ID code: '5DEA' 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 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' U A 3 beta 47 53 50 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' G A 6 beta 110 116 113 138 C1' G A 7 beta 133 139 136 161 C1' U A 8 beta 156 162 159 181 C1' G A 9 beta 176 182 179 204 C1' U A 10 beta 199 205 202 224 C1' G A 11 beta 219 225 222 247 C1' G A 12 beta 242 248 245 270 C1' A A 13 beta 265 271 268 292 C1' A A 14 beta 287 293 290 314 C1' G A 15 beta 309 315 312 337 C1' G A 16 beta 332 338 335 360 C1' A A 17 beta 355 361 358 382 C1' G A 18 beta 377 383 380 405 C1' U A 19 beta 400 406 403 425 C1' G A 20 beta 420 426 423 448 C1' G A 21 beta 443 449 446 471 C1' C A 22 beta 466 472 469 491 C1' U A 23 beta 486 492 489 511 C1' G A 24 beta 506 512 509 534 C1' G A 25 beta 529 535 532 557 C1' G A 26 beta 552 558 555 580 C1' U A 27 beta 575 581 578 600 C1' U A 28 beta 595 601 598 620 C1' G A 29 beta 615 621 618 643 C1' C A 30 beta 638 644 641 663 C1' G A 31 beta 658 664 661 686 C1' C A 32 beta 681 687 684 706 C1' A A 33 beta 701 707 704 728 C1' G A 34 beta 723 729 726 751 C1' C A 35 beta 746 752 749 854 C1' G C 1 beta 849 855 852 877 C1' C C 2 beta 872 878 875 897 C1' U C 3 beta 892 898 895 917 C1' G C 4 beta 912 918 915 940 C1' C C 5 beta 935 941 938 960 C1' G C 6 beta 955 961 958 983 C1' G C 7 beta 978 984 981 1006 C1' U C 8 beta 1001 1007 1004 1026 C1' G C 9 beta 1021 1027 1024 1049 C1' U C 10 beta 1044 1050 1047 1069 C1' G C 11 beta 1064 1070 1067 1092 C1' G C 12 beta 1087 1093 1090 1115 C1' A C 13 beta 1110 1116 1113 1137 C1' A C 14 beta 1132 1138 1135 1159 C1' G C 15 beta 1154 1160 1157 1182 C1' G C 16 beta 1177 1183 1180 1205 C1' A C 17 beta 1200 1206 1203 1227 C1' G C 18 beta 1222 1228 1225 1250 C1' U C 19 beta 1245 1251 1248 1270 C1' G C 20 beta 1265 1271 1268 1293 C1' G C 21 beta 1288 1294 1291 1316 C1' C C 22 beta 1311 1317 1314 1336 C1' U C 23 beta 1331 1337 1334 1356 C1' G C 24 beta 1351 1357 1354 1379 C1' G C 25 beta 1374 1380 1377 1402 C1' G C 26 beta 1397 1403 1400 1425 C1' U C 27 beta 1420 1426 1423 1445 C1' U C 28 beta 1440 1446 1443 1465 C1' G C 29 beta 1460 1466 1463 1488 C1' C C 30 beta 1483 1489 1486 1508 C1' G C 31 beta 1503 1509 1506 1531 C1' C C 32 beta 1526 1532 1529 1551 C1' A C 33 beta 1546 1552 1549 1573 C1' G C 34 beta 1568 1574 1571 1596 C1' C C 35 beta 1591 1597 1594 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' U A 3 OK 52 48 51 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' G A 6 OK 115 111 114 136 C2' G A 7 OK 138 134 137 159 C2' U A 8 OK 161 157 160 179 C2' G A 9 OK 181 177 180 202 C2' U A 10 OK 204 200 203 222 C2' G A 11 OK 224 220 223 245 C2' G A 12 OK 247 243 246 268 C2' A A 13 OK 270 266 269 290 C2' A A 14 OK 292 288 291 312 C2' G A 15 OK 314 310 313 335 C2' G A 16 OK 337 