ID code: '2MIY' 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' C A 1 alpha beta 39 59 45 42 75 C1' U A 2 alpha beta 70 90 76 73 105 C1' U A 3 alpha beta 100 120 106 103 135 C1' G A 4 alpha beta 130 153 136 133 169 C1' G A 5 alpha beta 164 187 170 167 203 C1' U A 6 alpha beta 198 218 204 201 233 C1' G A 7 alpha beta 228 251 234 231 267 C1' C A 8 alpha beta 262 282 268 265 298 C1' U A 9 alpha beta 293 313 299 296 328 C1' U A 10 alpha beta 323 343 329 326 358 C1' A A 11 alpha beta 353 375 359 356 391 C1' G A 12 alpha beta 386 409 392 389 425 C1' C A 13 alpha beta 420 440 426 423 456 C1' U A 14 alpha beta 451 471 457 454 486 C1' U A 15 alpha beta 481 501 487 484 516 C1' C A 16 alpha beta 511 531 517 514 547 C1' U A 17 alpha beta 542 562 548 545 577 C1' U A 18 alpha beta 572 592 578 575 607 C1' U A 19 alpha beta 602 622 608 605 637 C1' C A 20 alpha beta 632 652 638 635 668 C1' A A 21 alpha beta 663 685 669 666 701 C1' C A 22 alpha beta 696 716 702 699 732 C1' C A 23 alpha beta 727 747 733 730 763 C1' A A 24 alpha beta 758 780 764 761 796 C1' A A 25 alpha beta 791 813 797 794 829 C1' G A 26 alpha beta 824 847 830 827 863 C1' C A 27 alpha beta 858 878 864 861 894 C1' A A 28 alpha beta 889 911 895 892 927 C1' U A 29 alpha beta 922 942 928 925 957 C1' A A 30 alpha beta 952 974 958 955 990 C1' U A 31 alpha beta 985 1005 991 988 1020 C1' U A 32 alpha beta 1015 1035 1021 1018 1050 C1' A A 33 alpha beta 1045 1067 1051 1048 1083 C1' C A 34 alpha beta 1078 1098 1084 1081 1114 C1' A A 35 alpha beta 1109 1131 1115 1112 1147 C1' C A 36 alpha beta 1142 1162 1148 1145 1178 C1' G A 37 alpha beta 1173 1196 1179 1176 1212 C1' C A 38 alpha beta 1207 1227 1213 1210 1243 C1' G A 39 alpha beta 1238 1261 1244 1241 1277 C1' G A 40 alpha beta 1272 1295 1278 1275 1311 C1' A A 41 alpha beta 1306 1328 1312 1309 1344 C1' U A 42 alpha beta 1339 1359 1345 1342 1374 C1' A A 43 alpha beta 1369 1391 1375 1372 1407 C1' A A 44 alpha beta 1402 1424 1408 1405 1440 C1' C A 45 alpha beta 1435 1455 1441 1438 1471 C1' C A 46 alpha beta 1466 1486 1472 1469 1502 C1' G A 47 alpha beta 1497 1520 1503 1500 1536 C1' C A 48 alpha beta 1531 1551 1537 1534 1567 C1' C A 49 alpha beta 1562 1582 1568 1565 1598 C1' A A 50 alpha beta 1593 1615 1599 1596 1631 C1' A A 51 alpha beta 1626 1648 1632 1629 1664 C1' A A 52 alpha beta 1659 1681 1665 1662 1697 C1' G A 53 alpha beta 1692 1715 1698 1695 1731 C1' G A 54 alpha beta 1726 1749 1732 1729 1765 C1' A A 55 alpha beta 1760 1782 1766 1763 1798 C1' G A 56 alpha beta 1793 1816 1799 1796 1832 C1' A A 57 alpha beta 1827 1849 1833 1830 1865 C1' A A 58 alpha beta 1860 1883 1866 1863 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 1 OK OK 44 40 57 43 73 C2' U A 2 OK OK 75 71 88 74 103 C2' U A 3 OK OK 105 101 118 104 133 C2' G A 4 OK OK 135 131 151 134 167 C2' G A 5 OK OK 169 165 185 168 201 C2' U A 6 OK OK 203 199 216 202 231 C2' G A 7 OK OK 233 229 249 232 265 C2' C A 8 OK OK 267 263 280 266 296 C2' U A 9 OK OK 298 294 311 297 326 C2' U A 10 OK OK 