ID code: '1Z2J' 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' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' G A 6 alpha beta 173 196 179 176 212 C1' A A 7 alpha beta 207 229 213 210 245 C1' U A 8 alpha beta 240 260 246 243 275 C1' C A 9 alpha beta 270 290 276 273 306 C1' U A 10 alpha beta 301 321 307 304 336 C1' G A 11 alpha beta 331 354 337 334 370 C1' G A 12 alpha beta 365 388 371 368 404 C1' C A 13 alpha beta 399 419 405 402 435 C1' C A 14 alpha beta 430 450 436 433 466 C1' U A 15 alpha beta 461 481 467 464 496 C1' U A 16 alpha beta 491 511 497 494 526 C1' C A 17 alpha beta 521 541 527 524 557 C1' C A 18 alpha beta 552 572 558 555 588 C1' C A 19 alpha beta 583 603 589 586 619 C1' A A 20 alpha beta 614 636 620 617 652 C1' C A 21 alpha beta 647 667 653 650 683 C1' A A 22 alpha beta 678 700 684 681 716 C1' A A 23 alpha beta 711 733 717 714 749 C1' G A 24 alpha beta 744 767 750 747 783 C1' G A 25 alpha beta 778 801 784 781 817 C1' G A 26 alpha beta 812 835 818 815 851 C1' A A 27 alpha beta 846 868 852 849 884 C1' A A 28 alpha beta 879 901 885 882 917 C1' G A 29 alpha beta 912 935 918 915 951 C1' G A 30 alpha beta 946 969 952 949 985 C1' C A 31 alpha beta 980 1000 986 983 1016 C1' C A 32 alpha beta 1011 1031 1017 1014 1047 C1' A A 33 alpha beta 1042 1064 1048 1045 1080 C1' G A 34 alpha beta 1075 1098 1081 1078 1114 C1' G A 35 alpha beta 1109 1132 1115 1112 1148 C1' G A 36 alpha beta 1143 1166 1149 1146 1182 C1' A A 37 alpha beta 1177 1199 1183 1180 1215 C1' A A 38 alpha beta 1210 1232 1216 1213 1248 C1' U A 39 alpha beta 1243 1263 1249 1246 1278 C1' C A 40 alpha beta 1273 1293 1279 1276 1309 C1' U A 41 alpha beta 1304 1324 1310 1307 1339 C1' U A 42 alpha beta 1334 1354 1340 1337 1369 C1' C A 43 alpha beta 1364 1384 1370 1367 1400 C1' C A 44 alpha beta 1395 1415 1401 1398 1431 C1' C A 45 alpha beta 1426 1447 1432 1429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' A A 5 OK OK 145 141 160 144 176 C2' G A 6 OK OK 178 174 194 177 210 C2' A A 7 OK OK 212 208 227 211 243 C2' U A 8 OK OK 245 241 258 244 273 C2' C A 9 OK OK 275 271 288 274 304 C2' U A 10 OK OK 306 302 319 305 334 C2' G A 11 OK OK 336 332 352 335 368 C2' G A 12 OK OK 370 366 386 369 402 C2' C A 13 OK OK 404 400 417 403 433 C2' C A 14 OK OK 435 431 448 434 464 C2' U A 15 OK OK 466 462 479 465 494 C2' U A 16 OK OK 496 492 509 495 524 C2' C A 17 OK OK 526 522 539 525 555 C2' C A 18 OK OK 557 553 570 556 586 C2' C A 19 OK OK 588 584 601 587 617 C2' A A 20 OK OK 619 615 634 618 650 C2' C A 21 OK OK 652 648 665 651 681 C2' A A 22 OK OK 683 679 698 682 714 C2' A A 23 OK OK 716 712 731 715 747 C2' G A 24 OK OK 749 745 765 748 781 C2' G A 25 OK OK 783 779 799 782 815 C2' G A 26 OK OK 817 813 833 816 849 C2' A A 27 OK OK 851 847 866 850 882 C2' A A 28 OK OK 884 880 899 883 915 C2' G A 29 OK OK 917 913 933 916 949 C2' G A 30 OK OK 951 947 967 950 983 C2' C A 31 OK OK 985 981 998 984 1014 C2' C A 32 OK OK 1016 1012 1029 1015 1045 C2' A A 33 OK OK 1047 1043 1062 1046 1078 C2' G A 34 OK OK 1080 1076 1096 1079 1112 C2' G A 35 OK OK 1114 1110 1130 1113 1146 C2' G A 36 OK OK 1148 1144 1164 1147 1180 C2' A A 37 OK OK 1182 1178 1197 1181 1213 C2' A A 38 OK OK 1215 1211 1230 1214 1246 C2' U A 39 OK OK 1248 1244 1261 1247 1276 C2' C A 40 OK OK 1278 1274 1291 1277 1307 C2' U A 41 OK OK 1309 1305 1322 1308 1337 C2' U A 42 OK OK 1339 1335 1352 1338 1367 C2' C A 43 OK OK 1369 1365 1382 1368 1398 C2' C A 44 OK OK 1400 1396 1413 1399 1429 C2' C A 45 OK OK 1431 1427 1445 1430 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' A