ID code: '3R1D' 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' --------------------------------------------------------------------------------- 186 C1' C A 5 beta 181 187 184 206 C1' G A 6 beta 201 207 204 229 C1' G A 7 beta 224 230 227 252 C1' C A 8 beta 247 253 250 272 C1' G A 9 beta 267 273 270 295 C1' G A 10 beta 290 296 293 318 C1' C A 11 beta 313 319 316 421 C1' GRB B 3 beta 427 420 422 443 C1' G B 4 beta 438 444 441 466 C1' C B 5 beta 461 467 464 486 C1' G B 6 beta 481 487 484 509 C1' G B 7 beta 504 510 507 532 C1' C B 8 beta 527 533 530 552 C1' G B 9 beta 547 553 550 575 C1' G B 10 beta 570 576 573 598 C1' C B 11 beta 593 599 596 799 C1' C C 5 beta 794 800 797 865 C1' G C 7 beta 860 866 863 888 C1' C C 8 beta 883 889 886 908 C1' G C 9 beta 903 909 906 931 C1' G C 10 beta 926 932 929 954 C1' C C 11 beta 949 955 952 972 C1' G D 1 beta 967 973 970 995 C1' C D 2 beta 990 996 993 1017 C1' GRB D 3 beta 1023 1016 1018 1039 C1' G D 4 beta 1034 1040 1037 1062 C1' C D 5 beta 1057 1063 1060 1174 C1' C D 8 beta 1169 1175 1172 1194 C1' G D 9 beta 1189 1195 1192 1217 C1' G D 10 beta 1212 1218 1215 1240 C1' C D 11 beta 1235 1241 1238 1435 C1' C E 5 beta 1430 1436 1433 1547 C1' C E 8 beta 1542 1548 1545 1567 C1' G E 9 beta 1562 1568 1565 1590 C1' G E 10 beta 1585 1591 1588 1613 C1' C E 11 beta 1608 1614 1611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 184 C2' C A 5 OK 186 182 185 204 C2' G A 6 OK 206 202 205 227 C2' G A 7 OK 229 225 228 250 C2' C A 8 OK 252 248 251 270 C2' G A 9 OK 272 268 271 293 C2' G A 10 OK 295 291 294 316 C2' C A 11 OK 318 314 317 422 C2' GRB B 3 OK 421 424 423 441 C2' G B 4 OK 443 439 442 464 C2' C B 5 OK 466 462 465 484 C2' G B 6 OK 486 482 485 507 C2' G B 7 OK 509 505 508 530 C2' C B 8 OK 532 528 531 550 C2' G B 9 OK 552 548 551 573 C2' G B 10 OK 575 571 574 596 C2' C B 11 OK 598 594 597 797 C2' C C 5 OK 799 795 798 863 C2' G C 7 OK 865 861 864 886 C2' C C 8 OK 888 884 887 906 C2' G C 9 OK 908 904 907 929 C2' G C 10 OK 931 927 930 952 C2' C C 11 OK 954 950 953 970 C2' G D 1 OK 972 968 971 993 C2' C D 2 OK 995 991 994 1018 C2' GRB D 3 OK 1017 1020 1019 1037 C2' G D 4 OK 1039 1035 1038 1060 C2' C D 5 OK 1062 1058 1061 1172 C2' C D 8 OK 1174 1170 1173 1192 C2' G D 9 OK 1194 1190 1193 1215 C2' G D 10 OK 1217 1213 1216 1238 C2' C D 11 OK 1240 1236 1239 1433 C2' C E 5 OK 1435 1431 1434 1545 C2' C E 8 OK 1547 1543 1546 1565 C2' G E 9 OK 1567 1563 1566 1588 C2' G E 10 OK 1590 1586 1589 1611 C2' C E 11 OK 1613 1609 1612 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 182 C3' C A 5 OK 180 183 184 202 C3' G A 6 OK 200 203 204 225 C3' G A 7 OK 223 