ID code: '5C7U' 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' G B 15 beta 7 13 10 35 C1' G B 16 beta 30 36 33 58 C1' A B 17 beta 53 59 56 80 C1' C B 18 beta 75 81 78 100 C1' A B 19 beta 95 101 98 122 C1' U B 20 beta 117 123 120 142 C1' A B 21 beta 137 143 140 164 C1' U B 22 beta 159 165 162 184 C1' A B 23 beta 179 185 182 206 C1' A B 24 beta 201 207 204 228 C1' U B 25 beta 223 229 226 248 C1' C B 26 beta 243 249 246 268 C1' G B 27 beta 263 269 266 291 C1' C B 28 beta 286 292 289 311 C1' G B 29 beta 306 312 309 334 C1' U B 30 beta 329 335 332 354 C1' G B 31 beta 349 355 352 377 C1' G B 32 beta 372 378 375 400 C1' A B 33 beta 395 401 398 422 C1' U B 34 beta 417 423 420 442 C1' A B 35 beta 437 443 440 464 C1' U B 36 beta 459 465 462 484 C1' G B 37 beta 479 485 482 507 C1' G B 38 beta 502 508 505 530 C1' C B 39 beta 525 531 528 550 C1' A B 40 beta 545 551 548 572 C1' C B 41 beta 567 573 570 592 C1' G B 42 beta 587 593 590 615 C1' C B 43 beta 610 616 613 635 C1' A B 44 beta 630 636 633 657 C1' A B 45 beta 652 658 655 679 C1' G B 46 beta 674 680 677 702 C1' U B 47 beta 697 703 700 722 C1' U B 48 beta 717 723 720 742 C1' U B 49 beta 737 743 740 762 C1' C B 50 beta 757 763 760 782 C1' U B 51 beta 777 783 780 802 C1' A B 52 beta 797 803 800 824 C1' C B 53 beta 819 825 822 844 C1' C B 54 beta 839 845 842 864 C1' G B 55 beta 859 865 862 887 C1' G B 56 beta 882 888 885 910 C1' G B 57 beta 905 911 908 933 C1' C B 58 beta 928 934 931 953 C1' A B 59 beta 948 954 951 975 C1' C B 60 beta 970 976 973 995 C1' C B 61 beta 990 996 993 1015 C1' G B 62 beta 1010 1016 1013 1038 C1' U B 63 beta 1033 1039 1036 1058 C1' A B 64 beta 1053 1059 1056 1080 C1' A B 65 beta 1075 1081 1078 1102 C1' A B 66 beta 1097 1103 1100 1124 C1' U B 67 beta 1119 1125 1122 1144 C1' G B 68 beta 1139 1145 1142 1167 C1' U B 69 beta 1162 1168 1165 1187 C1' C B 70 beta 1182 1188 1185 1207 C1' C B 71 beta 1202 1208 1205 1227 C1' G B 72 beta 1222 1228 1225 1250 C1' A B 73 beta 1245 1251 1248 1272 C1' C B 74 beta 1267 1273 1270 1292 C1' U B 75 beta 1287 1293 1290 1312 C1' A B 76 beta 1307 1313 1310 1334 C1' U B 77 beta 1329 1335 1332 1354 C1' G B 78 beta 1349 1355 1352 1377 C1' U B 79 beta 1372 1378 1375 1397 C1' C B 80 beta 1392 1398 1395 1417 C1' C B 81 beta 1412 1418 1415 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 15 OK 12 8 11 33 C2' G B 16 OK 35 31 34 56 C2' A B 17 OK 58 54 57 78 C2' C B 18 OK 80 76 79 98 C2' A B 19 OK 100 96 99 120 C2' U B 20 OK 122 118 121 140 C2' A B 21 OK 142 138 141 162 C2' U B 22 OK 164 160 163 182 C2' A B 23 OK 184 180 183 204 C2' A B 24 OK 206 202 205 226 C2' U B 25 OK 228 224 227 246 C2' C B 26 OK 248 244 247 266 C2' G B 27 OK 268 264 267 289 C2' C B 28 OK 291 287 290 309 C2' G B 29 OK 311 307 310 