ID code: '3CQS' 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 84 106 C1' A A 5 beta 101 107 104 128 C1' G A 6 beta 123 129 126 151 C1' U A 7 beta 146 152 149 171 C1' C A 8 beta 166 172 169 191 C1' C A 9 beta 186 192 189 211 C1' A A 10 beta 206 212 209 233 C1' C A 11 beta 228 234 231 253 C1' C A 12 beta 248 254 251 273 C1' G A 13 beta 268 274 271 294 C1' C B 2 beta 289 295 292 314 C1' G B 3 beta 309 315 312 337 C1' G B 4 beta 332 338 335 360 C1' U B 5 beta 355 361 358 380 C1' G B 6 beta 375 381 378 403 C1' A B 7 beta 398 404 401 425 C1' G B 8 beta 420 426 423 448 C1' A B 9 beta 443 449 446 470 C1' A B 10 beta 465 471 468 492 C1' G B 11 beta 487 493 490 515 C1' G B 12 beta 510 516 513 538 C1' G B 13 beta 533 539 536 574 C1' G B 15 beta 569 575 572 597 C1' G B 16 beta 592 598 595 620 C1' C B 17 beta 615 621 618 640 C1' A B 18 beta 635 641 638 662 C1' G B 19 beta 657 663 660 685 C1' A B 20 beta 680 686 683 707 C1' G B 21 beta 702 708 705 730 C1' A B 22 beta 725 731 728 752 C1' A B 23 beta 747 753 750 774 C1' A B 24 beta 769 775 772 796 C1' C B 25 beta 791 797 794 816 C1' A B 26 beta 811 817 814 838 C1' C B 27 beta 833 839 836 858 C1' A B 28 beta 853 859 856 880 C1' C B 29 beta 875 881 878 900 C1' G B 30 beta 895 901 898 923 C1' A B 31 beta 918 924 921 943 C1' U C 31 beta 938 944 941 963 C1' C C 32 beta 958 964 961 983 C1' G C 33 beta 978 984 981 1006 C1' U C 34 beta 1001 1007 1004 1026 C1' G C 35 beta 1021 1027 1024 1049 C1' G C 36 beta 1044 1050 1047 1072 C1' U C 37 beta 1067 1073 1070 1092 C1' A C 38 beta 1087 1093 1090 1114 C1' C C 39 beta 1109 1115 1112 1134 C1' A C 40 beta 1129 1135 1132 1156 C1' U C 41 beta 1151 1157 1154 1176 C1' U C 42 beta 1171 1177 1174 1196 C1' A C 43 beta 1191 1197 1194 1218 C1' C C 44 beta 1213 1219 1216 1238 C1' C C 45 beta 1233 1239 1236 1258 C1' U C 46 beta 1253 1259 1256 1278 C1' G C 47 beta 1273 1279 1276 1301 C1' C C 48 beta 1296 1302 1299 1321 C1' C C 49 beta 1316 1322 1319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 85 104 C2' A A 5 OK 106 102 105 126 C2' G A 6 OK 128 124 127 149 C2' U A 7 OK 151 147 150 169 C2' C A 8 OK 171 167 170 189 C2' C A 9 OK 191 187 190 209 C2' A A 10 OK 211 207 210 231 C2' C A 11 OK 233 229 232 251 C2' C A 12 OK 253 249 252 271 C2' G A 13 OK 273 269 272 292 C2' C B 2 OK 294 290 293 312 C2' G B 3 OK 314 310 313 335 C2' G B 4 OK 337 333 336 358 C2' U B 5 OK 360 356 359 378 C2' G B 6 OK 380 376 379 401 C2' A B 7 OK 403 399 402 423 C2' G B 8 OK 425 421 424 446 C2' A B 9 OK 448 444 447 468 C2' A B 10 OK 470 466 469 490 C2' G B 11 OK 492 488 491 513 C2' G B 12 OK 515 511 514 536 C2' G B 13 OK 538 534 537 572 C2' G B 15 OK 574 570 573 595 C2' G B 16 OK 597 593 596 618 C2' C B 17 OK 620 616 619 638 C2' A B 18 OK 640 636 639 660 C2' G B 19 OK 662 658 661 683 C2' A B 20 OK 685 681 684 705 C2' G B 21 OK 707 703 706 728 C2' A B 22 OK 730 726 729 750 C2' A B 23 OK 752 748 751 772 C2' A B 24 OK 774 770 773 