226 227 248 C3' C A 8 OK 246 249 250 268 C3' G A 9 OK 266 269 270 291 C3' G A 10 OK 289 292 293 314 C3' C A 11 OK 312 315 316 424 C3' GRB B 3 OK 426 425 422 439 C3' G B 4 OK 437 440 441 462 C3' C B 5 OK 460 463 464 482 C3' G B 6 OK 480 483 484 505 C3' G B 7 OK 503 506 507 528 C3' C B 8 OK 526 529 530 548 C3' G B 9 OK 546 549 550 571 C3' G B 10 OK 569 572 573 594 C3' C B 11 OK 592 595 596 795 C3' C C 5 796 797 861 C3' G C 7 OK 859 862 863 884 C3' C C 8 OK 882 885 886 904 C3' G C 9 OK 902 905 906 927 C3' G C 10 OK 925 928 929 950 C3' C C 11 OK 948 951 952 968 C3' G D 1 OK 966 969 970 991 C3' C D 2 OK 989 992 993 1020 C3' GRB D 3 OK 1022 1021 1018 1035 C3' G D 4 OK 1033 1036 1037 1058 C3' C D 5 OK 1056 1059 1060 1170 C3' C D 8 OK 1168 1171 1172 1190 C3' G D 9 OK 1188 1191 1192 1213 C3' G D 10 OK 1211 1214 1215 1236 C3' C D 11 OK 1234 1237 1238 1431 C3' C E 5 OK 1429 1432 1433 1543 C3' C E 8 OK 1541 1544 1545 1563 C3' G E 9 OK 1561 1564 1565 1586 C3' G E 10 OK 1584 1587 1588 1609 C3' C E 11 OK 1607 1610 1611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 180 C4' C A 5 OK 182 179 181 200 C4' G A 6 OK 202 199 201 223 C4' G A 7 OK 225 222 224 246 C4' C A 8 OK 248 245 247 266 C4' G A 9 OK 268 265 267 289 C4' G A 10 OK 291 288 290 312 C4' C A 11 OK 314 311 313 426 C4' GRB B 3 OK 424 428 427 437 C4' G B 4 OK 439 436 438 460 C4' C B 5 OK 462 459 461 480 C4' G B 6 OK 482 479 481 503 C4' G B 7 OK 505 502 504 526 C4' C B 8 OK 528 525 527 546 C4' G B 9 OK 548 545 547 569 C4' G B 10 OK 571 568 570 592 C4' C B 11 OK 594 591 593 859 C4' G C 7 OK 861 858 860 882 C4' C C 8 OK 884 881 883 902 C4' G C 9 OK 904 901 903 925 C4' G C 10 OK 927 924 926 948 C4' C C 11 OK 950 947 949 966 C4' G D 1 OK 968 965 967 989 C4' C D 2 OK 991 988 990 1022 C4' GRB D 3 OK 1020 1024 1023 1033 C4' G D 4 OK 1035 1032 1034 1056 C4' C D 5 OK 1058 1055 1057 1168 C4' C D 8 OK 1170 1167 1169 1188 C4' G D 9 OK 1190 1187 1189 1211 C4' G D 10 OK 1213 1210 1212 1234 C4' C D 11 OK 1236 1233 1235 1429 C4' C E 5 OK 1431 1428 1430 1541 C4' C E 8 OK 1543 1540 1542 1561 C4' G E 9 OK 1563 1560 1562 1584 C4' G E 10 OK 1586 1583 1585 1607 C4' C E 11 OK 1609 1606 1608 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 179 C5' C A 5 178 180 199 C5' G A 6 198 200 222 C5' G A 7 221 223 245 C5' C A 8 244 246 265 C5' G A 9 264 266 288 C5' G A 10 287 289 311 C5' C A 11 310 312 428 C5' GRB B 3 429 426 436 C5' G B 4 435 437 459 C5' C B 5 458 460 479 C5' G B 6 478 480 502 C5' G B 7 501 503 525 C5' C B 8 524 526 545 C5' G B 9 544 546 568 C5' G B 10 567 569 591 C5' C B 11 590 592 858 C5' G C 7 857 859 881 C5' C C 8 880 882 901 C5' G C 9 