332 C2' U B 30 OK 334 330 333 352 C2' G B 31 OK 354 350 353 375 C2' G B 32 OK 377 373 376 398 C2' A B 33 OK 400 396 399 420 C2' U B 34 OK 422 418 421 440 C2' A B 35 OK 442 438 441 462 C2' U B 36 OK 464 460 463 482 C2' G B 37 OK 484 480 483 505 C2' G B 38 OK 507 503 506 528 C2' C B 39 OK 530 526 529 548 C2' A B 40 OK 550 546 549 570 C2' C B 41 OK 572 568 571 590 C2' G B 42 OK 592 588 591 613 C2' C B 43 OK 615 611 614 633 C2' A B 44 OK 635 631 634 655 C2' A B 45 OK 657 653 656 677 C2' G B 46 OK 679 675 678 700 C2' U B 47 OK 702 698 701 720 C2' U B 48 OK 722 718 721 740 C2' U B 49 OK 742 738 741 760 C2' C B 50 OK 762 758 761 780 C2' U B 51 OK 782 778 781 800 C2' A B 52 OK 802 798 801 822 C2' C B 53 OK 824 820 823 842 C2' C B 54 OK 844 840 843 862 C2' G B 55 OK 864 860 863 885 C2' G B 56 OK 887 883 886 908 C2' G B 57 OK 910 906 909 931 C2' C B 58 OK 933 929 932 951 C2' A B 59 OK 953 949 952 973 C2' C B 60 OK 975 971 974 993 C2' C B 61 OK 995 991 994 1013 C2' G B 62 OK 1015 1011 1014 1036 C2' U B 63 OK 1038 1034 1037 1056 C2' A B 64 OK 1058 1054 1057 1078 C2' A B 65 OK 1080 1076 1079 1100 C2' A B 66 OK 1102 1098 1101 1122 C2' U B 67 OK 1124 1120 1123 1142 C2' G B 68 OK 1144 1140 1143 1165 C2' U B 69 OK 1167 1163 1166 1185 C2' C B 70 OK 1187 1183 1186 1205 C2' C B 71 OK 1207 1203 1206 1225 C2' G B 72 OK 1227 1223 1226 1248 C2' A B 73 OK 1250 1246 1249 1270 C2' C B 74 OK 1272 1268 1271 1290 C2' U B 75 OK 1292 1288 1291 1310 C2' A B 76 OK 1312 1308 1311 1332 C2' U B 77 OK 1334 1330 1333 1352 C2' G B 78 OK 1354 1350 1353 1375 C2' U B 79 OK 1377 1373 1376 1395 C2' C B 80 OK 1397 1393 1396 1415 C2' C B 81 OK 1417 1413 1416 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 15 OK 6 9 10 31 C3' G B 16 OK 29 32 33 54 C3' A B 17 OK 52 55 56 76 C3' C B 18 OK 74 77 78 96 C3' A B 19 OK 94 97 98 118 C3' U B 20 OK 116 119 120 138 C3' A B 21 OK 136 139 140 160 C3' U B 22 OK 158 161 162 180 C3' A B 23 OK 178 181 182 202 C3' A B 24 OK 200 203 204 224 C3' U B 25 OK 222 225 226 244 C3' C B 26 OK 242 245 246 264 C3' G B 27 OK 262 265 266 287 C3' C B 28 OK 285 288 289 307 C3' G B 29 OK 305 308 309 330 C3' U B 30 OK 328 331 332 350 C3' G B 31 OK 348 351 352 373 C3' G B 32 OK 371 374 375 396 C3' A B 33 OK 394 397 398 418 C3' U B 34 OK 416 419 420 438 C3' A B 35 OK 436 439 440 460 C3' U B 36 OK 458 461 462 480 C3' G B 37 OK 478 481 482 503 C3' G B 38 OK 501 504 505 526 C3' C B 39 OK 524 527 528 546 C3' A B 40 OK 544 547 548 568 C3' C B 41 OK 566 569 570 588 C3' G B 42 OK 586 589 590 611 C3' C B 43 OK 609 612 613 631 C3' A B 44 OK 629 632 633 653 C3' A B 45 OK 651 654 655 675 C3' G B 46 OK 673 676 677 698 C3' U B 47 OK 696 699 700 718 C3' U B 48 OK 716 719 720 738 C3' U B 49 OK 736 739 740 758 C3' C B 50 OK 756 759 760 