ID code: '3R4F' 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' G A 2 beta 27 33 30 55 C1' C A 3 beta 50 56 53 75 C1' G A 4 beta 70 76 73 98 C1' U A 5 beta 93 99 96 118 C1' G A 6 beta 113 119 116 141 C1' U A 7 beta 136 142 139 161 C1' A A 8 beta 156 162 159 183 C1' U A 9 beta 178 184 181 203 C1' G A 10 beta 198 204 201 226 C1' U A 11 beta 221 227 224 246 C1' G A 12 beta 241 247 244 269 C1' G A 13 beta 264 270 267 292 C1' G A 14 beta 287 293 290 315 C1' G A 15 beta 310 316 313 338 C1' A A 16 beta 333 339 336 360 C1' A A 17 beta 355 361 358 382 C1' A A 18 beta 377 383 380 404 C1' C A 19 beta 399 405 402 424 C1' C A 20 beta 419 425 422 444 C1' C A 21 beta 439 445 442 464 C1' U A 22 beta 459 465 462 484 C1' G A 23 beta 479 485 482 507 C1' A A 24 beta 502 508 505 529 C1' U A 25 beta 524 530 527 549 C1' U A 26 beta 544 550 547 569 C1' G A 27 beta 564 570 567 592 C1' A A 28 beta 587 593 590 614 C1' G A 29 beta 609 615 612 637 C1' U A 30 beta 632 638 635 657 C1' U A 31 beta 652 658 655 677 C1' C A 32 beta 672 678 675 697 C1' A A 33 beta 692 698 695 719 C1' G A 34 beta 714 720 717 742 C1' C A 35 beta 737 743 740 762 C1' C A 36 beta 757 763 760 782 C1' C A 37 beta 777 783 780 802 C1' A A 38 beta 797 803 800 824 C1' C A 39 beta 819 825 822 844 C1' A A 40 beta 839 845 842 866 C1' U A 41 beta 861 867 864 886 C1' A A 42 beta 881 887 884 908 C1' C A 43 beta 903 909 906 928 C1' U A 44 beta 923 929 926 948 C1' U A 45 beta 943 949 946 968 C1' U A 46 beta 963 969 966 988 C1' G A 47 beta 983 989 986 1011 C1' U A 48 beta 1006 1012 1009 1031 C1' U A 49 beta 1026 1032 1029 1051 C1' G A 50 beta 1046 1052 1049 1074 C1' A A 51 beta 1069 1075 1072 1096 C1' U A 52 beta 1091 1097 1094 1116 C1' G A 53 beta 1111 1117 1114 1139 C1' G A 54 beta 1134 1140 1137 1162 C1' U A 55 beta 1157 1163 1160 1182 C1' U A 56 beta 1177 1183 1180 1202 C1' G A 57 beta 1197 1203 1200 1225 C1' U A 58 beta 1220 1226 1223 1245 C1' C A 59 beta 1240 1246 1243 1265 C1' A A 60 beta 1260 1266 1263 1287 C1' A A 61 beta 1282 1288 1285 1309 C1' U A 62 beta 1304 1310 1307 1329 C1' C A 63 beta 1324 1330 1327 1349 C1' G A 64 beta 1344 1350 1347 1372 C1' C A 65 beta 1367 1373 1370 1392 C1' C A 66 beta 1387 1393 1390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK 32 28 31 53 C2' C A 3 OK 55 51 54 73 C2' G A 4 OK 75 71 74 96 C2' U A 5 OK 98 94 97 116 C2' G A 6 OK 118 114 117 139 C2' U A 7 OK 141 137 140 159 C2' A A 8 OK 161 157 160 181 C2' U A 9 OK 183 179 182 201 C2' G A 10 OK 203 199 202 224 C2' U A 11 OK 226 222 225 244 C2' G A 12 OK 246 242 245 267 C2' G A 13 OK 269 265 268 290 C2' G A 14 OK 292 288 291 313 C2' G A 15 OK 315 311 314 336 