ID code: '5VJB' 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' C A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' G A 4 beta 70 76 73 98 C1' G A 5 beta 93 99 96 121 C1' G A 6 beta 116 122 119 144 C1' A A 7 beta 139 145 142 166 C1' C A 8 beta 161 167 164 186 C1' G A 9 beta 181 187 184 209 C1' A A 10 beta 204 210 207 231 C1' C A 11 beta 226 232 229 251 C1' C A 12 beta 246 252 249 271 C1' C A 13 beta 266 272 269 291 C1' 5BU A 14 beta 286 292 289 312 C1' G A 15 beta 307 313 310 335 C1' C A 16 beta 330 336 333 353 C1' G B 1 beta 348 354 351 376 C1' C B 2 beta 371 377 374 396 C1' G B 3 beta 391 397 394 419 C1' G B 4 beta 414 420 417 442 C1' G B 5 beta 437 443 440 465 C1' G B 6 beta 460 466 463 488 C1' A B 7 beta 483 489 486 510 C1' C B 8 beta 505 511 508 530 C1' G B 9 beta 525 531 528 553 C1' A B 10 beta 548 554 551 575 C1' C B 11 beta 570 576 573 595 C1' C B 12 beta 590 596 593 615 C1' C B 13 beta 610 616 613 635 C1' 5BU B 14 beta 630 636 633 656 C1' G B 15 beta 651 657 654 679 C1' C B 16 beta 674 680 677 697 C1' G C 1 beta 692 698 695 720 C1' C C 2 beta 715 721 718 740 C1' G C 3 beta 735 741 738 763 C1' G C 4 beta 758 764 761 786 C1' G C 5 beta 781 787 784 809 C1' G C 6 beta 804 810 807 832 C1' A C 7 beta 827 833 830 854 C1' C C 8 beta 849 855 852 874 C1' G C 9 beta 869 875 872 897 C1' A C 10 beta 892 898 895 919 C1' C C 11 beta 914 920 917 939 C1' C C 12 beta 934 940 937 959 C1' C C 13 beta 954 960 957 979 C1' 5BU C 14 beta 974 980 977 1000 C1' G C 15 beta 995 1001 998 1023 C1' C C 16 beta 1018 1024 1021 1041 C1' G D 1 beta 1036 1042 1039 1064 C1' C D 2 beta 1059 1065 1062 1084 C1' G D 3 beta 1079 1085 1082 1107 C1' G D 4 beta 1102 1108 1105 1130 C1' G D 5 beta 1125 1131 1128 1153 C1' G D 6 beta 1148 1154 1151 1176 C1' A D 7 beta 1171 1177 1174 1198 C1' C D 8 beta 1193 1199 1196 1218 C1' G D 9 beta 1213 1219 1216 1241 C1' A D 10 beta 1236 1242 1239 1263 C1' C D 11 beta 1258 1264 1261 1283 C1' C D 12 beta 1278 1284 1281 1303 C1' C D 13 beta 1298 1304 1301 1323 C1' 5BU D 14 beta 1318 1324 1321 1344 C1' G D 15 beta 1339 1345 1342 1367 C1' C D 16 beta 1362 1368 1365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' G A 4 OK 75 71 74 96 C2' G A 5 OK 98 94 97 119 C2' G A 6 OK 121 117 120 142 C2' A A 7 OK 144 140 143 164 C2' C A 8 OK 166 162 165 184 C2' G A 9 OK 186 182 185 207 C2' A A 10 OK 209 205 208 229 C2' C A 11 OK 231 227 230 249 C2' C A 12 OK 251 247 250 269 C2' C A 13 OK 271 267 270 289 C2' 5BU A 14 OK 291 287 290 310 C2' G A 15 OK 312 308 311 333 C2' C A 16 OK 335 331 334 351 C2' G B 1 OK 353 349 352 374 C2' C B 2 OK 376 372 375 394 C2' G B 3 OK 396 392 395 417 C2' G B 4 OK 419 415 418 440 C2' G B 5 OK 442 438 441 463 C2' G B 6 OK 465 461 464 486 C2' A B 7 OK 488 484 487 508 C2' C B 8 OK 510 506 509 528 C2' G B 9 OK 530 526 529 551 C2' A B 10 OK 553 549 552 573 C2' C B 11 OK 575 571 574 593 C2' C B 12 OK 595 591 594 613 C2' C B 13 OK 615 611 614 633 C2' 5BU B 14 OK 635 631 634 654 C2' G B 15 OK 656 652 655 677 C2' C B 16 OK 679 675 678 695 C2' G C 1 OK 697 693 696 718 C2' C C 2 OK 720 716 719 738 C2' G C 3 OK 740 