328 324 341 327 356 C2' A A 11 OK OK 358 354 373 357 389 C2' G A 12 OK OK 391 387 407 390 423 C2' C A 13 OK OK 425 421 438 424 454 C2' U A 14 OK OK 456 452 469 455 484 C2' U A 15 OK OK 486 482 499 485 514 C2' C A 16 OK OK 516 512 529 515 545 C2' U A 17 OK OK 547 543 560 546 575 C2' U A 18 OK OK 577 573 590 576 605 C2' U A 19 OK OK 607 603 620 606 635 C2' C A 20 OK OK 637 633 650 636 666 C2' A A 21 OK OK 668 664 683 667 699 C2' C A 22 OK OK 701 697 714 700 730 C2' C A 23 OK OK 732 728 745 731 761 C2' A A 24 OK OK 763 759 778 762 794 C2' A A 25 OK OK 796 792 811 795 827 C2' G A 26 OK OK 829 825 845 828 861 C2' C A 27 OK OK 863 859 876 862 892 C2' A A 28 OK OK 894 890 909 893 925 C2' U A 29 OK OK 927 923 940 926 955 C2' A A 30 OK OK 957 953 972 956 988 C2' U A 31 OK OK 990 986 1003 989 1018 C2' U A 32 OK OK 1020 1016 1033 1019 1048 C2' A A 33 OK OK 1050 1046 1065 1049 1081 C2' C A 34 OK OK 1083 1079 1096 1082 1112 C2' A A 35 OK OK 1114 1110 1129 1113 1145 C2' C A 36 OK OK 1147 1143 1160 1146 1176 C2' G A 37 OK OK 1178 1174 1194 1177 1210 C2' C A 38 OK OK 1212 1208 1225 1211 1241 C2' G A 39 OK OK 1243 1239 1259 1242 1275 C2' G A 40 OK OK 1277 1273 1293 1276 1309 C2' A A 41 OK OK 1311 1307 1326 1310 1342 C2' U A 42 OK OK 1344 1340 1357 1343 1372 C2' A A 43 OK OK 1374 1370 1389 1373 1405 C2' A A 44 OK OK 1407 1403 1422 1406 1438 C2' C A 45 OK OK 1440 1436 1453 1439 1469 C2' C A 46 OK OK 1471 1467 1484 1470 1500 C2' G A 47 OK OK 1502 1498 1518 1501 1534 C2' C A 48 OK OK 1536 1532 1549 1535 1565 C2' C A 49 OK OK 1567 1563 1580 1566 1596 C2' A A 50 OK OK 1598 1594 1613 1597 1629 C2' A A 51 OK OK 1631 1627 1646 1630 1662 C2' A A 52 OK OK 1664 1660 1679 1663 1695 C2' G A 53 OK OK 1697 1693 1713 1696 1729 C2' G A 54 OK OK 1731 1727 1747 1730 1763 C2' A A 55 OK OK 1765 1761 1780 1764 1796 C2' G A 56 OK OK 1798 1794 1814 1797 1830 C2' A A 57 OK OK 1832 1828 1847 1831 1863 C2' A A 58 OK OK 1865 1861 1881 1864 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A -1 OK OK 3 24 6 7 40 C3' C A 1 OK OK 38 56 41 42 71 C3' U A 2 OK OK 69 87 72 73 101 C3' U A 3 OK OK 99 117 102 103 131 C3' G A 4 OK OK 129 150 132 133 165 C3' G A 5 OK OK 163 184 166 167 199 C3' U A 6 OK OK 197 215 200 201 229 C3' G A 7 OK OK 227 248 230 231 263 C3' C A 8 OK OK 261 279 264 265 294 C3' U A 9 OK OK 292 310 295 296 324 C3' U A 10 OK OK 322 340 325 326 354 C3' A A 11 OK OK 352 372 355 356 387 C3' G A 12 OK OK 385 406 388 389 421 C3' C A 13 OK OK 419 437 422 423 452 C3' U A 14 OK OK 450 468 453 454 482 C3' U A 15 OK OK 480 498 483 484 512 C3' C A 16 OK OK 510 528 513 514 543 C3' U A 17 OK OK 541 559 544 545 573 C3' U A 18 OK OK 571 589 574 575 603 C3' U A 19 OK OK 601 619 604 605 633 C3' C A 20 OK OK 631 649 634 635 664 C3' A A 21 OK OK 662 682 665 666 697 C3' C A 22 OK OK 695 713 698 699 728 C3' C A 23 OK OK 726 744 729 730 759 C3' A A 24 OK OK 757 777 760 761 792 C3' A A 25 OK OK 790 810 793 794 825 C3' G A 26 OK OK 823 844 826 827 859 C3' C A 27 OK OK 857 875 860 861 890 C3' A A 28 