C2' A A 16 OK 338 334 337 358 C2' A A 17 OK 360 356 359 380 C2' A A 18 OK 382 378 381 402 C2' C A 19 OK 404 400 403 422 C2' C A 20 OK 424 420 423 442 C2' C A 21 OK 444 440 443 462 C2' U A 22 OK 464 460 463 482 C2' G A 23 OK 484 480 483 505 C2' A A 24 OK 507 503 506 527 C2' U A 25 OK 529 525 528 547 C2' U A 26 OK 549 545 548 567 C2' G A 27 OK 569 565 568 590 C2' A A 28 OK 592 588 591 612 C2' G A 29 OK 614 610 613 635 C2' U A 30 OK 637 633 636 655 C2' U A 31 OK 657 653 656 675 C2' C A 32 OK 677 673 676 695 C2' A A 33 OK 697 693 696 717 C2' G A 34 OK 719 715 718 740 C2' C A 35 OK 742 738 741 760 C2' C A 36 OK 762 758 761 780 C2' C A 37 OK 782 778 781 800 C2' A A 38 OK 802 798 801 822 C2' C A 39 OK 824 820 823 842 C2' A A 40 OK 844 840 843 864 C2' U A 41 OK 866 862 865 884 C2' A A 42 OK 886 882 885 906 C2' C A 43 OK 908 904 907 926 C2' U A 44 OK 928 924 927 946 C2' U A 45 OK 948 944 947 966 C2' U A 46 OK 968 964 967 986 C2' G A 47 OK 988 984 987 1009 C2' U A 48 OK 1011 1007 1010 1029 C2' U A 49 OK 1031 1027 1030 1049 C2' G A 50 OK 1051 1047 1050 1072 C2' A A 51 OK 1074 1070 1073 1094 C2' U A 52 OK 1096 1092 1095 1114 C2' G A 53 OK 1116 1112 1115 1137 C2' G A 54 OK 1139 1135 1138 1160 C2' U A 55 OK 1162 1158 1161 1180 C2' U A 56 OK 1182 1178 1181 1200 C2' G A 57 OK 1202 1198 1201 1223 C2' U A 58 OK 1225 1221 1224 1243 C2' C A 59 OK 1245 1241 1244 1263 C2' A A 60 OK 1265 1261 1264 1285 C2' A A 61 OK 1287 1283 1286 1307 C2' U A 62 OK 1309 1305 1308 1327 C2' C A 63 OK 1329 1325 1328 1347 C2' G A 64 OK 1349 1345 1348 1370 C2' C A 65 OK 1372 1368 1371 1390 C2' C A 66 OK 1392 1388 1391 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' C A 3 OK 49 52 53 71 C3' G A 4 OK 69 72 73 94 C3' U A 5 OK 92 95 96 114 C3' G A 6 OK 112 115 116 137 C3' U A 7 OK 135 138 139 157 C3' A A 8 OK 155 158 159 179 C3' U A 9 OK 177 180 181 199 C3' G A 10 OK 197 200 201 222 C3' U A 11 OK 220 223 224 242 C3' G A 12 OK 240 243 244 265 C3' G A 13 OK 263 266 267 288 C3' G A 14 OK 286 289 290 311 C3' G A 15 OK 309 312 313 334 C3' A A 16 OK 332 335 336 356 C3' A A 17 OK 354 357 358 378 C3' A A 18 OK 376 379 380 400 C3' C A 19 OK 398 401 402 420 C3' C A 20 OK 418 421 422 440 C3' C A 21 OK 438 441 442 460 C3' U A 22 OK 458 461 462 480 C3' G A 23 OK 478 481 482 503 C3' A A 24 OK 501 504 505 525 C3' U A 25 OK 523 526 527 545 C3' U A 26 OK 543 546 547 565 C3' G A 27 OK 563 566 567 588 C3' A A 28 OK 586 589 590 610 C3' G A 29 OK 608 611 612 633 C3' U A 30 OK 631 634 635 653 C3' U A 31 OK 651 654 655 673 C3' C A 32 OK 671 674 675 693 C3' A A 33 OK 691 694 695 715 C3' G A 34 OK 713 716 717 738 C3' C A 35 OK 736 739 740 758 C3' C A 36 OK 