794 C2' C B 25 OK 796 792 795 814 C2' A B 26 OK 816 812 815 836 C2' C B 27 OK 838 834 837 856 C2' A B 28 OK 858 854 857 878 C2' C B 29 OK 880 876 879 898 C2' G B 30 OK 900 896 899 921 C2' A B 31 OK 923 919 922 941 C2' U C 31 OK 943 939 942 961 C2' C C 32 OK 963 959 962 981 C2' G C 33 OK 983 979 982 1004 C2' U C 34 OK 1006 1002 1005 1024 C2' G C 35 OK 1026 1022 1025 1047 C2' G C 36 OK 1049 1045 1048 1070 C2' U C 37 OK 1072 1068 1071 1090 C2' A C 38 OK 1092 1088 1091 1112 C2' C C 39 OK 1114 1110 1113 1132 C2' A C 40 OK 1134 1130 1133 1154 C2' U C 41 OK 1156 1152 1155 1174 C2' U C 42 OK 1176 1172 1175 1194 C2' A C 43 OK 1196 1192 1195 1216 C2' C C 44 OK 1218 1214 1217 1236 C2' C C 45 OK 1238 1234 1237 1256 C2' U C 46 OK 1258 1254 1257 1276 C2' G C 47 OK 1278 1274 1277 1299 C2' C C 48 OK 1301 1297 1300 1319 C2' C C 49 OK 1321 1317 1320 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 84 102 C3' A A 5 OK 100 103 104 124 C3' G A 6 OK 122 125 126 147 C3' U A 7 OK 145 148 149 167 C3' C A 8 OK 165 168 169 187 C3' C A 9 OK 185 188 189 207 C3' A A 10 OK 205 208 209 229 C3' C A 11 OK 227 230 231 249 C3' C A 12 OK 247 250 251 269 C3' G A 13 OK 267 270 271 290 C3' C B 2 OK 288 291 292 310 C3' G B 3 OK 308 311 312 333 C3' G B 4 OK 331 334 335 356 C3' U B 5 OK 354 357 358 376 C3' G B 6 OK 374 377 378 399 C3' A B 7 OK 397 400 401 421 C3' G B 8 OK 419 422 423 444 C3' A B 9 OK 442 445 446 466 C3' A B 10 OK 464 467 468 488 C3' G B 11 OK 486 489 490 511 C3' G B 12 OK 509 512 513 534 C3' G B 13 OK 532 535 536 570 C3' G B 15 OK 568 571 572 593 C3' G B 16 OK 591 594 595 616 C3' C B 17 OK 614 617 618 636 C3' A B 18 OK 634 637 638 658 C3' G B 19 OK 656 659 660 681 C3' A B 20 OK 679 682 683 703 C3' G B 21 OK 701 704 705 726 C3' A B 22 OK 724 727 728 748 C3' A B 23 OK 746 749 750 770 C3' A B 24 OK 768 771 772 792 C3' C B 25 OK 790 793 794 812 C3' A B 26 OK 810 813 814 834 C3' C B 27 OK 832 835 836 854 C3' A B 28 OK 852 855 856 876 C3' C B 29 OK 874 877 878 896 C3' G B 30 OK 894 897 898 919 C3' A B 31 OK 917 920 921 939 C3' U C 31 OK 937 940 941 959 C3' C C 32 OK 957 960 961 979 C3' G C 33 OK 977 980 981 1002 C3' U C 34 OK 1000 1003 1004 1022 C3' G C 35 OK 1020 1023 1024 1045 C3' G C 36 OK 1043 1046 1047 1068 C3' U C 37 OK 1066 1069 1070 1088 C3' A C 38 OK 1086 1089 1090 1110 C3' C C 39 OK 1108 1111 1112 1130 C3' A C 40 OK 1128 1131 1132 1152 C3' U C 41 OK 1150 1153 1154 1172 C3' U C 42 OK 1170 1173 1174 1192 C3' A C 43 OK 1190 1193 1194 1214 C3' C C 44 OK 1212 1215 1216 1234 C3' C C 45 OK 1232 1235 1236 1254 C3' U C 46 OK 1252 1255 1256 1274 C3' G C 47 OK 1272 1275 1276 1297 C3' C C 48 OK 1295 1298 1299 1317 C3' C C 49 OK 1315 1318 1319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 81 100 C4' A A 5 OK 102 99 101 122 C4' G A 6 OK 124 121 123 145 C4' U A 7 OK 147 144 146 165 C4' C A 8 OK 167 164 166 185 C4' C A 9 OK 187 184 186 205 C4' A A 10 OK 207 204 206 227 C4' C A 11 OK 229 226 228 247 