ID code: '1VFG' 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' --------------------------------------------------------------------------------- 13 C1' G C 1 beta 8 14 11 36 C1' G C 2 beta 31 37 34 59 C1' C C 3 beta 54 60 57 79 C1' C C 4 beta 74 80 77 99 C1' A C 5 beta 94 100 97 121 C1' G C 6 beta 116 122 119 144 C1' G C 7 beta 139 145 142 167 C1' G C 49 beta 162 168 165 190 C1' G C 50 beta 185 191 188 213 C1' C C 51 beta 208 214 211 233 C1' G C 52 beta 228 234 231 256 C1' G C 53 beta 251 257 254 279 C1' U C 54 beta 274 280 277 299 C1' U C 55 beta 294 300 297 319 C1' C C 56 beta 314 320 317 339 C1' G C 57 beta 334 340 337 362 C1' A C 58 beta 357 363 360 384 C1' U C 59 beta 379 385 382 404 C1' U C 60 beta 399 405 402 424 C1' C C 61 beta 419 425 422 444 C1' C C 62 beta 439 445 442 464 C1' G C 63 beta 459 465 462 487 C1' C C 64 beta 482 488 485 507 C1' C C 65 beta 502 508 505 527 C1' C C 66 beta 522 528 525 547 C1' C C 67 beta 542 548 545 567 C1' U C 68 beta 562 568 565 587 C1' G C 69 beta 582 588 585 610 C1' G C 70 beta 605 611 608 633 C1' C C 71 beta 628 634 631 653 C1' C C 72 beta 648 654 651 675 C1' G D 1 beta 670 676 673 698 C1' G D 2 beta 693 699 696 721 C1' C D 3 beta 716 722 719 741 C1' C D 4 beta 736 742 739 761 C1' A D 5 beta 756 762 759 783 C1' G D 6 beta 778 784 781 806 C1' G D 7 beta 801 807 804 829 C1' G D 49 beta 824 830 827 852 C1' G D 50 beta 847 853 850 875 C1' C D 51 beta 870 876 873 895 C1' G D 52 beta 890 896 893 918 C1' G D 53 beta 913 919 916 941 C1' U D 54 beta 936 942 939 961 C1' U D 55 beta 956 962 959 981 C1' C D 56 beta 976 982 979 1001 C1' G D 57 beta 996 1002 999 1024 C1' A D 58 beta 1019 1025 1022 1046 C1' U D 59 beta 1041 1047 1044 1066 C1' U D 60 beta 1061 1067 1064 1086 C1' C D 61 beta 1081 1087 1084 1106 C1' C D 62 beta 1101 1107 1104 1126 C1' G D 63 beta 1121 1127 1124 1149 C1' C D 64 beta 1144 1150 1147 1169 C1' C D 65 beta 1164 1170 1167 1189 C1' C D 66 beta 1184 1190 1187 1209 C1' C D 67 beta 1204 1210 1207 1229 C1' U D 68 beta 1224 1230 1227 1249 C1' G D 69 beta 1244 1250 1247 1272 C1' G D 70 beta 1267 1273 1270 1295 C1' C D 71 beta 1290 1296 1293 1315 C1' C D 72 beta 1310 1316 1313 1335 C1' A D 73 beta 1330 1336 1333 1357 C1' C D 74 beta 1352 1358 1355 1377 C1' C D 75 beta 1372 1378 1375 7203 C1' APC A 500 beta 7198 7204 7201 7234 C1' APC B1500 beta 7229 7235 7232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G C 1 OK 13 9 12 34 C2' G C 2 OK 36 32 35 57 C2' C C 3 OK 59 55 58 77 C2' C C 4 OK 79 75 78 97 C2' A C 5 OK 99 95 98 119 C2' G C 6 OK 121 117 120 142 C2' G C 7 OK 144 140 143 165 C2' G C 49 OK 167 163 166 188 C2' G C 50 OK 190 186 189 211 C2' C C 51 OK 213 209 212 231 C2' G C 52 OK 233 229 232 254 C2' G C 53 OK 256 