756 759 760 778 C3' C A 37 OK 776 779 780 798 C3' A A 38 OK 796 799 800 820 C3' C A 39 OK 818 821 822 840 C3' A A 40 OK 838 841 842 862 C3' U A 41 OK 860 863 864 882 C3' A A 42 OK 880 883 884 904 C3' C A 43 OK 902 905 906 924 C3' U A 44 OK 922 925 926 944 C3' U A 45 OK 942 945 946 964 C3' U A 46 OK 962 965 966 984 C3' G A 47 OK 982 985 986 1007 C3' U A 48 OK 1005 1008 1009 1027 C3' U A 49 OK 1025 1028 1029 1047 C3' G A 50 OK 1045 1048 1049 1070 C3' A A 51 OK 1068 1071 1072 1092 C3' U A 52 OK 1090 1093 1094 1112 C3' G A 53 OK 1110 1113 1114 1135 C3' G A 54 OK 1133 1136 1137 1158 C3' U A 55 OK 1156 1159 1160 1178 C3' U A 56 OK 1176 1179 1180 1198 C3' G A 57 OK 1196 1199 1200 1221 C3' U A 58 OK 1219 1222 1223 1241 C3' C A 59 OK 1239 1242 1243 1261 C3' A A 60 OK 1259 1262 1263 1283 C3' A A 61 OK 1281 1284 1285 1305 C3' U A 62 OK 1303 1306 1307 1325 C3' C A 63 OK 1323 1326 1327 1345 C3' G A 64 OK 1343 1346 1347 1368 C3' C A 65 OK 1366 1369 1370 1388 C3' C A 66 OK 1386 1389 1390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' C A 3 OK 51 48 50 69 C4' G A 4 OK 71 68 70 92 C4' U A 5 OK 94 91 93 112 C4' G A 6 OK 114 111 113 135 C4' U A 7 OK 137 134 136 155 C4' A A 8 OK 157 154 156 177 C4' U A 9 OK 179 176 178 197 C4' G A 10 OK 199 196 198 220 C4' U A 11 OK 222 219 221 240 C4' G A 12 OK 242 239 241 263 C4' G A 13 OK 265 262 264 286 C4' G A 14 OK 288 285 287 309 C4' G A 15 OK 311 308 310 332 C4' A A 16 OK 334 331 333 354 C4' A A 17 OK 356 353 355 376 C4' A A 18 OK 378 375 377 398 C4' C A 19 OK 400 397 399 418 C4' C A 20 OK 420 417 419 438 C4' C A 21 OK 440 437 439 458 C4' U A 22 OK 460 457 459 478 C4' G A 23 OK 480 477 479 501 C4' A A 24 OK 503 500 502 523 C4' U A 25 OK 525 522 524 543 C4' U A 26 OK 545 542 544 563 C4' G A 27 OK 565 562 564 586 C4' A A 28 OK 588 585 587 608 C4' G A 29 OK 610 607 609 631 C4' U A 30 OK 633 630 632 651 C4' U A 31 OK 653 650 652 671 C4' C A 32 OK 673 670 672 691 C4' A A 33 OK 693 690 692 713 C4' G A 34 OK 715 712 714 736 C4' C A 35 OK 738 735 737 756 C4' C A 36 OK 758 755 757 776 C4' C A 37 OK 778 775 777 796 C4' A A 38 OK 798 795 797 818 C4' C A 39 OK 820 817 819 838 C4' A A 40 OK 840 837 839 860 C4' U A 41 OK 862 859 861 880 C4' A A 42 OK 882 879 881 902 C4' C A 43 OK 904 901 903 922 C4' U A 44 OK 924 921 923 942 C4' U A 45 OK 944 941 943 962 C4' U A 46 OK 964 961 963 982 C4' G A 47 OK 984 981 983 1005 C4' U A 48 OK 1007 1004 1006 1025 C4' U A 49 OK 1027 1024 1026 1045 C4' G A 50 OK 1047 1044 1046 1068 C4' A A 51 OK 1070 1067 1069 1090 C4' U A 52 OK 1092 1089 1091 1110 C4' G A 53 OK 1112 1109 1111 1133 C4' G A 54 OK 1135 1132 1134 1156 C4' U A 55 OK 1158 1155 1157 