ID code: '2D2K' 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' --------------------------------------------------------------------------------- 46 C1' C A 2 beta 41 47 44 66 C1' C A 3 beta 61 67 64 86 C1' C A 4 beta 81 87 84 105 C1' A2M A 5 beta 100 107 103 129 C1' G A 6 beta 124 130 127 152 C1' U A 7 beta 147 153 150 172 C1' C A 8 beta 167 173 170 192 C1' C A 9 beta 187 193 190 212 C1' A A 10 beta 207 213 210 234 C1' C A 11 beta 229 235 232 254 C1' C A 12 beta 249 255 252 274 C1' G A 13 beta 269 275 272 295 C1' C B 2 beta 290 296 293 315 C1' G B 3 beta 310 316 313 338 C1' G B 4 beta 333 339 336 361 C1' U B 5 beta 356 362 359 381 C1' G B 6 beta 376 382 379 404 C1' A B 7 beta 399 405 402 426 C1' G B 8 beta 421 427 424 449 C1' A B 9 beta 444 450 447 471 C1' A B 10 beta 466 472 469 493 C1' G B 11 beta 488 494 491 516 C1' G B 12 beta 511 517 514 539 C1' G B 13 beta 534 540 537 560 C1' G C 15 beta 555 561 558 583 C1' G C 16 beta 578 584 581 606 C1' C C 17 beta 601 607 604 626 C1' A C 18 beta 621 627 624 648 C1' G C 19 beta 643 649 646 671 C1' A C 20 beta 666 672 669 693 C1' G C 21 beta 688 694 691 716 C1' A C 22 beta 711 717 714 738 C1' A C 23 beta 733 739 736 760 C1' A C 24 beta 755 761 758 782 C1' C C 25 beta 777 783 780 802 C1' A C 26 beta 797 803 800 824 C1' C C 27 beta 819 825 822 844 C1' A C 28 beta 839 845 842 866 C1' C C 29 beta 861 867 864 886 C1' G C 30 beta 881 887 884 909 C1' A C 31 beta 904 910 907 929 C1' U D 31 beta 924 930 927 949 C1' C D 32 beta 944 950 947 969 C1' G D 33 beta 964 970 967 992 C1' U D 34 beta 987 993 990 1012 C1' G D 35 beta 1007 1013 1010 1035 C1' G D 36 beta 1030 1036 1033 1182 C1' A D 40 beta 1177 1183 1180 1204 C1' U D 41 beta 1199 1205 1202 1224 C1' U D 42 beta 1219 1225 1222 1244 C1' A D 43 beta 1239 1245 1242 1266 C1' C D 44 beta 1261 1267 1264 1286 C1' C D 45 beta 1281 1287 1284 1306 C1' U D 46 beta 1301 1307 1304 1326 C1' G D 47 beta 1321 1327 1324 1349 C1' C D 48 beta 1344 1350 1347 1369 C1' C D 49 beta 1364 1370 1367 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 44 C2' C A 2 OK 46 42 45 64 C2' C A 3 OK 66 62 65 84 C2' C A 4 OK 86 82 85 103 C2' A2M A 5 OK 105 101 104 127 C2' G A 6 OK 129 125 128 150 C2' U A 7 OK 152 148 151 170 C2' C A 8 OK 172 168 171 190 C2' C A 9 OK 192 188 191 210 C2' A A 10 OK 212 208 211 232 C2' C A 11 OK 234 230 233 252 C2' C A 12 OK 254 250 253 272 C2' G A 13 OK 274 270 273 293 C2' C B 2 OK 295 291 294 313 C2' G B 3 OK 315 311 314 336 C2' G B 4 OK 338 334 337 359 C2' U B 5 OK 361 357 360 379 C2' G B 6 OK 381 377 380 402 C2' A B 7 OK 404 400 403 424 C2' G B 8 OK 426 422 425 447 C2' A B 9 OK 449 445 448 469 C2' A B 10 OK 471 467 470 491 C2' G B 11 OK 493 489 492 514 C2' G B 12 OK 516 512 515 537 C2' G B 13 OK 539 535 538 558 C2' G C 15 OK 560 556 559 581 C2' G C 16 OK 583 579 582 604 C2' C C 17 OK 606 602 605 624 C2' A C 18 OK 626 622 625 646 C2' G C 19 OK 648 644 647 669 C2' A