OK OK 888 908 891 892 923 C3' U A 29 OK OK 921 939 924 925 953 C3' A A 30 OK OK 951 971 954 955 986 C3' U A 31 OK OK 984 1002 987 988 1016 C3' U A 32 OK OK 1014 1032 1017 1018 1046 C3' A A 33 OK OK 1044 1064 1047 1048 1079 C3' C A 34 OK OK 1077 1095 1080 1081 1110 C3' A A 35 OK OK 1108 1128 1111 1112 1143 C3' C A 36 OK OK 1141 1159 1144 1145 1174 C3' G A 37 OK OK 1172 1193 1175 1176 1208 C3' C A 38 OK OK 1206 1224 1209 1210 1239 C3' G A 39 OK OK 1237 1258 1240 1241 1273 C3' G A 40 OK OK 1271 1292 1274 1275 1307 C3' A A 41 OK OK 1305 1325 1308 1309 1340 C3' U A 42 OK OK 1338 1356 1341 1342 1370 C3' A A 43 OK OK 1368 1388 1371 1372 1403 C3' A A 44 OK OK 1401 1421 1404 1405 1436 C3' C A 45 OK OK 1434 1452 1437 1438 1467 C3' C A 46 OK OK 1465 1483 1468 1469 1498 C3' G A 47 OK OK 1496 1517 1499 1500 1532 C3' C A 48 OK OK 1530 1548 1533 1534 1563 C3' C A 49 OK OK 1561 1579 1564 1565 1594 C3' A A 50 OK OK 1592 1612 1595 1596 1627 C3' A A 51 OK OK 1625 1645 1628 1629 1660 C3' A A 52 OK OK 1658 1678 1661 1662 1693 C3' G A 53 OK OK 1691 1712 1694 1695 1727 C3' G A 54 OK OK 1725 1746 1728 1729 1761 C3' A A 55 OK OK 1759 1779 1762 1763 1794 C3' G A 56 OK OK 1792 1813 1795 1796 1828 C3' A A 57 OK OK 1826 1846 1829 1830 1861 C3' A A 58 OK OK 1859 1879 1862 1863 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A -1 OK OK 5 23 2 4 38 C4' C A 1 OK OK 40 55 37 39 69 C4' U A 2 OK OK 71 86 68 70 99 C4' U A 3 OK OK 101 116 98 100 129 C4' G A 4 OK OK 131 149 128 130 163 C4' G A 5 OK OK 165 183 162 164 197 C4' U A 6 OK OK 199 214 196 198 227 C4' G A 7 OK OK 229 247 226 228 261 C4' C A 8 OK OK 263 278 260 262 292 C4' U A 9 OK OK 294 309 291 293 322 C4' U A 10 OK OK 324 339 321 323 352 C4' A A 11 OK OK 354 371 351 353 385 C4' G A 12 OK OK 387 405 384 386 419 C4' C A 13 OK OK 421 436 418 420 450 C4' U A 14 OK OK 452 467 449 451 480 C4' U A 15 OK OK 482 497 479 481 510 C4' C A 16 OK OK 512 527 509 511 541 C4' U A 17 OK OK 543 558 540 542 571 C4' U A 18 OK OK 573 588 570 572 601 C4' U A 19 OK OK 603 618 600 602 631 C4' C A 20 OK OK 633 648 630 632 662 C4' A A 21 OK OK 664 681 661 663 695 C4' C A 22 OK OK 697 712 694 696 726 C4' C A 23 OK OK 728 743 725 727 757 C4' A A 24 OK OK 759 776 756 758 790 C4' A A 25 OK OK 792 809 789 791 823 C4' G A 26 OK OK 825 843 822 824 857 C4' C A 27 OK OK 859 874 856 858 888 C4' A A 28 OK OK 890 907 887 889 921 C4' U A 29 OK OK 923 938 920 922 951 C4' A A 30 OK OK 953 970 950 952 984 C4' U A 31 OK OK 986 1001 983 985 1014 C4' U A 32 OK OK 1016 1031 1013 1015 1044 C4' A A 33 OK OK 1046 1063 1043 1045 1077 C4' C A 34 OK OK 1079 1094 1076 1078 1108 C4' A A 35 OK OK 1110 1127 1107 1109 1141 C4' C A 36 OK OK 1143 1158 1140 1142 1172 C4' G A 37 OK OK 1174 1192 1171 1173 1206 C4' C A 38 OK OK 1208 1223 1205 1207 1237 C4' G A 39 OK OK 1239 1257 1236 1238 1271 C4' G A 40 OK OK 1273 1291 1270 1272 1305 C4' A A 41 OK OK 1307 1324 1304 1306 1338 C4' U A 42 OK OK 1340 1355 1337 1339 1368 C4' A A 43 OK OK 1370 1387 1367 1369 1401 C4' A A 44 OK OK 