1176 C4' U A 56 OK 1178 1175 1177 1196 C4' G A 57 OK 1198 1195 1197 1219 C4' U A 58 OK 1221 1218 1220 1239 C4' C A 59 OK 1241 1238 1240 1259 C4' A A 60 OK 1261 1258 1260 1281 C4' A A 61 OK 1283 1280 1282 1303 C4' U A 62 OK 1305 1302 1304 1323 C4' C A 63 OK 1325 1322 1324 1343 C4' G A 64 OK 1345 1342 1344 1366 C4' C A 65 OK 1368 1365 1367 1386 C4' C A 66 OK 1388 1385 1387 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' C A 3 47 49 68 C5' G A 4 67 69 91 C5' U A 5 90 92 111 C5' G A 6 110 112 134 C5' U A 7 133 135 154 C5' A A 8 153 155 176 C5' U A 9 175 177 196 C5' G A 10 195 197 219 C5' U A 11 218 220 239 C5' G A 12 238 240 262 C5' G A 13 261 263 285 C5' G A 14 284 286 308 C5' G A 15 307 309 331 C5' A A 16 330 332 353 C5' A A 17 352 354 375 C5' A A 18 374 376 397 C5' C A 19 396 398 417 C5' C A 20 416 418 437 C5' C A 21 436 438 457 C5' U A 22 456 458 477 C5' G A 23 476 478 500 C5' A A 24 499 501 522 C5' U A 25 521 523 542 C5' U A 26 541 543 562 C5' G A 27 561 563 585 C5' A A 28 584 586 607 C5' G A 29 606 608 630 C5' U A 30 629 631 650 C5' U A 31 649 651 670 C5' C A 32 669 671 690 C5' A A 33 689 691 712 C5' G A 34 711 713 735 C5' C A 35 734 736 755 C5' C A 36 754 756 775 C5' C A 37 774 776 795 C5' A A 38 794 796 817 C5' C A 39 816 818 837 C5' A A 40 836 838 859 C5' U A 41 858 860 879 C5' A A 42 878 880 901 C5' C A 43 900 902 921 C5' U A 44 920 922 941 C5' U A 45 940 942 961 C5' U A 46 960 962 981 C5' G A 47 980 982 1004 C5' U A 48 1003 1005 1024 C5' U A 49 1023 1025 1044 C5' G A 50 1043 1045 1067 C5' A A 51 1066 1068 1089 C5' U A 52 1088 1090 1109 C5' G A 53 1108 1110 1132 C5' G A 54 1131 1133 1155 C5' U A 55 1154 1156 1175 C5' U A 56 1174 1176 1195 C5' G A 57 1194 1196 1218 C5' U A 58 1217 1219 1238 C5' C A 59 1237 1239 1258 C5' A A 60 1257 1259 1280 C5' A A 61 1279 1281 1302 C5' U A 62 1301 1303 1322 C5' C A 63 1321 1323 1342 C5' G A 64 1341 1343 1365 C5' C A 65 1364 1366 1385 C5' C A 66 1384 1386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P C A 3 distorted distorted 29 45 46 47 64 P G A 4 distorted distorted 52 65 66 67 87 P U A 5 distorted distorted 72 88 89 90 107 P G A 6 distorted distorted 95 108 109 110 130 P U A 7 distorted distorted 115 131 132 133 150 P A A 8 distorted distorted 138 151 152 153 172 P U A 9 distorted distorted 158 173 174 175 192 P G A 10 distorted distorted 180 193 194 195 215 P U A 11 distorted distorted 200 216 217 218 235 P G A 12 distorted distorted 223 236 237 238 258 P G A 13 distorted distorted 243 259 260 261 281 P G A 14 distorted distorted 266 282 283 284 304 P G A 15 distorted distorted 289 305 306 307 327 P A A 16 distorted distorted 312 