252 255 277 C2' U C 54 OK 279 275 278 297 C2' U C 55 OK 299 295 298 317 C2' C C 56 OK 319 315 318 337 C2' G C 57 OK 339 335 338 360 C2' A C 58 OK 362 358 361 382 C2' U C 59 OK 384 380 383 402 C2' U C 60 OK 404 400 403 422 C2' C C 61 OK 424 420 423 442 C2' C C 62 OK 444 440 443 462 C2' G C 63 OK 464 460 463 485 C2' C C 64 OK 487 483 486 505 C2' C C 65 OK 507 503 506 525 C2' C C 66 OK 527 523 526 545 C2' C C 67 OK 547 543 546 565 C2' U C 68 OK 567 563 566 585 C2' G C 69 OK 587 583 586 608 C2' G C 70 OK 610 606 609 631 C2' C C 71 OK 633 629 632 651 C2' C C 72 OK 653 649 652 673 C2' G D 1 OK 675 671 674 696 C2' G D 2 OK 698 694 697 719 C2' C D 3 OK 721 717 720 739 C2' C D 4 OK 741 737 740 759 C2' A D 5 OK 761 757 760 781 C2' G D 6 OK 783 779 782 804 C2' G D 7 OK 806 802 805 827 C2' G D 49 OK 829 825 828 850 C2' G D 50 OK 852 848 851 873 C2' C D 51 OK 875 871 874 893 C2' G D 52 OK 895 891 894 916 C2' G D 53 OK 918 914 917 939 C2' U D 54 OK 941 937 940 959 C2' U D 55 OK 961 957 960 979 C2' C D 56 OK 981 977 980 999 C2' G D 57 OK 1001 997 1000 1022 C2' A D 58 OK 1024 1020 1023 1044 C2' U D 59 OK 1046 1042 1045 1064 C2' U D 60 OK 1066 1062 1065 1084 C2' C D 61 OK 1086 1082 1085 1104 C2' C D 62 OK 1106 1102 1105 1124 C2' G D 63 OK 1126 1122 1125 1147 C2' C D 64 OK 1149 1145 1148 1167 C2' C D 65 OK 1169 1165 1168 1187 C2' C D 66 OK 1189 1185 1188 1207 C2' C D 67 OK 1209 1205 1208 1227 C2' U D 68 OK 1229 1225 1228 1247 C2' G D 69 OK 1249 1245 1248 1270 C2' G D 70 OK 1272 1268 1271 1293 C2' C D 71 OK 1295 1291 1294 1313 C2' C D 72 OK 1315 1311 1314 1333 C2' A D 73 OK 1335 1331 1334 1355 C2' C D 74 OK 1357 1353 1356 1375 C2' C D 75 OK 1377 1373 1376 7201 C2' APC A 500 OK 7203 7199 7202 7232 C2' APC B1500 OK 7234 7230 7233 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G C 1 OK 7 10 11 32 C3' G C 2 OK 30 33 34 55 C3' C C 3 OK 53 56 57 75 C3' C C 4 OK 73 76 77 95 C3' A C 5 OK 93 96 97 117 C3' G C 6 OK 115 118 119 140 C3' G C 7 OK 138 141 142 163 C3' G C 49 OK 161 164 165 186 C3' G C 50 OK 184 187 188 209 C3' C C 51 OK 207 210 211 229 C3' G C 52 OK 227 230 231 252 C3' G C 53 OK 250 253 254 275 C3' U C 54 OK 273 276 277 295 C3' U C 55 OK 293 296 297 315 C3' C C 56 OK 313 316 317 335 C3' G C 57 OK 333 336 337 358 C3' A C 58 OK 356 359 360 380 C3' U C 59 OK 378 381 382 400 C3' U C 60 OK 398 401 402 420 C3' C C 61 OK 418 421 422 440 C3' C C 62 OK 438 441 442 460 C3' G C 63 OK 458 461 462 483 C3' C C 64 OK 481 484 485 503 C3' C C 65 OK 501 504 505 523 C3' C C 66 OK 521 524 525 543 C3' C C 67 OK 541 544 545 563 C3' U C 68 OK 561 564 565 583 C3' G C 69 OK 581 584 585 606 C3' G C 70 OK 604 607 608 629 C3' C C 71 OK 627 630 631 649 C3' C C 72 OK 647 650 651 671 C3' G D 1 OK 669 672 673 694 C3' G