C 20 OK 671 667 670 691 C2' G C 21 OK 693 689 692 714 C2' A C 22 OK 716 712 715 736 C2' A C 23 OK 738 734 737 758 C2' A C 24 OK 760 756 759 780 C2' C C 25 OK 782 778 781 800 C2' A C 26 OK 802 798 801 822 C2' C C 27 OK 824 820 823 842 C2' A C 28 OK 844 840 843 864 C2' C C 29 OK 866 862 865 884 C2' G C 30 OK 886 882 885 907 C2' A C 31 OK 909 905 908 927 C2' U D 31 OK 929 925 928 947 C2' C D 32 OK 949 945 948 967 C2' G D 33 OK 969 965 968 990 C2' U D 34 OK 992 988 991 1010 C2' G D 35 OK 1012 1008 1011 1033 C2' G D 36 OK 1035 1031 1034 1180 C2' A D 40 OK 1182 1178 1181 1202 C2' U D 41 OK 1204 1200 1203 1222 C2' U D 42 OK 1224 1220 1223 1242 C2' A D 43 OK 1244 1240 1243 1264 C2' C D 44 OK 1266 1262 1265 1284 C2' C D 45 OK 1286 1282 1285 1304 C2' U D 46 OK 1306 1302 1305 1324 C2' G D 47 OK 1326 1322 1325 1347 C2' C D 48 OK 1349 1345 1348 1367 C2' C D 49 OK 1369 1365 1368 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 42 C3' C A 2 OK 40 43 44 62 C3' C A 3 OK 60 63 64 82 C3' C A 4 OK 80 83 84 101 C3' A2M A 5 OK 99 102 103 125 C3' G A 6 OK 123 126 127 148 C3' U A 7 OK 146 149 150 168 C3' C A 8 OK 166 169 170 188 C3' C A 9 OK 186 189 190 208 C3' A A 10 OK 206 209 210 230 C3' C A 11 OK 228 231 232 250 C3' C A 12 OK 248 251 252 270 C3' G A 13 OK 268 271 272 291 C3' C B 2 OK 289 292 293 311 C3' G B 3 OK 309 312 313 334 C3' G B 4 OK 332 335 336 357 C3' U B 5 OK 355 358 359 377 C3' G B 6 OK 375 378 379 400 C3' A B 7 OK 398 401 402 422 C3' G B 8 OK 420 423 424 445 C3' A B 9 OK 443 446 447 467 C3' A B 10 OK 465 468 469 489 C3' G B 11 OK 487 490 491 512 C3' G B 12 OK 510 513 514 535 C3' G B 13 OK 533 536 537 556 C3' G C 15 OK 554 557 558 579 C3' G C 16 OK 577 580 581 602 C3' C C 17 OK 600 603 604 622 C3' A C 18 OK 620 623 624 644 C3' G C 19 OK 642 645 646 667 C3' A C 20 OK 665 668 669 689 C3' G C 21 OK 687 690 691 712 C3' A C 22 OK 710 713 714 734 C3' A C 23 OK 732 735 736 756 C3' A C 24 OK 754 757 758 778 C3' C C 25 OK 776 779 780 798 C3' A C 26 OK 796 799 800 820 C3' C C 27 OK 818 821 822 840 C3' A C 28 OK 838 841 842 862 C3' C C 29 OK 860 863 864 882 C3' G C 30 OK 880 883 884 905 C3' A C 31 OK 903 906 907 925 C3' U D 31 OK 923 926 927 945 C3' C D 32 OK 943 946 947 965 C3' G D 33 OK 963 966 967 988 C3' U D 34 OK 986 989 990 1008 C3' G D 35 OK 1006 1009 1010 1031 C3' G D 36 OK 1029 1032 1033 1178 C3' A D 40 OK 1176 1179 1180 1200 C3' U D 41 OK 1198 1201 1202 1220 C3' U D 42 OK 1218 1221 1222 1240 C3' A D 43 OK 1238 1241 1242 1262 C3' C D 44 OK 1260 1263 1264 1282 C3' C D 45 OK 1280 1283 1284 1302 C3' U D 46 OK 1300 1303 1304 1322 C3' G D 47 OK 1320 1323 1324 1345 C3' C D 48 OK 1343 1346 1347 1365 C3' C D 49 OK 1363 1366 1367 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 40 C4' C A 2 OK 42 39 41 60 C4' C A 3 OK 62 59 61 80 C4' C A 4 OK 82 79 81 99 C4' A2M A 5 OK 101 98 100 123 C4' G A 6 OK 125 122 124 146 C4' U A 7 OK 148 145 147 166 C4' C A 8 OK 168 165 