OK 981 984 985 1003 C3' A B 148 OK 1001 1004 1005 1025 C3' U B 149 OK 1023 1026 1027 1045 C3' U B 150 OK 1043 1046 1047 1065 C3' G B 151 OK 1063 1066 1067 1088 C3' C B 152 OK 1086 1089 1090 1108 C3' A B 153 OK 1106 1109 1110 1130 C3' C B 154 OK 1128 1131 1132 1150 C3' U B 155 OK 1148 1151 1152 1170 C3' C B 156 OK 1168 1171 1172 1190 C3' C B 157 OK 1188 1191 1192 1210 C3' G B 158 OK 1208 1211 1212 1233 C3' G B 159 OK 1231 1234 1235 1256 C3' U B 160 OK 1254 1257 1258 1276 C3' G B 161 OK 1274 1277 1278 1299 C3' G B 162 OK 1297 1300 1301 1322 C3' U B 163 OK 1320 1323 1324 1342 C3' G B 164 OK 1340 1343 1344 1365 C3' A B 165 OK 1363 1366 1367 1387 C3' A B 166 OK 1385 1388 1389 1409 C3' U B 167 OK 1407 1410 1411 1429 C3' G B 168 OK 1427 1430 1431 1452 C3' G B 169 OK 1450 1453 1454 1475 C3' G B 170 OK 1473 1476 1477 1498 C3' A B 171 OK 1496 1499 1500 1520 C3' C B 172 OK 1518 1521 1522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 101 OK 5 2 4 26 C4' G B 102 OK 28 25 27 49 C4' C B 103 OK 51 48 50 69 C4' C B 104 OK 71 68 70 89 C4' G B 105 OK 91 88 90 112 C4' G B 106 OK 114 111 113 135 C4' C B 107 OK 137 134 136 155 C4' A B 108 OK 157 154 156 177 C4' U B 109 OK 179 176 178 197 C4' G B 110 OK 199 196 198 220 C4' G B 111 OK 222 219 221 243 C4' U B 112 OK 245 242 244 263 C4' C B 113 OK 265 262 264 283 C4' C B 114 OK 285 282 284 303 C4' C B 115 OK 305 302 304 323 C4' A B 116 OK 325 322 324 345 C4' G B 117 OK 347 344 346 368 C4' C B 118 OK 370 367 369 388 C4' C B 119 OK 390 387 389 408 C4' U B 120 OK 410 407 409 428 C4' C B 121 OK 430 427 429 448 C4' C B 122 OK 450 447 449 468 C4' U B 123 OK 470 467 469 488 C4' C B 124 OK 490 487 489 508 C4' G B 125 OK 510 507 509 531 C4' C B 126 OK 533 530 532 551 C4' U B 127 OK 553 550 552 571 C4' G B 128 OK 573 570 572 594 C4' G B 129 OK 596 593 595 617 C4' C B 130 OK 619 616 618 637 C4' G B 131 OK 639 636 638 660 C4' C B 132 OK 662 659 661 680 C4' C B 133 OK 682 679 681 700 C4' G B 134 OK 702 699 701 723 C4' G B 135 OK 725 722 724 746 C4' C B 136 OK 748 745 747 766 C4' U B 137 OK 768 765 767 786 C4' G B 138 OK 788 785 787 809 C4' G B 139 OK 811 808 810 832 C4' G B 140 OK 834 831 833 855 C4' C B 141 OK 857 854 856 875 C4' A B 142 OK 877 874 876 897 C4' A B 143 OK 899 896 898 919 C4' C B 144 OK 921 918 920 939 C4' A B 145 OK 941 938 940 961 C4' C B 146 OK 963 960 962 981 C4' C B 147 OK 983 980 982 1001 C4' A B 148 OK 1003 1000 1002 1023 C4' U B 149 OK 1025 1022 1024 1043 C4' U B 150 OK 1045 1042 1044 1063 C4' G B 151 OK 1065 1062 1064 1086 C4' C B 152 OK 1088 1085 1087 1106 C4' A B 153 OK 1108 1105 1107 1128 C4' C B 154 OK 1130 1127 1129 1148 C4' U B 155 OK 1150 1147 1149 1168 C4' C B 156 OK 1170 1167 1169 1188 C4' C B 157 OK 1190 1187 1189 1208 C4' G B 158 OK 1210 1207 1209 1231 C4' G B 159 OK 1233 1230 1232 1254 C4' U B 160 OK 1256 1253 1255 1274 C4' G B 161 OK 1276 1273 1275 1297 C4' G B 162 OK 1299 1296 1298 1320 C4' U B 163 OK 1322 1319 1321 1340 C4' G B 