D 2 OK 692 695 696 717 C3' C D 3 OK 715 718 719 737 C3' C D 4 OK 735 738 739 757 C3' A D 5 OK 755 758 759 779 C3' G D 6 OK 777 780 781 802 C3' G D 7 OK 800 803 804 825 C3' G D 49 OK 823 826 827 848 C3' G D 50 OK 846 849 850 871 C3' C D 51 OK 869 872 873 891 C3' G D 52 OK 889 892 893 914 C3' G D 53 OK 912 915 916 937 C3' U D 54 OK 935 938 939 957 C3' U D 55 OK 955 958 959 977 C3' C D 56 OK 975 978 979 997 C3' G D 57 OK 995 998 999 1020 C3' A D 58 OK 1018 1021 1022 1042 C3' U D 59 OK 1040 1043 1044 1062 C3' U D 60 OK 1060 1063 1064 1082 C3' C D 61 OK 1080 1083 1084 1102 C3' C D 62 OK 1100 1103 1104 1122 C3' G D 63 OK 1120 1123 1124 1145 C3' C D 64 OK 1143 1146 1147 1165 C3' C D 65 OK 1163 1166 1167 1185 C3' C D 66 OK 1183 1186 1187 1205 C3' C D 67 OK 1203 1206 1207 1225 C3' U D 68 OK 1223 1226 1227 1245 C3' G D 69 OK 1243 1246 1247 1268 C3' G D 70 OK 1266 1269 1270 1291 C3' C D 71 OK 1289 1292 1293 1311 C3' C D 72 OK 1309 1312 1313 1331 C3' A D 73 OK 1329 1332 1333 1353 C3' C D 74 OK 1351 1354 1355 1373 C3' C D 75 OK 1371 1374 1375 7199 C3' APC A 500 OK 7197 7200 7201 7230 C3' APC B1500 OK 7228 7231 7232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G C 1 OK 9 6 8 30 C4' G C 2 OK 32 29 31 53 C4' C C 3 OK 55 52 54 73 C4' C C 4 OK 75 72 74 93 C4' A C 5 OK 95 92 94 115 C4' G C 6 OK 117 114 116 138 C4' G C 7 OK 140 137 139 161 C4' G C 49 OK 163 160 162 184 C4' G C 50 OK 186 183 185 207 C4' C C 51 OK 209 206 208 227 C4' G C 52 OK 229 226 228 250 C4' G C 53 OK 252 249 251 273 C4' U C 54 OK 275 272 274 293 C4' U C 55 OK 295 292 294 313 C4' C C 56 OK 315 312 314 333 C4' G C 57 OK 335 332 334 356 C4' A C 58 OK 358 355 357 378 C4' U C 59 OK 380 377 379 398 C4' U C 60 OK 400 397 399 418 C4' C C 61 OK 420 417 419 438 C4' C C 62 OK 440 437 439 458 C4' G C 63 OK 460 457 459 481 C4' C C 64 OK 483 480 482 501 C4' C C 65 OK 503 500 502 521 C4' C C 66 OK 523 520 522 541 C4' C C 67 OK 543 540 542 561 C4' U C 68 OK 563 560 562 581 C4' G C 69 OK 583 580 582 604 C4' G C 70 OK 606 603 605 627 C4' C C 71 OK 629 626 628 647 C4' C C 72 OK 649 646 648 669 C4' G D 1 OK 671 668 670 692 C4' G D 2 OK 694 691 693 715 C4' C D 3 OK 717 714 716 735 C4' C D 4 OK 737 734 736 755 C4' A D 5 OK 757 754 756 777 C4' G D 6 OK 779 776 778 800 C4' G D 7 OK 802 799 801 823 C4' G D 49 OK 825 822 824 846 C4' G D 50 OK 848 845 847 869 C4' C D 51 OK 871 868 870 889 C4' G D 52 OK 891 888 890 912 C4' G D 53 OK 914 911 913 935 C4' U D 54 OK 937 934 936 955 C4' U D 55 OK 957 954 956 975 C4' C D 56 OK 977 974 976 995 C4' G D 57 OK 997 994 996 1018 C4' A D 58 OK 1020 1017 1019 1040 C4' U D 59 OK 1042 1039 1041 1060 C4' U D 60 OK 1062 1059 1061 1080 C4' C D 61 OK 1082 1079 1081 1100 C4' C D 62 OK 1102 1099 1101 1120 C4' G