A 5 OK OK 139 159 142 143 174 C3' G A 6 OK OK 172 193 175 176 208 C3' A A 7 OK OK 206 226 209 210 241 C3' U A 8 OK OK 239 257 242 243 271 C3' C A 9 OK OK 269 287 272 273 302 C3' U A 10 OK OK 300 318 303 304 332 C3' G A 11 OK OK 330 351 333 334 366 C3' G A 12 OK OK 364 385 367 368 400 C3' C A 13 OK OK 398 416 401 402 431 C3' C A 14 OK OK 429 447 432 433 462 C3' U A 15 OK OK 460 478 463 464 492 C3' U A 16 OK OK 490 508 493 494 522 C3' C A 17 OK OK 520 538 523 524 553 C3' C A 18 OK OK 551 569 554 555 584 C3' C A 19 OK OK 582 600 585 586 615 C3' A A 20 OK OK 613 633 616 617 648 C3' C A 21 OK OK 646 664 649 650 679 C3' A A 22 OK OK 677 697 680 681 712 C3' A A 23 OK OK 710 730 713 714 745 C3' G A 24 OK OK 743 764 746 747 779 C3' G A 25 OK OK 777 798 780 781 813 C3' G A 26 OK OK 811 832 814 815 847 C3' A A 27 OK OK 845 865 848 849 880 C3' A A 28 OK OK 878 898 881 882 913 C3' G A 29 OK OK 911 932 914 915 947 C3' G A 30 OK OK 945 966 948 949 981 C3' C A 31 OK OK 979 997 982 983 1012 C3' C A 32 OK OK 1010 1028 1013 1014 1043 C3' A A 33 OK OK 1041 1061 1044 1045 1076 C3' G A 34 OK OK 1074 1095 1077 1078 1110 C3' G A 35 OK OK 1108 1129 1111 1112 1144 C3' G A 36 OK OK 1142 1163 1145 1146 1178 C3' A A 37 OK OK 1176 1196 1179 1180 1211 C3' A A 38 OK OK 1209 1229 1212 1213 1244 C3' U A 39 OK OK 1242 1260 1245 1246 1274 C3' C A 40 OK OK 1272 1290 1275 1276 1305 C3' U A 41 OK OK 1303 1321 1306 1307 1335 C3' U A 42 OK OK 1333 1351 1336 1337 1365 C3' C A 43 OK OK 1363 1381 1366 1367 1396 C3' C A 44 OK OK 1394 1412 1397 1398 1427 C3' C A 45 OK OK 1425 1443 1428 1429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' A A 5 OK OK 141 158 138 140 172 C4' G A 6 OK OK 174 192 171 173 206 C4' A A 7 OK OK 208 225 205 207 239 C4' U A 8 OK OK 241 256 238 240 269 C4' C A 9 OK OK 271 286 268 270 300 C4' U A 10 OK OK 302 317 299 301 330 C4' G A 11 OK OK 332 350 329 331 364 C4' G A 12 OK OK 366 384 363 365 398 C4' C A 13 OK OK 400 415 397 399 429 C4' C A 14 OK OK 431 446 428 430 460 C4' U A 15 OK OK 462 477 459 461 490 C4' U A 16 OK OK 492 507 489 491 520 C4' C A 17 OK OK 522 537 519 521 551 C4' C A 18 OK OK 553 568 550 552 582 C4' C A 19 OK OK 584 599 581 583 613 C4' A A 20 OK OK 615 632 612 614 646 C4' C A 21 OK OK 648 663 645 647 677 C4' A A 22 OK OK 679 696 676 678 710 C4' A A 23 OK OK 712 729 709 711 743 C4' G A 24 OK OK 745 763 742 744 777 C4' G A 25 OK OK 779 797 776 778 811 C4' G A 26 OK OK 813 831 810 812 845 C4' A A 27 OK OK 847 864 844 846 878 C4' A A 28 OK OK 880 897 877 879 911 C4' G A 29 OK OK 913 931 910 912 945 C4' G A 30 OK OK 947 965 944 946 979 C4' C A 31 OK OK 981 996 978 980 1010 C4' C A 32 OK OK 1012 1027 1009 1011 1041 C4' A A 33 OK OK 1043 1060 1040 1042 1074 C4' G A 34 OK OK 1076 1094 1073 1075 1108 C4' G A 35 OK OK 1110 1128 1107 1109 1142 C4' G A 36 OK OK 1144 1162 1141 1143 1176 C4' A A 37 OK OK 1178 1195 1175 1177 1209 C4' A A 38 OK OK 1211 1228 1208 1210 1242 C4' U A 39 OK OK 1244 1259 1241 1243 1272 C4' C A 40 OK OK 1274 1289 1271 1273 1303 C4' U A 41 OK OK 1305 1320 1302 1304 1333 C4' U A 42 OK OK 1335 1350 1332 1334 1363 C4' C A 43 OK OK 1365 1380 1362 1364 1394 C4' C A 44 OK OK 1396 1411 1393 1395 1425 C4' C A 45 OK OK 1427 1442 1424 1426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' A A 5 OK OK 137 156 157 139 171 C5' G A 6 OK OK 170 190 191 172 205 C5' A A 7 OK OK 204 223 224 206 238 C5' U A 8 OK OK 237 254 255 239 268 C5' C A 9 OK OK 267 284 285 269 299 C5' U A 10 OK OK 298 315 316 300 329 C5' G A 11 OK OK 328 348 349 330 363 