1403 1420 1400 1402 1434 C4' C A 45 OK OK 1436 1451 1433 1435 1465 C4' C A 46 OK OK 1467 1482 1464 1466 1496 C4' G A 47 OK OK 1498 1516 1495 1497 1530 C4' C A 48 OK OK 1532 1547 1529 1531 1561 C4' C A 49 OK OK 1563 1578 1560 1562 1592 C4' A A 50 OK OK 1594 1611 1591 1593 1625 C4' A A 51 OK OK 1627 1644 1624 1626 1658 C4' A A 52 OK OK 1660 1677 1657 1659 1691 C4' G A 53 OK OK 1693 1711 1690 1692 1725 C4' G A 54 OK OK 1727 1745 1724 1726 1759 C4' A A 55 OK OK 1761 1778 1758 1760 1792 C4' G A 56 OK OK 1794 1812 1791 1793 1826 C4' A A 57 OK OK 1828 1845 1825 1827 1859 C4' A A 58 OK OK 1861 1878 1858 1860 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 1 OK OK 36 53 54 38 68 C5' U A 2 OK OK 67 84 85 69 98 C5' U A 3 OK OK 97 114 115 99 128 C5' G A 4 OK OK 127 147 148 129 162 C5' G A 5 OK OK 161 181 182 163 196 C5' U A 6 OK OK 195 212 213 197 226 C5' G A 7 OK OK 225 245 246 227 260 C5' C A 8 OK OK 259 276 277 261 291 C5' U A 9 OK OK 290 307 308 292 321 C5' U A 10 OK OK 320 337 338 322 351 C5' A A 11 OK OK 350 369 370 352 384 C5' G A 12 OK OK 383 403 404 385 418 C5' C A 13 OK OK 417 434 435 419 449 C5' U A 14 OK OK 448 465 466 450 479 C5' U A 15 OK OK 478 495 496 480 509 C5' C A 16 OK OK 508 525 526 510 540 C5' U A 17 OK OK 539 556 557 541 570 C5' U A 18 OK OK 569 586 587 571 600 C5' U A 19 OK OK 599 616 617 601 630 C5' C A 20 OK OK 629 646 647 631 661 C5' A A 21 OK OK 660 679 680 662 694 C5' C A 22 OK OK 693 710 711 695 725 C5' C A 23 OK OK 724 741 742 726 756 C5' A A 24 OK OK 755 774 775 757 789 C5' A A 25 OK OK 788 807 808 790 822 C5' G A 26 OK OK 821 841 842 823 856 C5' C A 27 OK OK 855 872 873 857 887 C5' A A 28 OK OK 886 905 906 888 920 C5' U A 29 OK OK 919 936 937 921 950 C5' A A 30 OK OK 949 968 969 951 983 C5' U A 31 OK OK 982 999 1000 984 1013 C5' U A 32 OK OK 1012 1029 1030 1014 1043 C5' A A 33 OK OK 1042 1061 1062 1044 1076 C5' C A 34 OK OK 1075 1092 1093 1077 1107 C5' A A 35 OK OK 1106 1125 1126 1108 1140 C5' C A 36 OK OK 1139 1156 1157 1141 1171 C5' G A 37 OK OK 1170 1190 1191 1172 1205 C5' C A 38 OK OK 1204 1221 1222 1206 1236 C5' G A 39 OK OK 1235 1255 1256 1237 1270 C5' G A 40 OK OK 1269 1289 1290 1271 1304 C5' A A 41 OK OK 1303 1322 1323 1305 1337 C5' U A 42 OK OK 1336 1353 1354 1338 1367 C5' A A 43 OK OK 1366 1385 1386 1368 1400 C5' A A 44 OK OK 1399 1418 1419 1401 1433 C5' C A 45 OK OK 1432 1449 1450 1434 1464 C5' C A 46 OK OK 1463 1480 1481 1465 1495 C5' G A 47 OK OK 1494 1514 1515 1496 1529 C5' C A 48 OK OK 1528 1545 1546 1530 1560 C5' C A 49 OK OK 1559 1576 1577 1561 1591 C5' A A 50 OK OK 1590 1609 1610 1592 1624 C5' A A 51 OK OK 1623 1642 1643 1625 1657 C5' A A 52 OK OK 1656 1675 1676 1658 1690 C5' G A 53 OK OK 1689 1709 1710 1691 1724 C5' G A 54 OK OK 1723 1743 1744 1725 1758 C5' A A 55 OK OK 1757 1776 1777 1759 1791 C5' G A 56 OK OK 1790 1810 1811 1792 1825 C5' A A 57 OK OK 1824 1843 1844 1826 1858 C5' A A 58 OK OK 1857 1876 1877 1859 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 1 distorted distorted 6 34 35 