ID code: '1ILI' 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' --------------------------------------------------------------------------------- 12 C1' C A 1 alpha beta 7 27 13 10 43 C1' U A 2 alpha beta 38 58 44 41 73 C1' C A 3 alpha beta 68 88 74 71 104 C1' U A 4 alpha beta 99 119 105 102 134 C1' G A 5 alpha beta 129 152 135 132 168 C1' U A 6 alpha beta 163 183 169 166 198 C1' U A 7 alpha beta 193 213 199 196 228 C1' U A 8 alpha beta 223 243 229 226 258 C1' A A 9 alpha beta 253 275 259 256 291 C1' C A 10 alpha beta 286 306 292 289 322 C1' C A 11 alpha beta 317 337 323 320 353 C1' A A 12 alpha beta 348 370 354 351 386 C1' G A 13 alpha beta 381 404 387 384 420 C1' G A 14 alpha beta 415 438 421 418 454 C1' U A 15 alpha beta 449 469 455 452 484 C1' C A 16 alpha beta 479 499 485 482 515 C1' A A 17 alpha beta 510 532 516 513 548 C1' G A 18 alpha beta 543 566 549 546 582 C1' G A 19 alpha beta 577 600 583 580 616 C1' U A 20 alpha beta 611 631 617 614 646 C1' C A 21 alpha beta 641 661 647 644 677 C1' C A 22 alpha beta 672 692 678 675 708 C1' G A 23 alpha beta 703 726 709 706 742 C1' G A 24 alpha beta 737 760 743 740 776 C1' A A 25 alpha beta 771 793 777 774 809 C1' A A 26 alpha beta 804 826 810 807 842 C1' G A 27 alpha beta 837 860 843 840 876 C1' G A 28 alpha beta 871 894 877 874 910 C1' A A 29 alpha beta 905 927 911 908 943 C1' A A 30 alpha beta 938 960 944 941 976 C1' G A 31 alpha beta 971 994 977 974 1010 C1' C A 32 alpha beta 1005 1025 1011 1008 1041 C1' A A 33 alpha beta 1036 1058 1042 1039 1074 C1' G A 34 alpha beta 1069 1092 1075 1072 1108 C1' C A 35 alpha beta 1103 1123 1109 1106 1139 C1' C A 36 alpha beta 1134 1154 1140 1137 1170 C1' A A 37 alpha beta 1165 1187 1171 1168 1203 C1' A A 38 alpha beta 1198 1220 1204 1201 1236 C1' G A 39 alpha beta 1231 1254 1237 1234 1270 C1' G A 40 alpha beta 1265 1288 1271 1268 1304 C1' C A 41 alpha beta 1299 1319 1305 1302 1335 C1' A A 42 alpha beta 1330 1352 1336 1333 1368 C1' G A 43 alpha beta 1363 1386 1369 1366 1402 C1' A A 44 alpha beta 1397 1419 1403 1400 1435 C1' G A 45 alpha beta 1430 1453 1436 1433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 1 OK OK 12 8 25 11 41 C2' U A 2 OK OK 43 39 56 42 71 C2' C A 3 OK OK 73 69 86 72 102 C2' U A 4 OK OK 104 100 117 103 132 C2' G A 5 OK OK 134 130 150 133 166 C2' U A 6 OK OK 168 164 181 167 196 C2' U A 7 OK OK 198 194 211 197 226 C2' U A 8 OK OK 228 224 241 227 256 C2' A A 9 OK OK 258 254 273 257 289 C2' C A 10 OK OK 291 287 304 290 320 C2' C A 11 OK OK 322 318 335 321 351 C2' A A 12 OK OK 353 349 368 352 384 C2' G A 13 OK OK 386 382 402 385 418 C2' G A 14 OK OK 420 416 436 419 452 C2' U A 15 OK OK 454 450 467 453 482 C2' C A 16 OK OK 484 480 497 483 513 C2' A A 17 OK OK 515 511 530 514 546 C2' G A 18 OK OK 548 544 564 547 580 C2' G A 19 OK OK 582 578 598 581 614 C2' U A 20 OK OK 616 612 629 615 644 C2' C A 21 