ID code: '3CR1' 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 534 540 537 575 C1' G B 15 beta 570 576 573 598 C1' G B 16 beta 593 599 596 621 C1' C B 17 beta 616 622 619 641 C1' A B 18 beta 636 642 639 663 C1' G B 19 beta 658 664 661 686 C1' A B 20 beta 681 687 684 708 C1' G B 21 beta 703 709 706 731 C1' A B 22 beta 726 732 729 753 C1' A B 23 beta 748 754 751 775 C1' A B 24 beta 770 776 773 797 C1' C B 25 beta 792 798 795 817 C1' A B 26 beta 812 818 815 839 C1' C B 27 beta 834 840 837 859 C1' A B 28 beta 854 860 857 881 C1' C B 29 beta 876 882 879 901 C1' G B 30 beta 896 902 899 924 C1' A B 31 beta 919 925 922 944 C1' U C 31 beta 939 945 942 964 C1' C C 32 beta 959 965 962 984 C1' G C 33 beta 979 985 982 1007 C1' U C 34 beta 1002 1008 1005 1027 C1' G C 35 beta 1022 1028 1025 1050 C1' G C 36 beta 1045 1051 1048 1073 C1' U C 37 beta 1068 1074 1071 1093 C1' C C 38 beta 1088 1094 1091 1113 C1' C C 39 beta 1108 1114 1111 1133 C1' A C 40 beta 1128 1134 1131 1155 C1' U C 41 beta 1150 1156 1153 1175 C1' U C 42 beta 1170 1176 1173 1195 C1' A C 43 beta 1190 1196 1193 1217 C1' C C 44 beta 1212 1218 1215 1237 C1' C C 45 beta 1232 1238 1235 1257 C1' U C 46 beta 1252 1258 1255 1277 C1' G C 47 beta 1272 1278 1275 1300 C1' C C 48 beta 1295 1301 1298 1320 C1' C C 49 beta 1315 1321 1318 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 539 535 538 573 C2' G B 15 OK 575 571 574 596 C2' G B 16 OK 598 594 597 619 C2' C B 17 OK 621 617 620 639 C2' A B 18 OK 641 637 640 661 C2' G B 19 OK 663 659 662 684 C2' A B 20 OK 686 682 685 706 C2' G B 21 OK 708 704 707 729 C2' A B 22 OK 731 727 730 751 C2' A B 23 OK 753 749 752 773 C2' A B 24 OK 775 771 774 795 C2' C B 25 OK 797 793 796 815 C2' A B 26 OK 817 813 816 837 C2' C B 27 OK 839 835 838 857 C2' A B 28 OK 859 855 858 879 C2' C B 29 OK 881 877 880 899 C2' G B 30 OK 901 897 900 922 C2' A B 31 OK 924 920 923 942 C2' U C 31 OK 944 940 943 962 C2' C C 32 OK 964 960 963 982 C2' G C 33 OK 984 980 983 1005 C2' U C 34 OK 1007 1003 1006 1025 C2' G C 35 OK 1027 1023 1026 1048 C2' G C 36 OK 1050 1046 1049 1071 C2' U C 37 OK 1073 1069 1072 1091 C2' C C 38 OK 1093 1089 1092 1111 C2' C C 39 OK 1113 1109 1112 1131 C2' A C 40 OK 1133 1129 1132 1153 C2' U C 41 OK 1155 1151 1154 1173 C2' U C 42 OK 1175 1171 1174 1193 C2' A C 43 OK 1195 1191 1194 1215 C2' C C 44 OK 1217 1213 1216 1235 C2' C C 45 OK 1237 1233 1236 1255 C2' U C 46 OK 1257 1253 1256 1275 C2' G C 47 OK 1277 1273 1276 1298 C2' C C 48 OK 1300 1296 1299 1318 C2' C C 49 OK 1320 1316 1319 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 533 536 537 571 C3' G B 15 OK 569 572 573 594 C3' G B 16 OK 592 595 596 617 C3' C B 17 OK 615 618 619 637 C3' A B 18 OK 635 638 639 659 C3' G B 19 OK 657 660 661 682 C3' A B 20 OK 680 683 684 704 C3' G B 21 OK 702 705 706 727 C3' A B 22 OK 725 728 729 749 C3' A B 23 OK 747 750 751 771 C3' A B 24 OK 769 772 773 793 C3' C B 25 OK 791 794 795 813 C3' A B 26 OK 811 814 815 835 C3' C B 27 OK 833 836 837 855 C3' A B 28 OK 853 856 857 877 C3' C B 29 OK 875 878 879 897 C3' G B 30 OK 895 898 899 920 C3' A B 31 OK 918 921 922 940 C3' U C 31 OK 938 941 942 960 C3' C C 32 OK 958 961 962 980 C3' G C 33 OK 978 981 982 1003 C3' U C 34 OK 1001 1004 1005 1023 C3' G C 35 OK 1021 1024 1025 1046 C3' G C 36 OK 1044 1047 1048 1069 C3' U C 37 OK 1067 1070 1071 1089 C3' C C 38 OK 1087 1090 1091 1109 C3' C C 39 OK 1107 1110 1111 1129 C3' A C 40 OK 1127 1130 1131 1151 C3' U C 41 OK 1149 1152 1153 1171 C3' U C 42 OK 1169 1172 1173 1191 C3' A C 43 OK 1189 1192 1193 1213 C3' C C 44 OK 1211 1214 1215 1233 C3' C C 45 OK 1231 1234 1235 1253 C3' U C 46 OK 1251 1254 1255 1273 C3' G C 47 OK 1271 1274 1275 1296 C3' C C 48 OK 1294 1297 1298 1316 C3' C C 49 OK 1314 1317 1318 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 535 532 534 569 C4' G B 15 OK 571 568 570 592 C4' G B 16 OK 594 591 593 615 C4' C B 17 OK 617 614 616 635 C4' A B 18 OK 637 634 636 657 C4' G B 19 OK 659 656 