C4' C A 12 OK 249 246 248 267 C4' G A 13 OK 269 266 268 288 C4' C B 2 OK 290 287 289 308 C4' G B 3 OK 310 307 309 331 C4' G B 4 OK 333 330 332 354 C4' U B 5 OK 356 353 355 374 C4' G B 6 OK 376 373 375 397 C4' A B 7 OK 399 396 398 419 C4' G B 8 OK 421 418 420 442 C4' A B 9 OK 444 441 443 464 C4' A B 10 OK 466 463 465 486 C4' G B 11 OK 488 485 487 509 C4' G B 12 OK 511 508 510 532 C4' G B 13 OK 534 531 533 568 C4' G B 15 OK 570 567 569 591 C4' G B 16 OK 593 590 592 614 C4' C B 17 OK 616 613 615 634 C4' A B 18 OK 636 633 635 656 C4' G B 19 OK 658 655 657 679 C4' A B 20 OK 681 678 680 701 C4' G B 21 OK 703 700 702 724 C4' A B 22 OK 726 723 725 746 C4' A B 23 OK 748 745 747 768 C4' A B 24 OK 770 767 769 790 C4' C B 25 OK 792 789 791 810 C4' A B 26 OK 812 809 811 832 C4' C B 27 OK 834 831 833 852 C4' A B 28 OK 854 851 853 874 C4' C B 29 OK 876 873 875 894 C4' G B 30 OK 896 893 895 917 C4' A B 31 OK 919 916 918 937 C4' U C 31 OK 939 936 938 957 C4' C C 32 OK 959 956 958 977 C4' G C 33 OK 979 976 978 1000 C4' U C 34 OK 1002 999 1001 1020 C4' G C 35 OK 1022 1019 1021 1043 C4' G C 36 OK 1045 1042 1044 1066 C4' U C 37 OK 1068 1065 1067 1086 C4' A C 38 OK 1088 1085 1087 1108 C4' C C 39 OK 1110 1107 1109 1128 C4' A C 40 OK 1130 1127 1129 1150 C4' U C 41 OK 1152 1149 1151 1170 C4' U C 42 OK 1172 1169 1171 1190 C4' A C 43 OK 1192 1189 1191 1212 C4' C C 44 OK 1214 1211 1213 1232 C4' C C 45 OK 1234 1231 1233 1252 C4' U C 46 OK 1254 1251 1253 1272 C4' G C 47 OK 1274 1271 1273 1295 C4' C C 48 OK 1297 1294 1296 1315 C4' C C 49 OK 1317 1314 1316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 99 C5' A A 5 98 100 121 C5' G A 6 120 122 144 C5' U A 7 143 145 164 C5' C A 8 163 165 184 C5' C A 9 183 185 204 C5' A A 10 203 205 226 C5' C A 11 225 227 246 C5' C A 12 245 247 266 C5' G A 13 265 267 287 C5' C B 2 286 288 307 C5' G B 3 306 308 330 C5' G B 4 329 331 353 C5' U B 5 352 354 373 C5' G B 6 372 374 396 C5' A B 7 395 397 418 C5' G B 8 417 419 441 C5' A B 9 440 442 463 C5' A B 10 462 464 485 C5' G B 11 484 486 508 C5' G B 12 507 509 531 C5' G B 13 530 532 567 C5' G B 15 566 568 590 C5' G B 16 589 591 613 C5' C B 17 612 614 633 C5' A B 18 632 634 655 C5' G B 19 654 656 678 C5' A B 20 677 679 700 C5' G B 21 699 701 723 C5' A B 22 722 724 745 C5' A B 23 744 746 767 C5' A B 24 766 768 789 C5' C B 25 788 790 809 C5' A B 26 808 810 831 C5' C B 27 830 832 851 C5' A B 28 850 852 873 C5' C B 29 872 874 893 C5' G B 30 892 894 916 C5' A B 31 915 917 936 C5' U C 31 935 937 956 C5' C C 32 955 957 976 C5' G C 33 975 977 999 C5' U C 34 998 1000 1019 C5' G C 35 1018 1020 1042 C5' G C 36 1041 1043 1065 C5' U C 37 1064 1066 1085 C5' A C 38 1084 1086 1107 C5' C C 39 1106 1108 1127 C5' A C 40 1126 1128 1149 C5' U C 41 1148 1150 1169 C5' U C 42 1168 1170 1189 C5' A C 43 1188 1190 1211 C5' C C 44 1210 1212 1231 C5' C C 45 1230 1232 1251 C5' U C 46 1250 1252 1271 C5' G C 47 1270 1272 1294 C5' C C 48 1293 1295 