OK OK 646 642 659 645 675 C2' C A 22 OK OK 677 673 690 676 706 C2' G A 23 OK OK 708 704 724 707 740 C2' G A 24 OK OK 742 738 758 741 774 C2' A A 25 OK OK 776 772 791 775 807 C2' A A 26 OK OK 809 805 824 808 840 C2' G A 27 OK OK 842 838 858 841 874 C2' G A 28 OK OK 876 872 892 875 908 C2' A A 29 OK OK 910 906 925 909 941 C2' A A 30 OK OK 943 939 958 942 974 C2' G A 31 OK OK 976 972 992 975 1008 C2' C A 32 OK OK 1010 1006 1023 1009 1039 C2' A A 33 OK OK 1041 1037 1056 1040 1072 C2' G A 34 OK OK 1074 1070 1090 1073 1106 C2' C A 35 OK OK 1108 1104 1121 1107 1137 C2' C A 36 OK OK 1139 1135 1152 1138 1168 C2' A A 37 OK OK 1170 1166 1185 1169 1201 C2' A A 38 OK OK 1203 1199 1218 1202 1234 C2' G A 39 OK OK 1236 1232 1252 1235 1268 C2' G A 40 OK OK 1270 1266 1286 1269 1302 C2' C A 41 OK OK 1304 1300 1317 1303 1333 C2' A A 42 OK OK 1335 1331 1350 1334 1366 C2' G A 43 OK OK 1368 1364 1384 1367 1400 C2' A A 44 OK OK 1402 1398 1417 1401 1433 C2' G A 45 OK OK 1435 1431 1451 1434 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 1 OK OK 6 24 9 10 39 C3' U A 2 OK OK 37 55 40 41 69 C3' C A 3 OK OK 67 85 70 71 100 C3' U A 4 OK OK 98 116 101 102 130 C3' G A 5 OK OK 128 149 131 132 164 C3' U A 6 OK OK 162 180 165 166 194 C3' U A 7 OK OK 192 210 195 196 224 C3' U A 8 OK OK 222 240 225 226 254 C3' A A 9 OK OK 252 272 255 256 287 C3' C A 10 OK OK 285 303 288 289 318 C3' C A 11 OK OK 316 334 319 320 349 C3' A A 12 OK OK 347 367 350 351 382 C3' G A 13 OK OK 380 401 383 384 416 C3' G A 14 OK OK 414 435 417 418 450 C3' U A 15 OK OK 448 466 451 452 480 C3' C A 16 OK OK 478 496 481 482 511 C3' A A 17 OK OK 509 529 512 513 544 C3' G A 18 OK OK 542 563 545 546 578 C3' G A 19 OK OK 576 597 579 580 612 C3' U A 20 OK OK 610 628 613 614 642 C3' C A 21 OK OK 640 658 643 644 673 C3' C A 22 OK OK 671 689 674 675 704 C3' G A 23 OK OK 702 723 705 706 738 C3' G A 24 OK OK 736 757 739 740 772 C3' A A 25 OK OK 770 790 773 774 805 C3' A A 26 OK OK 803 823 806 807 838 C3' G A 27 OK OK 836 857 839 840 872 C3' G A 28 OK OK 870 891 873 874 906 C3' A A 29 OK OK 904 924 907 908 939 C3' A A 30 OK OK 937 957 940 941 972 C3' G A 31 OK OK 970 991 973 974 1006 C3' C A 32 OK OK 1004 1022 1007 1008 1037 C3' A A 33 OK OK 1035 1055 1038 1039 1070 C3' G A 34 OK OK 1068 1089 1071 1072 1104 C3' C A 35 OK OK 1102 1120 1105 1106 1135 C3' C A 36 OK OK 1133 1151 1136 1137 1166 C3' A A 37 OK OK 1164 1184 1167 1168 1199 C3' A A 38 OK OK 1197 1217 1200 1201 1232 C3' G A 39 OK OK 1230 1251 1233 1234 1266 C3' G A 40 OK OK 1264 1285 1267 1268 1300 C3' C A 41 OK OK 1298 1316 1301 1302 1331 C3' A A 42 OK OK 1329 1349 1332 1333 1364 C3' G A 43 OK OK 1362 1383 1365 1366 1398 C3' A A 44 OK OK 1396 1416 1399 1400 1431 C3' G A 45 OK OK 1429 1450 1432 1433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 1 OK OK 8 23 5 7 37 C4' U A 2 OK OK 39 54 36 38 67 C4' C A 3 OK OK 69 84 