736 739 761 C2' G C 4 OK 763 759 762 784 C2' G C 5 OK 786 782 785 807 C2' G C 6 OK 809 805 808 830 C2' A C 7 OK 832 828 831 852 C2' C C 8 OK 854 850 853 872 C2' G C 9 OK 874 870 873 895 C2' A C 10 OK 897 893 896 917 C2' C C 11 OK 919 915 918 937 C2' C C 12 OK 939 935 938 957 C2' C C 13 OK 959 955 958 977 C2' 5BU C 14 OK 979 975 978 998 C2' G C 15 OK 1000 996 999 1021 C2' C C 16 OK 1023 1019 1022 1039 C2' G D 1 OK 1041 1037 1040 1062 C2' C D 2 OK 1064 1060 1063 1082 C2' G D 3 OK 1084 1080 1083 1105 C2' G D 4 OK 1107 1103 1106 1128 C2' G D 5 OK 1130 1126 1129 1151 C2' G D 6 OK 1153 1149 1152 1174 C2' A D 7 OK 1176 1172 1175 1196 C2' C D 8 OK 1198 1194 1197 1216 C2' G D 9 OK 1218 1214 1217 1239 C2' A D 10 OK 1241 1237 1240 1261 C2' C D 11 OK 1263 1259 1262 1281 C2' C D 12 OK 1283 1279 1282 1301 C2' C D 13 OK 1303 1299 1302 1321 C2' 5BU D 14 OK 1323 1319 1322 1342 C2' G D 15 OK 1344 1340 1343 1365 C2' C D 16 OK 1367 1363 1366 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' G A 4 OK 69 72 73 94 C3' G A 5 OK 92 95 96 117 C3' G A 6 OK 115 118 119 140 C3' A A 7 OK 138 141 142 162 C3' C A 8 OK 160 163 164 182 C3' G A 9 OK 180 183 184 205 C3' A A 10 OK 203 206 207 227 C3' C A 11 OK 225 228 229 247 C3' C A 12 OK 245 248 249 267 C3' C A 13 OK 265 268 269 287 C3' 5BU A 14 OK 285 288 289 308 C3' G A 15 OK 306 309 310 331 C3' C A 16 OK 329 332 333 349 C3' G B 1 OK 347 350 351 372 C3' C B 2 OK 370 373 374 392 C3' G B 3 OK 390 393 394 415 C3' G B 4 OK 413 416 417 438 C3' G B 5 OK 436 439 440 461 C3' G B 6 OK 459 462 463 484 C3' A B 7 OK 482 485 486 506 C3' C B 8 OK 504 507 508 526 C3' G B 9 OK 524 527 528 549 C3' A B 10 OK 547 550 551 571 C3' C B 11 OK 569 572 573 591 C3' C B 12 OK 589 592 593 611 C3' C B 13 OK 609 612 613 631 C3' 5BU B 14 OK 629 632 633 652 C3' G B 15 OK 650 653 654 675 C3' C B 16 OK 673 676 677 693 C3' G C 1 OK 691 694 695 716 C3' C C 2 OK 714 717 718 736 C3' G C 3 OK 734 737 738 759 C3' G C 4 OK 757 760 761 782 C3' G C 5 OK 780 783 784 805 C3' G C 6 OK 803 806 807 828 C3' A C 7 OK 826 829 830 850 C3' C C 8 OK 848 851 852 870 C3' G C 9 OK 868 871 872 893 C3' A C 10 OK 891 894 895 915 C3' C C 11 OK 913 916 917 935 C3' C C 12 OK 933 936 937 955 C3' C C 13 OK 953 956 957 975 C3' 5BU C 14 OK 973 976 977 996 C3' G C 15 OK 994 997 998 1019 C3' C C 16 OK 1017 1020 1021 1037 C3' G D 1 OK 1035 1038 1039 1060 C3' C D 2 OK 1058 1061 1062 1080 C3' G D 3 OK 1078 1081 1082 1103 C3' G D 4 OK 1101 1104 1105 1126 C3' G D 5 OK 1124 1127 1128 1149 C3' G D 6 OK 1147 1150 1151 1172 C3' A D 7 OK 1170 1173 1174 1194 C3' C D 8 OK 1192 1195 1196 1214 C3' G D 9 OK 1212 1215 1216 1237 C3' A D 10 OK 1235 1238 1239 1259 C3' C D 11 OK 1257 1260 1261 1279 C3' C D 12 OK 1277 1280 1281 1299 C3' C D 13 OK 1297 1300 1301 1319 C3' 5BU D 14 OK 1317 1320 1321 1340 C3' G D 15 OK 1338 1341 1342 1363 C3' C D 16 OK 1361 1364 1365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' G A 4 OK 71 68 70 92 C4' G A 5 OK 94 91 93 115 C4' G A 6 OK 117 114 116 138 C4' A A 7 OK 140 137 139 160 C4' C A 8 OK 162 159 161 180 C4' G A 9 OK 182 179 181 203 C4' A A 10 OK 205 202 