333 336 358 C2' A A 17 OK 360 356 359 380 C2' G A 18 OK 382 378 381 403 C2' U A 19 OK 405 401 404 423 C2' G A 20 OK 425 421 424 446 C2' G A 21 OK 448 444 447 469 C2' C A 22 OK 471 467 470 489 C2' U A 23 OK 491 487 490 509 C2' G A 24 OK 511 507 510 532 C2' G A 25 OK 534 530 533 555 C2' G A 26 OK 557 553 556 578 C2' U A 27 OK 580 576 579 598 C2' U A 28 OK 600 596 599 618 C2' G A 29 OK 620 616 619 641 C2' C A 30 OK 643 639 642 661 C2' G A 31 OK 663 659 662 684 C2' C A 32 OK 686 682 685 704 C2' A A 33 OK 706 702 705 726 C2' G A 34 OK 728 724 727 749 C2' C A 35 OK 751 747 750 852 C2' G C 1 OK 854 850 853 875 C2' C C 2 OK 877 873 876 895 C2' U C 3 OK 897 893 896 915 C2' G C 4 OK 917 913 916 938 C2' C C 5 OK 940 936 939 958 C2' G C 6 OK 960 956 959 981 C2' G C 7 OK 983 979 982 1004 C2' U C 8 OK 1006 1002 1005 1024 C2' G C 9 OK 1026 1022 1025 1047 C2' U C 10 OK 1049 1045 1048 1067 C2' G C 11 OK 1069 1065 1068 1090 C2' G C 12 OK 1092 1088 1091 1113 C2' A C 13 OK 1115 1111 1114 1135 C2' A C 14 OK 1137 1133 1136 1157 C2' G C 15 OK 1159 1155 1158 1180 C2' G C 16 OK 1182 1178 1181 1203 C2' A C 17 OK 1205 1201 1204 1225 C2' G C 18 OK 1227 1223 1226 1248 C2' U C 19 OK 1250 1246 1249 1268 C2' G C 20 OK 1270 1266 1269 1291 C2' G C 21 OK 1293 1289 1292 1314 C2' C C 22 OK 1316 1312 1315 1334 C2' U C 23 OK 1336 1332 1335 1354 C2' G C 24 OK 1356 1352 1355 1377 C2' G C 25 OK 1379 1375 1378 1400 C2' G C 26 OK 1402 1398 1401 1423 C2' U C 27 OK 1425 1421 1424 1443 C2' U C 28 OK 1445 1441 1444 1463 C2' G C 29 OK 1465 1461 1464 1486 C2' C C 30 OK 1488 1484 1487 1506 C2' G C 31 OK 1508 1504 1507 1529 C2' C C 32 OK 1531 1527 1530 1549 C2' A C 33 OK 1551 1547 1550 1571 C2' G C 34 OK 1573 1569 1572 1594 C2' C C 35 OK 1596 1592 1595 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' U A 3 OK 46 49 50 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' G A 6 OK 109 112 113 134 C3' G A 7 OK 132 135 136 157 C3' U A 8 OK 155 158 159 177 C3' G A 9 OK 175 178 179 200 C3' U A 10 OK 198 201 202 220 C3' G A 11 OK 218 221 222 243 C3' G A 12 OK 241 244 245 266 C3' A A 13 OK 264 267 268 288 C3' A A 14 OK 286 289 290 310 C3' G A 15 OK 308 311 312 333 C3' G A 16 OK 331 334 335 356 C3' A A 17 OK 354 357 358 378 C3' G A 18 OK 376 379 380 401 C3' U A 19 OK 399 402 403 421 C3' G A 20 OK 419 422 423 444 C3' G A 21 OK 442 445 446 467 C3' C A 22 OK 465 468 469 487 C3' U A 23 OK 485 488 489 507 C3' G A 24 OK 505 508 509 530 C3' G A 25 OK 528 531 532 553 C3' G A 26 OK 551 554 555 576 C3' U A 27 OK 574 577 578 596 C3' U A 28 OK 594 597 598 616 C3' G A 29 OK 614 617 618 639 C3' C A 30 OK 637 640 641 659 C3' G A 31 OK 657 660 661 682 C3' C A 32 OK 680 683 684 702 C3' A A 33 OK 700 703 704 724 C3' G A 34 OK 722 725 726 747 C3' C A 35 OK 745 748 749 850 C3' G C 1 OK 848 851 852 873 C3' C C 2 OK 871 874 875 893 