164 OK 1342 1339 1341 1363 C4' A B 165 OK 1365 1362 1364 1385 C4' A B 166 OK 1387 1384 1386 1407 C4' U B 167 OK 1409 1406 1408 1427 C4' G B 168 OK 1429 1426 1428 1450 C4' G B 169 OK 1452 1449 1451 1473 C4' G B 170 OK 1475 1472 1474 1496 C4' A B 171 OK 1498 1495 1497 1518 C4' C B 172 OK 1520 1517 1519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 101 1 3 25 C5' G B 102 24 26 48 C5' C B 103 47 49 68 C5' C B 104 67 69 88 C5' G B 105 87 89 111 C5' G B 106 110 112 134 C5' C B 107 133 135 154 C5' A B 108 153 155 176 C5' U B 109 175 177 196 C5' G B 110 195 197 219 C5' G B 111 218 220 242 C5' U B 112 241 243 262 C5' C B 113 261 263 282 C5' C B 114 281 283 302 C5' C B 115 301 303 322 C5' A B 116 321 323 344 C5' G B 117 343 345 367 C5' C B 118 366 368 387 C5' C B 119 386 388 407 C5' U B 120 406 408 427 C5' C B 121 426 428 447 C5' C B 122 446 448 467 C5' U B 123 466 468 487 C5' C B 124 486 488 507 C5' G B 125 506 508 530 C5' C B 126 529 531 550 C5' U B 127 549 551 570 C5' G B 128 569 571 593 C5' G B 129 592 594 616 C5' C B 130 615 617 636 C5' G B 131 635 637 659 C5' C B 132 658 660 679 C5' C B 133 678 680 699 C5' G B 134 698 700 722 C5' G B 135 721 723 745 C5' C B 136 744 746 765 C5' U B 137 764 766 785 C5' G B 138 784 786 808 C5' G B 139 807 809 831 C5' G B 140 830 832 854 C5' C B 141 853 855 874 C5' A B 142 873 875 896 C5' A B 143 895 897 918 C5' C B 144 917 919 938 C5' A B 145 937 939 960 C5' C B 146 959 961 980 C5' C B 147 979 981 1000 C5' A B 148 999 1001 1022 C5' U B 149 1021 1023 1042 C5' U B 150 1041 1043 1062 C5' G B 151 1061 1063 1085 C5' C B 152 1084 1086 1105 C5' A B 153 1104 1106 1127 C5' C B 154 1126 1128 1147 C5' U B 155 1146 1148 1167 C5' C B 156 1166 1168 1187 C5' C B 157 1186 1188 1207 C5' G B 158 1206 1208 1230 C5' G B 159 1229 1231 1253 C5' U B 160 1252 1254 1273 C5' G B 161 1272 1274 1296 C5' G B 162 1295 1297 1319 C5' U B 163 1318 1320 1339 C5' G B 164 1338 1340 1362 C5' A B 165 1361 1363 1384 C5' A B 166 1383 1385 1406 C5' U B 167 1405 1407 1426 C5' G B 168 1425 1427 1449 C5' G B 169 1448 1450 1472 C5' G B 170 1471 1473 1495 C5' A B 171 1494 1496 1517 C5' C B 172 1516 1518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G B 102 distorted distorted 6 22 23 24 44 P C B 103 distorted distorted 29 45 46 47 64 P C B 104 distorted distorted 52 65 66 67 84 P G B 105 distorted distorted 72 85 86 87 107 P G B 106 distorted distorted 92 108 109 110 130 P C B 107 distorted distorted 115 131 132 133 150 P A B 108 distorted distorted 138 151 152 153 172 P U B 109 distorted distorted 158 173 174 175 192 P G B 110 distorted distorted 180 193 194 195 215 P G B 111 distorted distorted 200 216 217 218 238 P U B 112 distorted distorted 223 239 240 241 258 P C B 113 distorted distorted 246 259 260 261 278 P C B 114 distorted distorted 266 279 280 281 298 P C B 115 distorted distorted 286 299 300 301 318 P A B 116 distorted distorted 306 319 320 321 340 P G B 117 distorted distorted 