778 C3' U B 51 OK 776 779 780 798 C3' A B 52 OK 796 799 800 820 C3' C B 53 OK 818 821 822 840 C3' C B 54 OK 838 841 842 860 C3' G B 55 OK 858 861 862 883 C3' G B 56 OK 881 884 885 906 C3' G B 57 OK 904 907 908 929 C3' C B 58 OK 927 930 931 949 C3' A B 59 OK 947 950 951 971 C3' C B 60 OK 969 972 973 991 C3' C B 61 OK 989 992 993 1011 C3' G B 62 OK 1009 1012 1013 1034 C3' U B 63 OK 1032 1035 1036 1054 C3' A B 64 OK 1052 1055 1056 1076 C3' A B 65 OK 1074 1077 1078 1098 C3' A B 66 OK 1096 1099 1100 1120 C3' U B 67 OK 1118 1121 1122 1140 C3' G B 68 OK 1138 1141 1142 1163 C3' U B 69 OK 1161 1164 1165 1183 C3' C B 70 OK 1181 1184 1185 1203 C3' C B 71 OK 1201 1204 1205 1223 C3' G B 72 OK 1221 1224 1225 1246 C3' A B 73 OK 1244 1247 1248 1268 C3' C B 74 OK 1266 1269 1270 1288 C3' U B 75 OK 1286 1289 1290 1308 C3' A B 76 OK 1306 1309 1310 1330 C3' U B 77 OK 1328 1331 1332 1350 C3' G B 78 OK 1348 1351 1352 1373 C3' U B 79 OK 1371 1374 1375 1393 C3' C B 80 OK 1391 1394 1395 1413 C3' C B 81 OK 1411 1414 1415 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 15 OK 8 5 7 29 C4' G B 16 OK 31 28 30 52 C4' A B 17 OK 54 51 53 74 C4' C B 18 OK 76 73 75 94 C4' A B 19 OK 96 93 95 116 C4' U B 20 OK 118 115 117 136 C4' A B 21 OK 138 135 137 158 C4' U B 22 OK 160 157 159 178 C4' A B 23 OK 180 177 179 200 C4' A B 24 OK 202 199 201 222 C4' U B 25 OK 224 221 223 242 C4' C B 26 OK 244 241 243 262 C4' G B 27 OK 264 261 263 285 C4' C B 28 OK 287 284 286 305 C4' G B 29 OK 307 304 306 328 C4' U B 30 OK 330 327 329 348 C4' G B 31 OK 350 347 349 371 C4' G B 32 OK 373 370 372 394 C4' A B 33 OK 396 393 395 416 C4' U B 34 OK 418 415 417 436 C4' A B 35 OK 438 435 437 458 C4' U B 36 OK 460 457 459 478 C4' G B 37 OK 480 477 479 501 C4' G B 38 OK 503 500 502 524 C4' C B 39 OK 526 523 525 544 C4' A B 40 OK 546 543 545 566 C4' C B 41 OK 568 565 567 586 C4' G B 42 OK 588 585 587 609 C4' C B 43 OK 611 608 610 629 C4' A B 44 OK 631 628 630 651 C4' A B 45 OK 653 650 652 673 C4' G B 46 OK 675 672 674 696 C4' U B 47 OK 698 695 697 716 C4' U B 48 OK 718 715 717 736 C4' U B 49 OK 738 735 737 756 C4' C B 50 OK 758 755 757 776 C4' U B 51 OK 778 775 777 796 C4' A B 52 OK 798 795 797 818 C4' C B 53 OK 820 817 819 838 C4' C B 54 OK 840 837 839 858 C4' G B 55 OK 860 857 859 881 C4' G B 56 OK 883 880 882 904 C4' G B 57 OK 906 903 905 927 C4' C B 58 OK 929 926 928 947 C4' A B 59 OK 949 946 948 969 C4' C B 60 OK 971 968 970 989 C4' C B 61 OK 991 988 990 1009 C4' G B 62 OK 1011 1008 1010 1032 C4' U B 63 OK 1034 1031 1033 1052 C4' A B 64 OK 1054 1051 1053 1074 C4' A B 65 OK 1076 1073 1075 1096 C4' A B 66 OK 1098 1095 1097 1118 C4' U B 67 OK 1120 1117 1119 1138 C4' G B 68 OK 1140 1137 1139 1161 C4' U B 69 OK 1163 1160 1162 1181 C4' C B 70 OK 1183 1180 