167 186 C4' C A 9 OK 188 185 187 206 C4' A A 10 OK 208 205 207 228 C4' C A 11 OK 230 227 229 248 C4' C A 12 OK 250 247 249 268 C4' G A 13 OK 270 267 269 289 C4' C B 2 OK 291 288 290 309 C4' G B 3 OK 311 308 310 332 C4' G B 4 OK 334 331 333 355 C4' U B 5 OK 357 354 356 375 C4' G B 6 OK 377 374 376 398 C4' A B 7 OK 400 397 399 420 C4' G B 8 OK 422 419 421 443 C4' A B 9 OK 445 442 444 465 C4' A B 10 OK 467 464 466 487 C4' G B 11 OK 489 486 488 510 C4' G B 12 OK 512 509 511 533 C4' G B 13 OK 535 532 534 554 C4' G C 15 OK 556 553 555 577 C4' G C 16 OK 579 576 578 600 C4' C C 17 OK 602 599 601 620 C4' A C 18 OK 622 619 621 642 C4' G C 19 OK 644 641 643 665 C4' A C 20 OK 667 664 666 687 C4' G C 21 OK 689 686 688 710 C4' A C 22 OK 712 709 711 732 C4' A C 23 OK 734 731 733 754 C4' A C 24 OK 756 753 755 776 C4' C C 25 OK 778 775 777 796 C4' A C 26 OK 798 795 797 818 C4' C C 27 OK 820 817 819 838 C4' A C 28 OK 840 837 839 860 C4' C C 29 OK 862 859 861 880 C4' G C 30 OK 882 879 881 903 C4' A C 31 OK 905 902 904 923 C4' U D 31 OK 925 922 924 943 C4' C D 32 OK 945 942 944 963 C4' G D 33 OK 965 962 964 986 C4' U D 34 OK 988 985 987 1006 C4' G D 35 OK 1008 1005 1007 1029 C4' G D 36 OK 1031 1028 1030 1176 C4' A D 40 OK 1178 1175 1177 1198 C4' U D 41 OK 1200 1197 1199 1218 C4' U D 42 OK 1220 1217 1219 1238 C4' A D 43 OK 1240 1237 1239 1260 C4' C D 44 OK 1262 1259 1261 1280 C4' C D 45 OK 1282 1279 1281 1300 C4' U D 46 OK 1302 1299 1301 1320 C4' G D 47 OK 1322 1319 1321 1343 C4' C D 48 OK 1345 1342 1344 1363 C4' C D 49 OK 1365 1362 1364 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 39 C5' C A 2 38 40 59 C5' C A 3 58 60 79 C5' C A 4 78 80 98 C5' A2M A 5 97 99 122 C5' G A 6 121 123 145 C5' U A 7 144 146 165 C5' C A 8 164 166 185 C5' C A 9 184 186 205 C5' A A 10 204 206 227 C5' C A 11 226 228 247 C5' C A 12 246 248 267 C5' G A 13 266 268 288 C5' C B 2 287 289 308 C5' G B 3 307 309 331 C5' G B 4 330 332 354 C5' U B 5 353 355 374 C5' G B 6 373 375 397 C5' A B 7 396 398 419 C5' G B 8 418 420 442 C5' A B 9 441 443 464 C5' A B 10 463 465 486 C5' G B 11 485 487 509 C5' G B 12 508 510 532 C5' G B 13 531 533 553 C5' G C 15 552 554 576 C5' G C 16 575 577 599 C5' C C 17 598 600 619 C5' A C 18 618 620 641 C5' G C 19 640 642 664 C5' A C 20 663 665 686 C5' G C 21 685 687 709 C5' A C 22 708 710 731 C5' A C 23 730 732 753 C5' A C 24 752 754 775 C5' C C 25 774 776 795 C5' A C 26 794 796 817 C5' C C 27 816 818 837 C5' A C 28 836 838 859 C5' C C 29 858 860 879 C5' G C 30 878 880 902 C5' A C 31 901 903 922 C5' U D 31 921 923 942 C5' C D 32 941 943 962 C5' G D 33 961 963 985 C5' U D 34 984 986 1005 C5' G D 35 1004 1006 1028 C5' G D 36 1027 1029 1175 C5' A D 40 1174 1176 1197 C5' U D 41 1196 1198 1217 C5' U D 42 1216 1218 1237 C5' A D 43 1236 1238 1259 C5' C D 44 1258 1260 1279 C5' C D 45 1278 1280 1299 C5' U D 46 1298 1300 1319 C5' G D 47 1318 1320 1342 C5' C D 48 1341 1343 1362 C5' C D 