D 63 OK 1122 1119 1121 1143 C4' C D 64 OK 1145 1142 1144 1163 C4' C D 65 OK 1165 1162 1164 1183 C4' C D 66 OK 1185 1182 1184 1203 C4' C D 67 OK 1205 1202 1204 1223 C4' U D 68 OK 1225 1222 1224 1243 C4' G D 69 OK 1245 1242 1244 1266 C4' G D 70 OK 1268 1265 1267 1289 C4' C D 71 OK 1291 1288 1290 1309 C4' C D 72 OK 1311 1308 1310 1329 C4' A D 73 OK 1331 1328 1330 1351 C4' C D 74 OK 1353 1350 1352 1371 C4' C D 75 OK 1373 1370 1372 7197 C4' APC A 500 OK 7199 7196 7198 7228 C4' APC B1500 OK 7230 7227 7229 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G C 1 5 7 29 C5' G C 2 28 30 52 C5' C C 3 51 53 72 C5' C C 4 71 73 92 C5' A C 5 91 93 114 C5' G C 6 113 115 137 C5' G C 7 136 138 160 C5' G C 49 159 161 183 C5' G C 50 182 184 206 C5' C C 51 205 207 226 C5' G C 52 225 227 249 C5' G C 53 248 250 272 C5' U C 54 271 273 292 C5' U C 55 291 293 312 C5' C C 56 311 313 332 C5' G C 57 331 333 355 C5' A C 58 354 356 377 C5' U C 59 376 378 397 C5' U C 60 396 398 417 C5' C C 61 416 418 437 C5' C C 62 436 438 457 C5' G C 63 456 458 480 C5' C C 64 479 481 500 C5' C C 65 499 501 520 C5' C C 66 519 521 540 C5' C C 67 539 541 560 C5' U C 68 559 561 580 C5' G C 69 579 581 603 C5' G C 70 602 604 626 C5' C C 71 625 627 646 C5' C C 72 645 647 668 C5' G D 1 667 669 691 C5' G D 2 690 692 714 C5' C D 3 713 715 734 C5' C D 4 733 735 754 C5' A D 5 753 755 776 C5' G D 6 775 777 799 C5' G D 7 798 800 822 C5' G D 49 821 823 845 C5' G D 50 844 846 868 C5' C D 51 867 869 888 C5' G D 52 887 889 911 C5' G D 53 910 912 934 C5' U D 54 933 935 954 C5' U D 55 953 955 974 C5' C D 56 973 975 994 C5' G D 57 993 995 1017 C5' A D 58 1016 1018 1039 C5' U D 59 1038 1040 1059 C5' U D 60 1058 1060 1079 C5' C D 61 1078 1080 1099 C5' C D 62 1098 1100 1119 C5' G D 63 1118 1120 1142 C5' C D 64 1141 1143 1162 C5' C D 65 1161 1163 1182 C5' C D 66 1181 1183 1202 C5' C D 67 1201 1203 1222 C5' U D 68 1221 1223 1242 C5' G D 69 1241 1243 1265 C5' G D 70 1264 1266 1288 C5' C D 71 1287 1289 1308 C5' C D 72 1307 1309 1328 C5' A D 73 1327 1329 1350 C5' C D 74 1349 1351 1370 C5' C D 75 1369 1371 7196 C5' APC A 500 7195 7197 7227 C5' APC B1500 7226 7228 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G C 1 distorted distorted 3 4 5 25 P G C 2 distorted distorted 10 26 27 28 48 P C C 3 distorted distorted 33 49 50 51 68 P C C 4 distorted distorted 56 69 70 71 88 P A C 5 distorted distorted 76 89 90 91 110 P G C 6 distorted distorted 96 111 112 113 133 P G C 7 distorted distorted 118 134 135 136 156 P G C 49 OK OK 157 158 159 179 P G C 50 distorted distorted 164 180 181 182 202 P C C 51 distorted distorted 187 203 204 205 222 P G C 52 distorted distorted 210 223 224 225 245 P G C 53 distorted distorted 230 246 247 248 268 P U C 54 