204 225 C4' C A 11 OK 227 224 226 245 C4' C A 12 OK 247 244 246 265 C4' C A 13 OK 267 264 266 285 C4' 5BU A 14 OK 287 284 286 306 C4' G A 15 OK 308 305 307 329 C4' C A 16 OK 331 328 330 347 C4' G B 1 OK 349 346 348 370 C4' C B 2 OK 372 369 371 390 C4' G B 3 OK 392 389 391 413 C4' G B 4 OK 415 412 414 436 C4' G B 5 OK 438 435 437 459 C4' G B 6 OK 461 458 460 482 C4' A B 7 OK 484 481 483 504 C4' C B 8 OK 506 503 505 524 C4' G B 9 OK 526 523 525 547 C4' A B 10 OK 549 546 548 569 C4' C B 11 OK 571 568 570 589 C4' C B 12 OK 591 588 590 609 C4' C B 13 OK 611 608 610 629 C4' 5BU B 14 OK 631 628 630 650 C4' G B 15 OK 652 649 651 673 C4' C B 16 OK 675 672 674 691 C4' G C 1 OK 693 690 692 714 C4' C C 2 OK 716 713 715 734 C4' G C 3 OK 736 733 735 757 C4' G C 4 OK 759 756 758 780 C4' G C 5 OK 782 779 781 803 C4' G C 6 OK 805 802 804 826 C4' A C 7 OK 828 825 827 848 C4' C C 8 OK 850 847 849 868 C4' G C 9 OK 870 867 869 891 C4' A C 10 OK 893 890 892 913 C4' C C 11 OK 915 912 914 933 C4' C C 12 OK 935 932 934 953 C4' C C 13 OK 955 952 954 973 C4' 5BU C 14 OK 975 972 974 994 C4' G C 15 OK 996 993 995 1017 C4' C C 16 OK 1019 1016 1018 1035 C4' G D 1 OK 1037 1034 1036 1058 C4' C D 2 OK 1060 1057 1059 1078 C4' G D 3 OK 1080 1077 1079 1101 C4' G D 4 OK 1103 1100 1102 1124 C4' G D 5 OK 1126 1123 1125 1147 C4' G D 6 OK 1149 1146 1148 1170 C4' A D 7 OK 1172 1169 1171 1192 C4' C D 8 OK 1194 1191 1193 1212 C4' G D 9 OK 1214 1211 1213 1235 C4' A D 10 OK 1237 1234 1236 1257 C4' C D 11 OK 1259 1256 1258 1277 C4' C D 12 OK 1279 1276 1278 1297 C4' C D 13 OK 1299 1296 1298 1317 C4' 5BU D 14 OK 1319 1316 1318 1338 C4' G D 15 OK 1340 1337 1339 1361 C4' C D 16 OK 1363 1360 1362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' G A 3 44 46 68 C5' G A 4 67 69 91 C5' G A 5 90 92 114 C5' G A 6 113 115 137 C5' A A 7 136 138 159 C5' C A 8 158 160 179 C5' G A 9 178 180 202 C5' A A 10 201 203 224 C5' C A 11 223 225 244 C5' C A 12 243 245 264 C5' C A 13 263 265 284 C5' 5BU A 14 283 285 305 C5' G A 15 304 306 328 C5' C A 16 327 329 346 C5' G B 1 345 347 369 C5' C B 2 368 370 389 C5' G B 3 388 390 412 C5' G B 4 411 413 435 C5' G B 5 434 436 458 C5' G B 6 457 459 481 C5' A B 7 480 482 503 C5' C B 8 502 504 523 C5' G B 9 522 524 546 C5' A B 10 545 547 568 C5' C B 11 567 569 588 C5' C B 12 587 589 608 C5' C B 13 607 609 628 C5' 5BU B 14 627 629 649 C5' G B 15 648 650 672 C5' C B 16 671 673 690 C5' G C 1 689 691 713 C5' C C 2 712 714 733 C5' G C 3 732 734 756 C5' G C 4 755 757 779 C5' G C 5 778 780 802 C5' G C 6 801 803 825 C5' A C 7 824 826 847 C5' C C 8 846 848 867 C5' G C 9 866 868 890 C5' A C 10 889 891 912 C5' C C 11 911 913 932 C5' C C 12 931 933 952 C5' C C 13 951 953 972 C5' 5BU C 14 971 973 993 C5' G C 15 992 994 1016 C5' C C 16 1015 1017 1034 C5' G D 1 1033 1035 1057 C5' C D 2 1056 1058 1077 C5' G D 3 1076 1078 1100 C5' G D 4 1099 1101 1123 C5' G D 5 1122 1124 1146 C5' G D 6 1145 1147 1169 C5' A D 7 1168 1170 1191 C5' C D 8 1190 1192 1211 C5' G D 9 1210 1212 1234 C5' A D 10 1233 1235 1256 C5' C D 11 1255 1257 1276 C5' C D 12 1275 1277 1296 C5' C D 13 1295 1297 1316 C5' 