66 68 98 C4' U A 4 OK OK 100 115 97 99 128 C4' G A 5 OK OK 130 148 127 129 162 C4' U A 6 OK OK 164 179 161 163 192 C4' U A 7 OK OK 194 209 191 193 222 C4' U A 8 OK OK 224 239 221 223 252 C4' A A 9 OK OK 254 271 251 253 285 C4' C A 10 OK OK 287 302 284 286 316 C4' C A 11 OK OK 318 333 315 317 347 C4' A A 12 OK OK 349 366 346 348 380 C4' G A 13 OK OK 382 400 379 381 414 C4' G A 14 OK OK 416 434 413 415 448 C4' U A 15 OK OK 450 465 447 449 478 C4' C A 16 OK OK 480 495 477 479 509 C4' A A 17 OK OK 511 528 508 510 542 C4' G A 18 OK OK 544 562 541 543 576 C4' G A 19 OK OK 578 596 575 577 610 C4' U A 20 OK OK 612 627 609 611 640 C4' C A 21 OK OK 642 657 639 641 671 C4' C A 22 OK OK 673 688 670 672 702 C4' G A 23 OK OK 704 722 701 703 736 C4' G A 24 OK OK 738 756 735 737 770 C4' A A 25 OK OK 772 789 769 771 803 C4' A A 26 OK OK 805 822 802 804 836 C4' G A 27 OK OK 838 856 835 837 870 C4' G A 28 OK OK 872 890 869 871 904 C4' A A 29 OK OK 906 923 903 905 937 C4' A A 30 OK OK 939 956 936 938 970 C4' G A 31 OK OK 972 990 969 971 1004 C4' C A 32 OK OK 1006 1021 1003 1005 1035 C4' A A 33 OK OK 1037 1054 1034 1036 1068 C4' G A 34 OK OK 1070 1088 1067 1069 1102 C4' C A 35 OK OK 1104 1119 1101 1103 1133 C4' C A 36 OK OK 1135 1150 1132 1134 1164 C4' A A 37 OK OK 1166 1183 1163 1165 1197 C4' A A 38 OK OK 1199 1216 1196 1198 1230 C4' G A 39 OK OK 1232 1250 1229 1231 1264 C4' G A 40 OK OK 1266 1284 1263 1265 1298 C4' C A 41 OK OK 1300 1315 1297 1299 1329 C4' A A 42 OK OK 1331 1348 1328 1330 1362 C4' G A 43 OK OK 1364 1382 1361 1363 1396 C4' A A 44 OK OK 1398 1415 1395 1397 1429 C4' G A 45 OK OK 1431 1449 1428 1430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 1 OK OK 4 21 22 6 36 C5' U A 2 OK OK 35 52 53 37 66 C5' C A 3 OK OK 65 82 83 67 97 C5' U A 4 OK OK 96 113 114 98 127 C5' G A 5 OK OK 126 146 147 128 161 C5' U A 6 OK OK 160 177 178 162 191 C5' U A 7 OK OK 190 207 208 192 221 C5' U A 8 OK OK 220 237 238 222 251 C5' A A 9 OK OK 250 269 270 252 284 C5' C A 10 OK OK 283 300 301 285 315 C5' C A 11 OK OK 314 331 332 316 346 C5' A A 12 OK OK 345 364 365 347 379 C5' G A 13 OK OK 378 398 399 380 413 C5' G A 14 OK OK 412 432 433 414 447 C5' U A 15 OK OK 446 463 464 448 477 C5' C A 16 OK OK 476 493 494 478 508 C5' A A 17 OK OK 507 526 527 509 541 C5' G A 18 OK OK 540 560 561 542 575 C5' G A 19 OK OK 574 594 595 576 609 C5' U A 20 OK OK 608 625 626 610 639 C5' C A 21 OK OK 638 655 656 640 670 C5' C A 22 OK OK 669 686 687 671 701 C5' G A 23 OK OK 700 720 721 702 735 C5' G A 24 OK OK 734 754 755 736 769 C5' A A 25 OK OK 768 787 788 770 802 C5' A A 26 OK OK 801 820 821 803 835 C5' G A 27 OK OK 834 854 855 836 869 C5' G A 28 OK OK 868 888 889 870 903 C5' A A 29 OK OK 902 921 922 904 936 C5' A A 30 OK OK 935 954 955 937 969 C5' G A 31 OK OK 968 988 989 970 1003 C5' C A 32 OK OK 1002 1019 1020 1004 1034 C5' A A 33 OK OK 1033 1052 1053 