900 902 924 C5' G C 10 923 925 947 C5' C C 11 946 948 965 C5' G D 1 964 966 988 C5' C D 2 987 989 1024 C5' GRB D 3 1025 1022 1032 C5' G D 4 1031 1033 1055 C5' C D 5 1054 1056 1167 C5' C D 8 1166 1168 1187 C5' G D 9 1186 1188 1210 C5' G D 10 1209 1211 1233 C5' C D 11 1232 1234 1428 C5' C E 5 1427 1429 1540 C5' C E 8 1539 1541 1560 C5' G E 9 1559 1561 1583 C5' G E 10 1582 1584 1606 C5' C E 11 1605 1607 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 41 P C A 2 42 P C A 2 81 P GRB A 3 82 P GRB A 3 129 P G A 4 130 P G A 4 175 P C A 5 distorted distorted 176 177 178 195 P G A 6 distorted distorted 183 196 197 198 218 P G A 7 distorted distorted 203 219 220 221 241 P C A 8 distorted distorted 226 242 243 244 261 P G A 9 distorted distorted 249 262 263 264 284 P G A 10 distorted distorted 269 285 286 287 307 P C A 11 distorted distorted 292 308 309 310 368 P C B 2 369 P C B 2 408 P GRB B 3 OK OK 430 431 429 432 P G B 4 distorted distorted 425 433 434 435 455 P C B 5 distorted distorted 440 456 457 458 475 P G B 6 distorted distorted 463 476 477 478 498 P G B 7 distorted distorted 483 499 500 501 521 P C B 8 distorted distorted 506 522 523 524 541 P G B 9 distorted distorted 529 542 543 544 564 P G B 10 distorted distorted 549 565 566 567 587 P C B 11 distorted distorted 572 588 589 590 648 P C C 2 649 P C C 2 688 P GRB C 3 689 P GRB C 3 736 P G C 4 737 P G C 4 782 P C C 5 783 P C C 5 808 P G C 6 796 809 P G C 6 796 854 P G C 7 distorted distorted 855 856 857 877 P C C 8 distorted distorted 862 878 879 880 897 P G C 9 distorted distorted 885 898 899 900 920 P G C 10 distorted distorted 905 921 922 923 943 P C C 11 distorted distorted 928 944 945 946 984 P C D 2 distorted distorted 969 985 986 987 1004 P GRB D 3 OK OK 992 1026 1027 1025 1028 P G D 4 distorted distorted 1021 1029 1030 1031 1051 P C D 5 distorted distorted 1036 1052 1053 1054 1071 P G D 6 1059 1072 P G D 6 1059 1117 P G D 7 1118 P G D 7 1163 P C D 8 distorted distorted 1164 1165 1166 1183 P G D 9 distorted distorted 1171 1184 1185 1186 1206 P G D 10 distorted distorted 1191 1207 1208 1209 1229 P C D 11 distorted distorted 1214 1230 1231 1232 1290 P C E 2 1291 P C E 2 1330 P GRB E 3 1331 P GRB E 3 1378 P G E 4 1379 P G E 4 1424 P C E 5 distorted distorted 1425 1426 1427 1444 P G E 6 1432 1445 P G E 6 1432 1490 P G E 7 1491 P G E 7 1536 P C E 8 distorted distorted 1537 1538 1539 1556 P G E 9 distorted distorted 1544 1557 1558 1559 1579 P G E 10 distorted distorted 1564 1580 1581 1582 1602 P C E 11 distorted distorted 1587 1603 1604 1605 ---------------------------------------------------------------------------------