1182 1201 C4' C B 71 OK 1203 1200 1202 1221 C4' G B 72 OK 1223 1220 1222 1244 C4' A B 73 OK 1246 1243 1245 1266 C4' C B 74 OK 1268 1265 1267 1286 C4' U B 75 OK 1288 1285 1287 1306 C4' A B 76 OK 1308 1305 1307 1328 C4' U B 77 OK 1330 1327 1329 1348 C4' G B 78 OK 1350 1347 1349 1371 C4' U B 79 OK 1373 1370 1372 1391 C4' C B 80 OK 1393 1390 1392 1411 C4' C B 81 OK 1413 1410 1412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 15 4 6 28 C5' G B 16 27 29 51 C5' A B 17 50 52 73 C5' C B 18 72 74 93 C5' A B 19 92 94 115 C5' U B 20 114 116 135 C5' A B 21 134 136 157 C5' U B 22 156 158 177 C5' A B 23 176 178 199 C5' A B 24 198 200 221 C5' U B 25 220 222 241 C5' C B 26 240 242 261 C5' G B 27 260 262 284 C5' C B 28 283 285 304 C5' G B 29 303 305 327 C5' U B 30 326 328 347 C5' G B 31 346 348 370 C5' G B 32 369 371 393 C5' A B 33 392 394 415 C5' U B 34 414 416 435 C5' A B 35 434 436 457 C5' U B 36 456 458 477 C5' G B 37 476 478 500 C5' G B 38 499 501 523 C5' C B 39 522 524 543 C5' A B 40 542 544 565 C5' C B 41 564 566 585 C5' G B 42 584 586 608 C5' C B 43 607 609 628 C5' A B 44 627 629 650 C5' A B 45 649 651 672 C5' G B 46 671 673 695 C5' U B 47 694 696 715 C5' U B 48 714 716 735 C5' U B 49 734 736 755 C5' C B 50 754 756 775 C5' U B 51 774 776 795 C5' A B 52 794 796 817 C5' C B 53 816 818 837 C5' C B 54 836 838 857 C5' G B 55 856 858 880 C5' G B 56 879 881 903 C5' G B 57 902 904 926 C5' C B 58 925 927 946 C5' A B 59 945 947 968 C5' C B 60 967 969 988 C5' C B 61 987 989 1008 C5' G B 62 1007 1009 1031 C5' U B 63 1030 1032 1051 C5' A B 64 1050 1052 1073 C5' A B 65 1072 1074 1095 C5' A B 66 1094 1096 1117 C5' U B 67 1116 1118 1137 C5' G B 68 1136 1138 1160 C5' U B 69 1159 1161 1180 C5' C B 70 1179 1181 1200 C5' C B 71 1199 1201 1220 C5' G B 72 1219 1221 1243 C5' A B 73 1242 1244 1265 C5' C B 74 1264 1266 1285 C5' U B 75 1284 1286 1305 C5' A B 76 1304 1306 1327 C5' U B 77 1326 1328 1347 C5' G B 78 1346 1348 1370 C5' U B 79 1369 1371 1390 C5' C B 80 1389 1391 1410 C5' C B 81 1409 1411 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 15 distorted distorted 2 3 4 24 P G B 16 distorted distorted 9 25 26 27 47 P A B 17 distorted distorted 32 48 49 50 69 P C B 18 distorted distorted 55 70 71 72 89 P A B 19 distorted distorted 77 90 91 92 111 P U B 20 distorted distorted 97 112 113 114 131 P A B 21 distorted distorted 119 132 133 134 153 P U B 22 distorted distorted 139 154 155 156 173 P A B 23 distorted distorted 161 174 175 176 195 P A B 24 distorted distorted 181 196 197 198 217 P U B 25 distorted distorted 203 218 219 220 237 P C B 26 distorted distorted 225 238 239 240 257 P G B 27 distorted distorted 245 258 259 260 280 P C B 28 distorted distorted 265 281 282 283 300 P G B 29 distorted distorted 288 