658 680 C4' A B 20 OK 682 679 681 702 C4' G B 21 OK 704 701 703 725 C4' A B 22 OK 727 724 726 747 C4' A B 23 OK 749 746 748 769 C4' A B 24 OK 771 768 770 791 C4' C B 25 OK 793 790 792 811 C4' A B 26 OK 813 810 812 833 C4' C B 27 OK 835 832 834 853 C4' A B 28 OK 855 852 854 875 C4' C B 29 OK 877 874 876 895 C4' G B 30 OK 897 894 896 918 C4' A B 31 OK 920 917 919 938 C4' U C 31 OK 940 937 939 958 C4' C C 32 OK 960 957 959 978 C4' G C 33 OK 980 977 979 1001 C4' U C 34 OK 1003 1000 1002 1021 C4' G C 35 OK 1023 1020 1022 1044 C4' G C 36 OK 1046 1043 1045 1067 C4' U C 37 OK 1069 1066 1068 1087 C4' C C 38 OK 1089 1086 1088 1107 C4' C C 39 OK 1109 1106 1108 1127 C4' A C 40 OK 1129 1126 1128 1149 C4' U C 41 OK 1151 1148 1150 1169 C4' U C 42 OK 1171 1168 1170 1189 C4' A C 43 OK 1191 1188 1190 1211 C4' C C 44 OK 1213 1210 1212 1231 C4' C C 45 OK 1233 1230 1232 1251 C4' U C 46 OK 1253 1250 1252 1271 C4' G C 47 OK 1273 1270 1272 1294 C4' C C 48 OK 1296 1293 1295 1314 C4' C C 49 OK 1316 1313 1315 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 13 531 533 568 C5' G B 15 567 569 591 C5' G B 16 590 592 614 C5' C B 17 613 615 634 C5' A B 18 633 635 656 C5' G B 19 655 657 679 C5' A B 20 678 680 701 C5' G B 21 700 702 724 C5' A B 22 723 725 746 C5' A B 23 745 747 768 C5' A B 24 767 769 790 C5' C B 25 789 791 810 C5' A B 26 809 811 832 C5' C B 27 831 833 852 C5' A B 28 851 853 874 C5' C B 29 873 875 894 C5' G B 30 893 895 917 C5' A B 31 916 918 937 C5' U C 31 936 938 957 C5' C C 32 956 958 977 C5' G C 33 976 978 1000 C5' U C 34 999 1001 1020 C5' G C 35 1019 1021 1043 C5' G C 36 1042 1044 1066 C5' U C 37 1065 1067 1086 C5' C C 38 1085 1087 1106 C5' C C 39 1105 1107 1126 C5' A C 40 1125 1127 1148 C5' U C 41 1147 1149 1168 C5' U C 42 1167 1169 1188 C5' A C 43 1187 1189 1210 C5' C C 44 1209 1211 1230 C5' C C 45 1229 1231 1250 C5' U C 46 1249 1251 1270 C5' G C 47 1269 1271 1293 C5' C C 48 1292 1294 1313 C5' C C 49 1312 1314 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 513 529 530 531 551 P S9L B 14 distorted distorted 536 552 553 554 564 P G B 15 distorted distorted 563 565 566 567 587 P G B 16 distorted distorted 572 588 589 590 610 P C B 17 distorted distorted 595 611 612 613 630 P A B 18 distorted distorted 618 631 632 633 652 P G B 19 distorted distorted 638 653 654 655 675 P A B 20 distorted distorted 660 676 677 678 697 P G B 21 distorted distorted 683 698 699 700 720 P A B 22 distorted distorted 705 721 722 723 742 P A B 23 distorted distorted 728 743 744 745 764 P A B 24 distorted distorted 750 765 766 767 786 P C B 25 distorted distorted 772 787 788 789 806 P A B 26 distorted distorted 794 807 808 809 828 P C B 27 distorted distorted 814 829 830 831 848 P A B 28 distorted distorted 836 849 850 851 870 P C B 29 distorted distorted 856 871 872 873 890 P G B 30 distorted distorted 878 891 892 893 913 P A B 31 distorted distorted 898 914 915 916 953 P C C 32 distorted distorted 941 954 955 956 973 P G C 33 distorted distorted 961 974 975 976 996 P U C 34 distorted distorted 981 997 998 999 1016 P G C 35 distorted distorted 1004 1017 1018 1019 1039 P G C 36 distorted distorted 1024 1040 1041 1042 1062 P U C 37 distorted distorted 1047 1063 1064 1065 1082 P C C 38 distorted distorted 1070 1083 1084 1085 1102 P C C 39 distorted distorted 1090 1103 1104 1105 1122 P A C 40 distorted distorted 1110 1123 1124 1125 1144 P U C 41 distorted distorted 1130 1145 1146 1147 1164 P U C 42 distorted distorted 1152 1165 1166 1167 1184 P A C 43 distorted distorted 1172 1185 1186 1187 1206 P C C 44 distorted distorted 1192 1207 1208 1209 1226 P C C 45 distorted distorted 1214 1227 1228 1229 1246 P U C 46 distorted distorted 1234 1247 1248 1249 1266 P G C 47 distorted distorted 1254 1267 1268 1269 1289 P C C 48 distorted distorted 1274 1290 1291 1292 1309 P C C 49 distorted distorted 1297 1310 1311 1312 ---------------------------------------------------------------------------------