C3' U C 3 OK 891 894 895 913 C3' G C 4 OK 911 914 915 936 C3' C C 5 OK 934 937 938 956 C3' G C 6 OK 954 957 958 979 C3' G C 7 OK 977 980 981 1002 C3' U C 8 OK 1000 1003 1004 1022 C3' G C 9 OK 1020 1023 1024 1045 C3' U C 10 OK 1043 1046 1047 1065 C3' G C 11 OK 1063 1066 1067 1088 C3' G C 12 OK 1086 1089 1090 1111 C3' A C 13 OK 1109 1112 1113 1133 C3' A C 14 OK 1131 1134 1135 1155 C3' G C 15 OK 1153 1156 1157 1178 C3' G C 16 OK 1176 1179 1180 1201 C3' A C 17 OK 1199 1202 1203 1223 C3' G C 18 OK 1221 1224 1225 1246 C3' U C 19 OK 1244 1247 1248 1266 C3' G C 20 OK 1264 1267 1268 1289 C3' G C 21 OK 1287 1290 1291 1312 C3' C C 22 OK 1310 1313 1314 1332 C3' U C 23 OK 1330 1333 1334 1352 C3' G C 24 OK 1350 1353 1354 1375 C3' G C 25 OK 1373 1376 1377 1398 C3' G C 26 OK 1396 1399 1400 1421 C3' U C 27 OK 1419 1422 1423 1441 C3' U C 28 OK 1439 1442 1443 1461 C3' G C 29 OK 1459 1462 1463 1484 C3' C C 30 OK 1482 1485 1486 1504 C3' G C 31 OK 1502 1505 1506 1527 C3' C C 32 OK 1525 1528 1529 1547 C3' A C 33 OK 1545 1548 1549 1569 C3' G C 34 OK 1567 1570 1571 1592 C3' C C 35 OK 1590 1593 1594 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' U A 3 OK 48 45 47 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' G A 6 OK 111 108 110 132 C4' G A 7 OK 134 131 133 155 C4' U A 8 OK 157 154 156 175 C4' G A 9 OK 177 174 176 198 C4' U A 10 OK 200 197 199 218 C4' G A 11 OK 220 217 219 241 C4' G A 12 OK 243 240 242 264 C4' A A 13 OK 266 263 265 286 C4' A A 14 OK 288 285 287 308 C4' G A 15 OK 310 307 309 331 C4' G A 16 OK 333 330 332 354 C4' A A 17 OK 356 353 355 376 C4' G A 18 OK 378 375 377 399 C4' U A 19 OK 401 398 400 419 C4' G A 20 OK 421 418 420 442 C4' G A 21 OK 444 441 443 465 C4' C A 22 OK 467 464 466 485 C4' U A 23 OK 487 484 486 505 C4' G A 24 OK 507 504 506 528 C4' G A 25 OK 530 527 529 551 C4' G A 26 OK 553 550 552 574 C4' U A 27 OK 576 573 575 594 C4' U A 28 OK 596 593 595 614 C4' G A 29 OK 616 613 615 637 C4' C A 30 OK 639 636 638 657 C4' G A 31 OK 659 656 658 680 C4' C A 32 OK 682 679 681 700 C4' A A 33 OK 702 699 701 722 C4' G A 34 OK 724 721 723 745 C4' C A 35 OK 747 744 746 848 C4' G C 1 OK 850 847 849 871 C4' C C 2 OK 873 870 872 891 C4' U C 3 OK 893 890 892 911 C4' G C 4 OK 913 910 912 934 C4' C C 5 OK 936 933 935 954 C4' G C 6 OK 956 953 955 977 C4' G C 7 OK 979 976 978 1000 C4' U C 8 OK 1002 999 1001 1020 C4' G C 9 OK 1022 1019 1021 1043 C4' U C 10 OK 1045 1042 1044 1063 C4' G C 11 OK 1065 1062 1064 1086 C4' G C 12 OK 1088 1085 1087 1109 C4' A C 13 OK 1111 1108 1110 1131 C4' A C 14 OK 1133 1130 1132 1153 C4' G C 15 OK 1155 1152 1154 1176 C4' G C 16 OK 1178 1175 1177 1199 C4' A C 17 OK 1201 1198 1200 1221 C4' G C 18 OK 1223 1220 1222 1244 C4' U C 19 OK 1246 1243 1245 1264 C4' G C 20 OK 1266 1263 1265 1287 C4' G C 21 OK 1289 1286 1288 1310 C4' C C 22 OK 1312 