301 302 303 323 P U B 30 distorted distorted 308 324 325 326 343 P G B 31 distorted distorted 331 344 345 346 366 P G B 32 distorted distorted 351 367 368 369 389 P A B 33 distorted distorted 374 390 391 392 411 P U B 34 distorted distorted 397 412 413 414 431 P A B 35 distorted distorted 419 432 433 434 453 P U B 36 distorted distorted 439 454 455 456 473 P G B 37 distorted distorted 461 474 475 476 496 P G B 38 distorted distorted 481 497 498 499 519 P C B 39 distorted distorted 504 520 521 522 539 P A B 40 distorted distorted 527 540 541 542 561 P C B 41 distorted distorted 547 562 563 564 581 P G B 42 distorted distorted 569 582 583 584 604 P C B 43 distorted distorted 589 605 606 607 624 P A B 44 distorted distorted 612 625 626 627 646 P A B 45 distorted distorted 632 647 648 649 668 P G B 46 distorted distorted 654 669 670 671 691 P U B 47 distorted distorted 676 692 693 694 711 P U B 48 distorted distorted 699 712 713 714 731 P U B 49 distorted distorted 719 732 733 734 751 P C B 50 distorted distorted 739 752 753 754 771 P U B 51 distorted distorted 759 772 773 774 791 P A B 52 distorted distorted 779 792 793 794 813 P C B 53 distorted distorted 799 814 815 816 833 P C B 54 distorted distorted 821 834 835 836 853 P G B 55 distorted distorted 841 854 855 856 876 P G B 56 distorted distorted 861 877 878 879 899 P G B 57 distorted distorted 884 900 901 902 922 P C B 58 distorted distorted 907 923 924 925 942 P A B 59 distorted distorted 930 943 944 945 964 P C B 60 distorted distorted 950 965 966 967 984 P C B 61 distorted distorted 972 985 986 987 1004 P G B 62 distorted distorted 992 1005 1006 1007 1027 P U B 63 distorted distorted 1012 1028 1029 1030 1047 P A B 64 distorted distorted 1035 1048 1049 1050 1069 P A B 65 distorted distorted 1055 1070 1071 1072 1091 P A B 66 distorted distorted 1077 1092 1093 1094 1113 P U B 67 distorted distorted 1099 1114 1115 1116 1133 P G B 68 distorted distorted 1121 1134 1135 1136 1156 P U B 69 distorted distorted 1141 1157 1158 1159 1176 P C B 70 distorted distorted 1164 1177 1178 1179 1196 P C B 71 distorted distorted 1184 1197 1198 1199 1216 P G B 72 distorted distorted 1204 1217 1218 1219 1239 P A B 73 distorted distorted 1224 1240 1241 1242 1261 P C B 74 distorted distorted 1247 1262 1263 1264 1281 P U B 75 distorted distorted 1269 1282 1283 1284 1301 P A B 76 distorted distorted 1289 1302 1303 1304 1323 P U B 77 distorted distorted 1309 1324 1325 1326 1343 P G B 78 distorted distorted 1331 1344 1345 1346 1366 P U B 79 distorted distorted 1351 1367 1368 1369 1386 P C B 80 distorted distorted 1374 1387 1388 1389 1406 P C B 81 distorted distorted 1394 1407 1408 1409 ---------------------------------------------------------------------------------