49 1361 1363 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 35 P C A 2 distorted distorted 36 37 38 55 P C A 3 distorted distorted 43 56 57 58 75 P C A 4 distorted distorted 63 76 77 78 95 P A2M A 5 distorted distorted 83 96 117 97 118 P G A 6 distorted distorted 102 119 120 121 141 P U A 7 distorted distorted 126 142 143 144 161 P C A 8 distorted distorted 149 162 163 164 181 P C A 9 distorted distorted 169 182 183 184 201 P A A 10 distorted distorted 189 202 203 204 223 P C A 11 distorted distorted 209 224 225 226 243 P C A 12 distorted distorted 231 244 245 246 263 P G A 13 distorted distorted 251 264 265 266 304 P G B 3 distorted distorted 292 305 306 307 327 P G B 4 distorted distorted 312 328 329 330 350 P U B 5 distorted distorted 335 351 352 353 370 P G B 6 distorted distorted 358 371 372 373 393 P A B 7 distorted distorted 378 394 395 396 415 P G B 8 distorted distorted 401 416 417 418 438 P A B 9 distorted distorted 423 439 440 441 460 P A B 10 distorted distorted 446 461 462 463 482 P G B 11 distorted distorted 468 483 484 485 505 P G B 12 distorted distorted 490 506 507 508 528 P G B 13 distorted distorted 513 529 530 531 572 P G C 16 distorted distorted 557 573 574 575 595 P C C 17 distorted distorted 580 596 597 598 615 P A C 18 distorted distorted 603 616 617 618 637 P G C 19 distorted distorted 623 638 639 640 660 P A C 20 distorted distorted 645 661 662 663 682 P G C 21 distorted distorted 668 683 684 685 705 P A C 22 distorted distorted 690 706 707 708 727 P A C 23 distorted distorted 713 728 729 730 749 P A C 24 distorted distorted 735 750 751 752 771 P C C 25 distorted distorted 757 772 773 774 791 P A C 26 distorted distorted 779 792 793 794 813 P C C 27 distorted distorted 799 814 815 816 833 P A C 28 distorted distorted 821 834 835 836 855 P C C 29 distorted distorted 841 856 857 858 875 P G C 30 distorted distorted 863 876 877 878 898 P A C 31 distorted distorted 883 899 900 901 938 P C D 32 distorted distorted 926 939 940 941 958 P G D 33 distorted distorted 946 959 960 961 981 P U D 34 distorted distorted 966 982 983 984 1001 P G D 35 distorted distorted 989 1002 1003 1004 1024 P G D 36 distorted distorted 1009 1025 1026 1027 1047 P U D 37 1032 1048 P U D 37 1032 1087 P A D 38 1088 P A D 38 1131 P U D 39 1132 P U D 39 1171 P A D 40 distorted distorted 1172 1173 1174 1193 P U D 41 distorted distorted 1179 1194 1195 1196 1213 P U D 42 distorted distorted 1201 1214 1215 1216 1233 P A D 43 distorted distorted 1221 1234 1235 1236 1255 P C D 44 distorted distorted 1241 1256 1257 1258 1275 P C D 45 distorted distorted 1263 1276 1277 1278 1295 P U D 46 distorted distorted 1283 1296 1297 1298 1315 P G D 47 distorted distorted 1303 1316 1317 1318 1338 P C D 48 distorted distorted 1323 1339 1340 1341 1358 P C D 49 distorted distorted 1346 1359 1360 1361 ---------------------------------------------------------------------------------