1309 1311 1330 C4' U C 23 OK 1332 1329 1331 1350 C4' G C 24 OK 1352 1349 1351 1373 C4' G C 25 OK 1375 1372 1374 1396 C4' G C 26 OK 1398 1395 1397 1419 C4' U C 27 OK 1421 1418 1420 1439 C4' U C 28 OK 1441 1438 1440 1459 C4' G C 29 OK 1461 1458 1460 1482 C4' C C 30 OK 1484 1481 1483 1502 C4' G C 31 OK 1504 1501 1503 1525 C4' C C 32 OK 1527 1524 1526 1545 C4' A C 33 OK 1547 1544 1546 1567 C4' G C 34 OK 1569 1566 1568 1590 C4' C C 35 OK 1592 1589 1591 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' U A 3 44 46 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' G A 6 107 109 131 C5' G A 7 130 132 154 C5' U A 8 153 155 174 C5' G A 9 173 175 197 C5' U A 10 196 198 217 C5' G A 11 216 218 240 C5' G A 12 239 241 263 C5' A A 13 262 264 285 C5' A A 14 284 286 307 C5' G A 15 306 308 330 C5' G A 16 329 331 353 C5' A A 17 352 354 375 C5' G A 18 374 376 398 C5' U A 19 397 399 418 C5' G A 20 417 419 441 C5' G A 21 440 442 464 C5' C A 22 463 465 484 C5' U A 23 483 485 504 C5' G A 24 503 505 527 C5' G A 25 526 528 550 C5' G A 26 549 551 573 C5' U A 27 572 574 593 C5' U A 28 592 594 613 C5' G A 29 612 614 636 C5' C A 30 635 637 656 C5' G A 31 655 657 679 C5' C A 32 678 680 699 C5' A A 33 698 700 721 C5' G A 34 720 722 744 C5' C A 35 743 745 847 C5' G C 1 846 848 870 C5' C C 2 869 871 890 C5' U C 3 889 891 910 C5' G C 4 909 911 933 C5' C C 5 932 934 953 C5' G C 6 952 954 976 C5' G C 7 975 977 999 C5' U C 8 998 1000 1019 C5' G C 9 1018 1020 1042 C5' U C 10 1041 1043 1062 C5' G C 11 1061 1063 1085 C5' G C 12 1084 1086 1108 C5' A C 13 1107 1109 1130 C5' A C 14 1129 1131 1152 C5' G C 15 1151 1153 1175 C5' G C 16 1174 1176 1198 C5' A C 17 1197 1199 1220 C5' G C 18 1219 1221 1243 C5' U C 19 1242 1244 1263 C5' G C 20 1262 1264 1286 C5' G C 21 1285 1287 1309 C5' C C 22 1308 1310 1329 C5' U C 23 1328 1330 1349 C5' G C 24 1348 1350 1372 C5' G C 25 1371 1373 1395 C5' G C 26 1394 1396 1418 C5' U C 27 1417 1419 1438 C5' U C 28 1437 1439 1458 C5' G C 29 1457 1459 1481 C5' C C 30 1480 1482 1501 C5' G C 31 1500 1502 1524 C5' C C 32 1523 1525 1544 C5' A C 33 1543 1545 1566 C5' G C 34 1565 1567 1589 C5' C C 35 1588 1590 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P U A 3 distorted distorted 29 42 43 44 61 P G A 4 distorted distorted 49 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P G A 6 distorted distorted 92 105 106 107 127 P G A 7 distorted distorted 112 128 129 130 150 P U A 8 distorted distorted 135 151 152 153 170 P G A 9 distorted distorted 158 171 172 173 193 P U A 10 distorted distorted 178 194 195 196 213 P G A 11 distorted distorted 201 214 215 216 236 P G A 12 distorted distorted 221 237 238 239 259 P A A 13 distorted distorted 244 260 261 262 281 P A A 14 distorted distorted 267 282 283 284 303 P G A 15 distorted distorted 289 304 305 306 326 P G A 16 