1035 1067 C5' G A 34 OK OK 1066 1086 1087 1068 1101 C5' C A 35 OK OK 1100 1117 1118 1102 1132 C5' C A 36 OK OK 1131 1148 1149 1133 1163 C5' A A 37 OK OK 1162 1181 1182 1164 1196 C5' A A 38 OK OK 1195 1214 1215 1197 1229 C5' G A 39 OK OK 1228 1248 1249 1230 1263 C5' G A 40 OK OK 1262 1282 1283 1264 1297 C5' C A 41 OK OK 1296 1313 1314 1298 1328 C5' A A 42 OK OK 1327 1346 1347 1329 1361 C5' G A 43 OK OK 1360 1380 1381 1362 1395 C5' A A 44 OK OK 1394 1413 1414 1396 1428 C5' G A 45 OK OK 1427 1447 1448 1429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 1 OK OK 2 3 4 32 P U A 2 distorted distorted 9 33 34 35 62 P C A 3 distorted distorted 40 63 64 65 93 P U A 4 distorted distorted 70 94 95 96 123 P G A 5 distorted distorted 101 124 125 126 157 P U A 6 distorted distorted 131 158 159 160 187 P U A 7 distorted distorted 165 188 189 190 217 P U A 8 distorted distorted 195 218 219 220 247 P A A 9 distorted distorted 225 248 249 250 280 P C A 10 distorted distorted 255 281 282 283 311 P C A 11 distorted distorted 288 312 313 314 342 P A A 12 distorted distorted 319 343 344 345 375 P G A 13 distorted distorted 350 376 377 378 409 P G A 14 distorted distorted 383 410 411 412 443 P U A 15 distorted distorted 417 444 445 446 473 P C A 16 distorted distorted 451 474 475 476 504 P A A 17 distorted distorted 481 505 506 507 537 P G A 18 distorted distorted 512 538 539 540 571 P G A 19 distorted distorted 545 572 573 574 605 P U A 20 distorted distorted 579 606 607 608 635 P C A 21 distorted distorted 613 636 637 638 666 P C A 22 distorted distorted 643 667 668 669 697 P G A 23 distorted distorted 674 698 699 700 731 P G A 24 distorted distorted 705 732 733 734 765 P A A 25 distorted distorted 739 766 767 768 798 P A A 26 distorted distorted 773 799 800 801 831 P G A 27 distorted distorted 806 832 833 834 865 P G A 28 distorted distorted 839 866 867 868 899 P A A 29 distorted distorted 873 900 901 902 932 P A A 30 distorted distorted 907 933 934 935 965 P G A 31 distorted distorted 940 966 967 968 999 P C A 32 distorted distorted 973 1000 1001 1002 1030 P A A 33 distorted distorted 1007 1031 1032 1033 1063 P G A 34 distorted distorted 1038 1064 1065 1066 1097 P C A 35 distorted distorted 1071 1098 1099 1100 1128 P C A 36 distorted distorted 1105 1129 1130 1131 1159 P A A 37 distorted distorted 1136 1160 1161 1162 1192 P A A 38 distorted distorted 1167 1193 1194 1195 1225 P G A 39 distorted distorted 1200 1226 1227 1228 1259 P G A 40 distorted distorted 1233 1260 1261 1262 1293 P C A 41 distorted distorted 1267 1294 1295 1296 1324 P A A 42 distorted distorted 1301 1325 1326 1327 1357 P G A 43 distorted distorted 1332 1358 1359 1360 1391 P A A 44 distorted distorted 1365 1392 1393 1394 1424 P G A 45 distorted distorted 1399 1425 1426 1427 ---------------------------------------------------------------------------------