36 64 P U A 2 distorted distorted 41 65 66 67 94 P U A 3 distorted distorted 72 95 96 97 124 P G A 4 distorted distorted 102 125 126 127 158 P G A 5 distorted distorted 132 159 160 161 192 P U A 6 distorted distorted 166 193 194 195 222 P G A 7 distorted distorted 200 223 224 225 256 P C A 8 distorted distorted 230 257 258 259 287 P U A 9 distorted distorted 264 288 289 290 317 P U A 10 distorted distorted 295 318 319 320 347 P A A 11 distorted distorted 325 348 349 350 380 P G A 12 distorted distorted 355 381 382 383 414 P C A 13 distorted distorted 388 415 416 417 445 P U A 14 distorted distorted 422 446 447 448 475 P U A 15 distorted distorted 453 476 477 478 505 P C A 16 distorted distorted 483 506 507 508 536 P U A 17 distorted distorted 513 537 538 539 566 P U A 18 distorted distorted 544 567 568 569 596 P U A 19 distorted distorted 574 597 598 599 626 P C A 20 distorted distorted 604 627 628 629 657 P A A 21 distorted distorted 634 658 659 660 690 P C A 22 distorted distorted 665 691 692 693 721 P C A 23 distorted distorted 698 722 723 724 752 P A A 24 distorted distorted 729 753 754 755 785 P A A 25 distorted distorted 760 786 787 788 818 P G A 26 distorted distorted 793 819 820 821 852 P C A 27 distorted distorted 826 853 854 855 883 P A A 28 distorted distorted 860 884 885 886 916 P U A 29 distorted distorted 891 917 918 919 946 P A A 30 distorted distorted 924 947 948 949 979 P U A 31 distorted distorted 954 980 981 982 1009 P U A 32 distorted distorted 987 1010 1011 1012 1039 P A A 33 distorted distorted 1017 1040 1041 1042 1072 P C A 34 distorted distorted 1047 1073 1074 1075 1103 P A A 35 distorted distorted 1080 1104 1105 1106 1136 P C A 36 distorted distorted 1111 1137 1138 1139 1167 P G A 37 distorted distorted 1144 1168 1169 1170 1201 P C A 38 distorted distorted 1175 1202 1203 1204 1232 P G A 39 distorted distorted 1209 1233 1234 1235 1266 P G A 40 distorted distorted 1240 1267 1268 1269 1300 P A A 41 distorted distorted 1274 1301 1302 1303 1333 P U A 42 distorted distorted 1308 1334 1335 1336 1363 P A A 43 distorted distorted 1341 1364 1365 1366 1396 P A A 44 distorted distorted 1371 1397 1398 1399 1429 P C A 45 distorted distorted 1404 1430 1431 1432 1460 P C A 46 distorted distorted 1437 1461 1462 1463 1491 P G A 47 distorted distorted 1468 1492 1493 1494 1525 P C A 48 distorted distorted 1499 1526 1527 1528 1556 P C A 49 distorted distorted 1533 1557 1558 1559 1587 P A A 50 distorted distorted 1564 1588 1589 1590 1620 P A A 51 distorted distorted 1595 1621 1622 1623 1653 P A A 52 distorted distorted 1628 1654 1655 1656 1686 P G A 53 distorted distorted 1661 1687 1688 1689 1720 P G A 54 distorted distorted 1694 1721 1722 1723 1754 P A A 55 distorted distorted 1728 1755 1756 1757 1787 P G A 56 distorted distorted 1762 1788 1789 1790 1821 P A A 57 distorted distorted 1795 1822 1823 1824 1854 P A A 58 distorted distorted 1829 1855 1856 1857 ---------------------------------------------------------------------------------