C5' G A 12 OK OK 362 382 383 364 397 C5' C A 13 OK OK 396 413 414 398 428 C5' C A 14 OK OK 427 444 445 429 459 C5' U A 15 OK OK 458 475 476 460 489 C5' U A 16 OK OK 488 505 506 490 519 C5' C A 17 OK OK 518 535 536 520 550 C5' C A 18 OK OK 549 566 567 551 581 C5' C A 19 OK OK 580 597 598 582 612 C5' A A 20 OK OK 611 630 631 613 645 C5' C A 21 OK OK 644 661 662 646 676 C5' A A 22 OK OK 675 694 695 677 709 C5' A A 23 OK OK 708 727 728 710 742 C5' G A 24 OK OK 741 761 762 743 776 C5' G A 25 OK OK 775 795 796 777 810 C5' G A 26 OK OK 809 829 830 811 844 C5' A A 27 OK OK 843 862 863 845 877 C5' A A 28 OK OK 876 895 896 878 910 C5' G A 29 OK OK 909 929 930 911 944 C5' G A 30 OK OK 943 963 964 945 978 C5' C A 31 OK OK 977 994 995 979 1009 C5' C A 32 OK OK 1008 1025 1026 1010 1040 C5' A A 33 OK OK 1039 1058 1059 1041 1073 C5' G A 34 OK OK 1072 1092 1093 1074 1107 C5' G A 35 OK OK 1106 1126 1127 1108 1141 C5' G A 36 OK OK 1140 1160 1161 1142 1175 C5' A A 37 OK OK 1174 1193 1194 1176 1208 C5' A A 38 OK OK 1207 1226 1227 1209 1241 C5' U A 39 OK OK 1240 1257 1258 1242 1271 C5' C A 40 OK OK 1270 1287 1288 1272 1302 C5' U A 41 OK OK 1301 1318 1319 1303 1332 C5' U A 42 OK OK 1331 1348 1349 1333 1362 C5' C A 43 OK OK 1361 1378 1379 1363 1393 C5' C A 44 OK OK 1392 1409 1410 1394 1424 C5' C A 45 OK OK 1423 1440 1441 1425 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P A A 5 distorted distorted 109 135 136 137 167 P G A 6 distorted distorted 142 168 169 170 201 P A A 7 distorted distorted 175 202 203 204 234 P U A 8 distorted distorted 209 235 236 237 264 P C A 9 distorted distorted 242 265 266 267 295 P U A 10 distorted distorted 272 296 297 298 325 P G A 11 distorted distorted 303 326 327 328 359 P G A 12 distorted distorted 333 360 361 362 393 P C A 13 distorted distorted 367 394 395 396 424 P C A 14 distorted distorted 401 425 426 427 455 P U A 15 distorted distorted 432 456 457 458 485 P U A 16 distorted distorted 463 486 487 488 515 P C A 17 distorted distorted 493 516 517 518 546 P C A 18 distorted distorted 523 547 548 549 577 P C A 19 distorted distorted 554 578 579 580 608 P A A 20 distorted distorted 585 609 610 611 641 P C A 21 distorted distorted 616 642 643 644 672 P A A 22 distorted distorted 649 673 674 675 705 P A A 23 distorted distorted 680 706 707 708 738 P G A 24 distorted distorted 713 739 740 741 772 P G A 25 distorted distorted 746 773 774 775 806 P G A 26 distorted distorted 780 807 808 809 840 P A A 27 distorted distorted 814 841 842 843 873 P A A 28 distorted distorted 848 874 875 876 906 P G A 29 distorted distorted 881 907 908 909 940 P G A 30 distorted distorted 914 941 942 943 974 P C A 31 distorted distorted 948 975 976 977 1005 P C A 32 distorted distorted 982 1006 1007 1008 1036 P A A 33 distorted distorted 1013 1037 1038 1039 1069 P G A 34 distorted distorted 1044 1070 1071 1072 1103 P G A 35 distorted distorted 1077 1104 1105 1106 1137 P G A 36 distorted distorted 1111 1138 1139 1140 1171 P A A 37 distorted distorted 1145 1172 1173 1174 1204 P A A 38 distorted distorted 1179 1205 1206 1207 1237 P U A 39 distorted distorted 1212 1238 1239 1240 1267 P C A 40 distorted distorted 1245 1268 1269 1270 1298 P U A 41 distorted distorted 1275 1299 1300 1301 1328 P U A 42 distorted distorted 1306 1329 1330 1331 1358 P C A 43 distorted distorted 1336 1359 1360 1361 1389 P C A 44 distorted distorted 1366 1390 1391 1392 1420 P C A 45 distorted distorted 1397 1421 1422 1423 ---------------------------------------------------------------------------------