328 329 330 349 P A A 17 distorted distorted 335 350 351 352 371 P A A 18 distorted distorted 357 372 373 374 393 P C A 19 distorted distorted 379 394 395 396 413 P C A 20 distorted distorted 401 414 415 416 433 P C A 21 distorted distorted 421 434 435 436 453 P U A 22 distorted distorted 441 454 455 456 473 P G A 23 distorted distorted 461 474 475 476 496 P A A 24 distorted distorted 481 497 498 499 518 P U A 25 distorted distorted 504 519 520 521 538 P U A 26 distorted distorted 526 539 540 541 558 P G A 27 distorted distorted 546 559 560 561 581 P A A 28 distorted distorted 566 582 583 584 603 P G A 29 distorted distorted 589 604 605 606 626 P U A 30 distorted distorted 611 627 628 629 646 P U A 31 distorted distorted 634 647 648 649 666 P C A 32 distorted distorted 654 667 668 669 686 P A A 33 distorted distorted 674 687 688 689 708 P G A 34 distorted distorted 694 709 710 711 731 P C A 35 distorted distorted 716 732 733 734 751 P C A 36 distorted distorted 739 752 753 754 771 P C A 37 distorted distorted 759 772 773 774 791 P A A 38 distorted distorted 779 792 793 794 813 P C A 39 distorted distorted 799 814 815 816 833 P A A 40 distorted distorted 821 834 835 836 855 P U A 41 distorted distorted 841 856 857 858 875 P A A 42 distorted distorted 863 876 877 878 897 P C A 43 distorted distorted 883 898 899 900 917 P U A 44 distorted distorted 905 918 919 920 937 P U A 45 distorted distorted 925 938 939 940 957 P U A 46 distorted distorted 945 958 959 960 977 P G A 47 distorted distorted 965 978 979 980 1000 P U A 48 distorted distorted 985 1001 1002 1003 1020 P U A 49 distorted distorted 1008 1021 1022 1023 1040 P G A 50 distorted distorted 1028 1041 1042 1043 1063 P A A 51 distorted distorted 1048 1064 1065 1066 1085 P U A 52 distorted distorted 1071 1086 1087 1088 1105 P G A 53 distorted distorted 1093 1106 1107 1108 1128 P G A 54 distorted distorted 1113 1129 1130 1131 1151 P U A 55 distorted distorted 1136 1152 1153 1154 1171 P U A 56 distorted distorted 1159 1172 1173 1174 1191 P G A 57 distorted distorted 1179 1192 1193 1194 1214 P U A 58 distorted distorted 1199 1215 1216 1217 1234 P C A 59 distorted distorted 1222 1235 1236 1237 1254 P A A 60 distorted distorted 1242 1255 1256 1257 1276 P A A 61 distorted distorted 1262 1277 1278 1279 1298 P U A 62 distorted distorted 1284 1299 1300 1301 1318 P C A 63 distorted distorted 1306 1319 1320 1321 1338 P G A 64 distorted distorted 1326 1339 1340 1341 1361 P C A 65 distorted distorted 1346 1362 1363 1364 1381 P C A 66 distorted distorted 1369 1382 1383 1384 ---------------------------------------------------------------------------------