1314 C5' C C 49 1313 1315 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 5 distorted distorted 83 96 97 98 117 P G A 6 OK OK 118 119 120 140 P U A 7 distorted distorted 125 141 142 143 160 P C A 8 distorted distorted 148 161 162 163 180 P C A 9 distorted distorted 168 181 182 183 200 P A A 10 distorted distorted 188 201 202 203 222 P C A 11 distorted distorted 208 223 224 225 242 P C A 12 distorted distorted 230 243 244 245 262 P G A 13 distorted distorted 250 263 264 265 303 P G B 3 distorted distorted 291 304 305 306 326 P G B 4 distorted distorted 311 327 328 329 349 P U B 5 distorted distorted 334 350 351 352 369 P G B 6 distorted distorted 357 370 371 372 392 P A B 7 distorted distorted 377 393 394 395 414 P G B 8 distorted distorted 400 415 416 417 437 P A B 9 distorted distorted 422 438 439 440 459 P A B 10 distorted distorted 445 460 461 462 481 P G B 11 distorted distorted 467 482 483 484 504 P G B 12 distorted distorted 489 505 506 507 527 P G B 13 distorted distorted 512 528 529 530 550 P S9L B 14 OK OK 535 551 552 553 563 P G B 15 distorted distorted 562 564 565 566 586 P G B 16 distorted distorted 571 587 588 589 609 P C B 17 distorted distorted 594 610 611 612 629 P A B 18 distorted distorted 617 630 631 632 651 P G B 19 distorted distorted 637 652 653 654 674 P A B 20 distorted distorted 659 675 676 677 696 P G B 21 distorted distorted 682 697 698 699 719 P A B 22 distorted distorted 704 720 721 722 741 P A B 23 distorted distorted 727 742 743 744 763 P A B 24 distorted distorted 749 764 765 766 785 P C B 25 distorted distorted 771 786 787 788 805 P A B 26 distorted distorted 793 806 807 808 827 P C B 27 distorted distorted 813 828 829 830 847 P A B 28 distorted distorted 835 848 849 850 869 P C B 29 distorted distorted 855 870 871 872 889 P G B 30 distorted distorted 877 890 891 892 912 P A B 31 distorted distorted 897 913 914 915 952 P C C 32 distorted distorted 940 953 954 955 972 P G C 33 distorted distorted 960 973 974 975 995 P U C 34 distorted distorted 980 996 997 998 1015 P G C 35 distorted distorted 1003 1016 1017 1018 1038 P G C 36 distorted distorted 1023 1039 1040 1041 1061 P U C 37 distorted distorted 1046 1062 1063 1064 1081 P A C 38 distorted distorted 1069 1082 1083 1084 1103 P C C 39 distorted distorted 1089 1104 1105 1106 1123 P A C 40 distorted distorted 1111 1124 1125 1126 1145 P U C 41 distorted distorted 1131 1146 1147 1148 1165 P U C 42 distorted distorted 1153 1166 1167 1168 1185 P A C 43 distorted distorted 1173 1186 1187 1188 1207 P C C 44 distorted distorted 1193 1208 1209 1210 1227 P C C 45 distorted distorted 1215 1228 1229 1230 1247 P U C 46 distorted distorted 1235 1248 1249 1250 1267 P G C 47 distorted distorted 1255 1268 1269 1270 1290 P C C 48 distorted distorted 1275 1291 1292 1293 1310 P C C 49 distorted distorted 1298 1311 1312 1313 ---------------------------------------------------------------------------------