326 341 342 343 363 P C B 118 distorted distorted 348 364 365 366 383 P C B 119 distorted distorted 371 384 385 386 403 P U B 120 distorted distorted 391 404 405 406 423 P C B 121 distorted distorted 411 424 425 426 443 P C B 122 distorted distorted 431 444 445 446 463 P U B 123 distorted distorted 451 464 465 466 483 P C B 124 distorted distorted 471 484 485 486 503 P G B 125 distorted distorted 491 504 505 506 526 P C B 126 distorted distorted 511 527 528 529 546 P U B 127 distorted distorted 534 547 548 549 566 P G B 128 distorted distorted 554 567 568 569 589 P G B 129 distorted distorted 574 590 591 592 612 P C B 130 distorted distorted 597 613 614 615 632 P G B 131 distorted distorted 620 633 634 635 655 P C B 132 distorted distorted 640 656 657 658 675 P C B 133 distorted distorted 663 676 677 678 695 P G B 134 distorted distorted 683 696 697 698 718 P G B 135 distorted distorted 703 719 720 721 741 P C B 136 distorted distorted 726 742 743 744 761 P U B 137 distorted distorted 749 762 763 764 781 P G B 138 distorted distorted 769 782 783 784 804 P G B 139 distorted distorted 789 805 806 807 827 P G B 140 distorted distorted 812 828 829 830 850 P C B 141 distorted distorted 835 851 852 853 870 P A B 142 distorted distorted 858 871 872 873 892 P A B 143 distorted distorted 878 893 894 895 914 P C B 144 distorted distorted 900 915 916 917 934 P A B 145 distorted distorted 922 935 936 937 956 P C B 146 distorted distorted 942 957 958 959 976 P C B 147 distorted distorted 964 977 978 979 996 P A B 148 distorted distorted 984 997 998 999 1018 P U B 149 distorted distorted 1004 1019 1020 1021 1038 P U B 150 distorted distorted 1026 1039 1040 1041 1058 P G B 151 distorted distorted 1046 1059 1060 1061 1081 P C B 152 distorted distorted 1066 1082 1083 1084 1101 P A B 153 distorted distorted 1089 1102 1103 1104 1123 P C B 154 distorted distorted 1109 1124 1125 1126 1143 P U B 155 distorted distorted 1131 1144 1145 1146 1163 P C B 156 distorted distorted 1151 1164 1165 1166 1183 P C B 157 distorted distorted 1171 1184 1185 1186 1203 P G B 158 distorted distorted 1191 1204 1205 1206 1226 P G B 159 distorted distorted 1211 1227 1228 1229 1249 P U B 160 distorted distorted 1234 1250 1251 1252 1269 P G B 161 distorted distorted 1257 1270 1271 1272 1292 P G B 162 distorted distorted 1277 1293 1294 1295 1315 P U B 163 distorted distorted 1300 1316 1317 1318 1335 P G B 164 distorted distorted 1323 1336 1337 1338 1358 P A B 165 distorted distorted 1343 1359 1360 1361 1380 P A B 166 distorted distorted 1366 1381 1382 1383 1402 P U B 167 distorted distorted 1388 1403 1404 1405 1422 P G B 168 distorted distorted 1410 1423 1424 1425 1445 P G B 169 distorted distorted 1430 1446 1447 1448 1468 P G B 170 distorted distorted 1453 1469 1470 1471 1491 P A B 171 distorted distorted 1476 1492 1493 1494 1513 P C B 172 distorted distorted 1499 1514 1515 1516 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