5BU D 14 1315 1317 1337 C5' G D 15 1336 1338 1360 C5' C D 16 1359 1361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P G A 4 distorted distorted 49 65 66 67 87 P G A 5 distorted distorted 72 88 89 90 110 P G A 6 distorted distorted 95 111 112 113 133 P A A 7 distorted distorted 118 134 135 136 155 P C A 8 distorted distorted 141 156 157 158 175 P G A 9 distorted distorted 163 176 177 178 198 P A A 10 distorted distorted 183 199 200 201 220 P C A 11 distorted distorted 206 221 222 223 240 P C A 12 distorted distorted 228 241 242 243 260 P C A 13 distorted distorted 248 261 262 263 280 P 5BU A 14 distorted distorted 268 281 282 283 301 P G A 15 distorted distorted 288 302 303 304 324 P C A 16 distorted distorted 309 325 326 327 365 P C B 2 distorted distorted 350 366 367 368 385 P G B 3 distorted distorted 373 386 387 388 408 P G B 4 distorted distorted 393 409 410 411 431 P G B 5 distorted distorted 416 432 433 434 454 P G B 6 distorted distorted 439 455 456 457 477 P A B 7 distorted distorted 462 478 479 480 499 P C B 8 distorted distorted 485 500 501 502 519 P G B 9 distorted distorted 507 520 521 522 542 P A B 10 distorted distorted 527 543 544 545 564 P C B 11 distorted distorted 550 565 566 567 584 P C B 12 distorted distorted 572 585 586 587 604 P C B 13 distorted distorted 592 605 606 607 624 P 5BU B 14 distorted distorted 612 625 626 627 645 P G B 15 distorted distorted 632 646 647 648 668 P C B 16 distorted distorted 653 669 670 671 709 P C C 2 distorted distorted 694 710 711 712 729 P G C 3 distorted distorted 717 730 731 732 752 P G C 4 distorted distorted 737 753 754 755 775 P G C 5 distorted distorted 760 776 777 778 798 P G C 6 distorted distorted 783 799 800 801 821 P A C 7 distorted distorted 806 822 823 824 843 P C C 8 distorted distorted 829 844 845 846 863 P G C 9 distorted distorted 851 864 865 866 886 P A C 10 distorted distorted 871 887 888 889 908 P C C 11 distorted distorted 894 909 910 911 928 P C C 12 distorted distorted 916 929 930 931 948 P C C 13 distorted distorted 936 949 950 951 968 P 5BU C 14 distorted distorted 956 969 970 971 989 P G C 15 distorted distorted 976 990 991 992 1012 P C C 16 distorted distorted 997 1013 1014 1015 1053 P C D 2 distorted distorted 1038 1054 1055 1056 1073 P G D 3 distorted distorted 1061 1074 1075 1076 1096 P G D 4 distorted distorted 1081 1097 1098 1099 1119 P G D 5 distorted distorted 1104 1120 1121 1122 1142 P G D 6 distorted distorted 1127 1143 1144 1145 1165 P A D 7 distorted distorted 1150 1166 1167 1168 1187 P C D 8 distorted distorted 1173 1188 1189 1190 1207 P G D 9 distorted distorted 1195 1208 1209 1210 1230 P A D 10 distorted distorted 1215 1231 1232 1233 1252 P C D 11 distorted distorted 1238 1253 1254 1255 1272 P C D 12 distorted distorted 1260 1273 1274 1275 1292 P C D 13 distorted distorted 1280 1293 1294 1295 1312 P 5BU D 14 distorted distorted 1300 1313 1314 1315 1333 P G D 15 distorted distorted 1320 1334 1335 1336 1356 P C D 16 distorted distorted 1341 1357 1358 1359 ---------------------------------------------------------------------------------