distorted distorted 311 327 328 329 349 P A A 17 distorted distorted 334 350 351 352 371 P G A 18 distorted distorted 357 372 373 374 394 P U A 19 distorted distorted 379 395 396 397 414 P G A 20 distorted distorted 402 415 416 417 437 P G A 21 distorted distorted 422 438 439 440 460 P C A 22 distorted distorted 445 461 462 463 480 P U A 23 distorted distorted 468 481 482 483 500 P G A 24 distorted distorted 488 501 502 503 523 P G A 25 distorted distorted 508 524 525 526 546 P G A 26 distorted distorted 531 547 548 549 569 P U A 27 distorted distorted 554 570 571 572 589 P U A 28 distorted distorted 577 590 591 592 609 P G A 29 distorted distorted 597 610 611 612 632 P C A 30 distorted distorted 617 633 634 635 652 P G A 31 distorted distorted 640 653 654 655 675 P C A 32 distorted distorted 660 676 677 678 695 P A A 33 distorted distorted 683 696 697 698 717 P G A 34 distorted distorted 703 718 719 720 740 P C A 35 distorted distorted 725 741 742 743 866 P C C 2 distorted distorted 851 867 868 869 886 P U C 3 distorted distorted 874 887 888 889 906 P G C 4 distorted distorted 894 907 908 909 929 P C C 5 distorted distorted 914 930 931 932 949 P G C 6 distorted distorted 937 950 951 952 972 P G C 7 distorted distorted 957 973 974 975 995 P U C 8 distorted distorted 980 996 997 998 1015 P G C 9 distorted distorted 1003 1016 1017 1018 1038 P U C 10 distorted distorted 1023 1039 1040 1041 1058 P G C 11 distorted distorted 1046 1059 1060 1061 1081 P G C 12 distorted distorted 1066 1082 1083 1084 1104 P A C 13 distorted distorted 1089 1105 1106 1107 1126 P A C 14 distorted distorted 1112 1127 1128 1129 1148 P G C 15 distorted distorted 1134 1149 1150 1151 1171 P G C 16 distorted distorted 1156 1172 1173 1174 1194 P A C 17 distorted distorted 1179 1195 1196 1197 1216 P G C 18 distorted distorted 1202 1217 1218 1219 1239 P U C 19 distorted distorted 1224 1240 1241 1242 1259 P G C 20 distorted distorted 1247 1260 1261 1262 1282 P G C 21 distorted distorted 1267 1283 1284 1285 1305 P C C 22 distorted distorted 1290 1306 1307 1308 1325 P U C 23 distorted distorted 1313 1326 1327 1328 1345 P G C 24 distorted distorted 1333 1346 1347 1348 1368 P G C 25 distorted distorted 1353 1369 1370 1371 1391 P G C 26 distorted distorted 1376 1392 1393 1394 1414 P U C 27 distorted distorted 1399 1415 1416 1417 1434 P U C 28 distorted distorted 1422 1435 1436 1437 1454 P G C 29 distorted distorted 1442 1455 1456 1457 1477 P C C 30 distorted distorted 1462 1478 1479 1480 1497 P G C 31 distorted distorted 1485 1498 1499 1500 1520 P C C 32 distorted distorted 1505 1521 1522 1523 1540 P A C 33 distorted distorted 1528 1541 1542 1543 1562 P G C 34 distorted distorted 1548 1563 1564 1565 1585 P C C 35 distorted distorted 1570 1586 1587 1588 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