distorted distorted 253 269 270 271 288 P U C 55 distorted distorted 276 289 290 291 308 P C C 56 distorted distorted 296 309 310 311 328 P G C 57 distorted distorted 316 329 330 331 351 P A C 58 distorted distorted 336 352 353 354 373 P U C 59 distorted distorted 359 374 375 376 393 P U C 60 distorted distorted 381 394 395 396 413 P C C 61 distorted distorted 401 414 415 416 433 P C C 62 distorted distorted 421 434 435 436 453 P G C 63 distorted distorted 441 454 455 456 476 P C C 64 distorted distorted 461 477 478 479 496 P C C 65 distorted distorted 484 497 498 499 516 P C C 66 distorted distorted 504 517 518 519 536 P C C 67 distorted distorted 524 537 538 539 556 P U C 68 distorted distorted 544 557 558 559 576 P G C 69 distorted distorted 564 577 578 579 599 P G C 70 distorted distorted 584 600 601 602 622 P C C 71 distorted distorted 607 623 624 625 642 P C C 72 distorted distorted 630 643 644 645 664 P G D 1 distorted distorted 665 666 667 687 P G D 2 distorted distorted 672 688 689 690 710 P C D 3 distorted distorted 695 711 712 713 730 P C D 4 distorted distorted 718 731 732 733 750 P A D 5 distorted distorted 738 751 752 753 772 P G D 6 distorted distorted 758 773 774 775 795 P G D 7 distorted distorted 780 796 797 798 818 P G D 49 OK OK 819 820 821 841 P G D 50 distorted distorted 826 842 843 844 864 P C D 51 distorted distorted 849 865 866 867 884 P G D 52 distorted distorted 872 885 886 887 907 P G D 53 distorted distorted 892 908 909 910 930 P U D 54 distorted distorted 915 931 932 933 950 P U D 55 distorted distorted 938 951 952 953 970 P C D 56 distorted distorted 958 971 972 973 990 P G D 57 distorted distorted 978 991 992 993 1013 P A D 58 distorted distorted 998 1014 1015 1016 1035 P U D 59 distorted distorted 1021 1036 1037 1038 1055 P U D 60 distorted distorted 1043 1056 1057 1058 1075 P C D 61 distorted distorted 1063 1076 1077 1078 1095 P C D 62 distorted distorted 1083 1096 1097 1098 1115 P G D 63 distorted distorted 1103 1116 1117 1118 1138 P C D 64 distorted distorted 1123 1139 1140 1141 1158 P C D 65 distorted distorted 1146 1159 1160 1161 1178 P C D 66 distorted distorted 1166 1179 1180 1181 1198 P C D 67 distorted distorted 1186 1199 1200 1201 1218 P U D 68 distorted distorted 1206 1219 1220 1221 1238 P G D 69 distorted distorted 1226 1239 1240 1241 1261 P G D 70 distorted distorted 1246 1262 1263 1264 1284 P C D 71 distorted distorted 1269 1285 1286 1287 1304 P C D 72 distorted distorted 1292 1305 1306 1307 1324 P A D 73 distorted distorted 1312 1325 1326 1327 1346 P C D 74 distorted distorted 1332 1347 1348 1349 1366 P C D 75 distorted distorted 1354 1367 1368 1369 ---------------------------------------------------------------------------------