ID code: '1ZFX' 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' U B 8 beta 420 426 423 445 C1' A B 9 beta 440 446 443 467 C1' A B 10 beta 462 468 465 489 C1' G B 11 beta 484 490 487 512 C1' G B 12 beta 507 513 510 535 C1' G B 13 beta 530 536 533 556 C1' G C 15 beta 551 557 554 579 C1' G C 16 beta 574 580 577 602 C1' C C 17 beta 597 603 600 622 C1' A C 18 beta 617 623 620 644 C1' G C 19 beta 639 645 642 667 C1' A C 20 beta 662 668 665 689 C1' G C 21 beta 684 690 687 712 C1' A C 22 beta 707 713 710 734 C1' A C 23 beta 729 735 732 756 C1' A C 24 beta 751 757 754 778 C1' C C 25 beta 773 779 776 798 C1' A C 26 beta 793 799 796 820 C1' C C 27 beta 815 821 818 840 C1' A C 28 beta 835 841 838 862 C1' C C 29 beta 857 863 860 882 C1' G C 30 beta 877 883 880 905 C1' A C 31 beta 900 906 903 925 C1' U D 31 beta 920 926 923 945 C1' C D 32 beta 940 946 943 965 C1' G D 33 beta 960 966 963 988 C1' U D 34 beta 983 989 986 1008 C1' G D 35 beta 1003 1009 1006 1031 C1' G D 36 beta 1026 1032 1029 1054 C1' U D 37 beta 1049 1055 1052 1074 C1' A D 38 beta 1069 1075 1072 1096 C1' C D 39 beta 1091 1097 1094 1116 C1' A D 40 beta 1111 1117 1114 1138 C1' U D 41 beta 1133 1139 1136 1158 C1' U D 42 beta 1153 1159 1156 1178 C1' A D 43 beta 1173 1179 1176 1200 C1' C D 44 beta 1195 1201 1198 1220 C1' C D 45 beta 1215 1221 1218 1240 C1' U D 46 beta 1235 1241 1238 1260 C1' G D 47 beta 1255 1261 1258 1283 C1' C D 48 beta 1278 1284 1281 1303 C1' C D 49 beta 1298 1304 1301 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U B 8 OK 425 421 424 443 C2' A B 9 OK 445 441 444 465 C2' A B 10 OK 467 463 466 487 C2' G B 11 OK 489 485 488 510 C2' G B 12 OK 512 508 511 533 C2' G B 13 OK 535 531 534 554 C2' G C 15 OK 556 552 555 577 C2' G C 16 OK 579 575 578 600 C2' C C 17 OK 602 598 601 620 C2' A C 18 OK 622 618 621 642 C2' G C 19 OK 644 640 643 665 C2' A C 20 OK 667 663 666 687 C2' G C 21 OK 689 685 688 710 C2' A C 22 OK 712 708 711 732 C2' A C 23 OK 734 730 733 754 C2' A C 24 OK 756 752 755 776 C2' C C 25 OK 778 774 777 796 C2' A C 26 OK 798 794 797 818 C2' C C 27 OK 820 816 819 838 C2' A C 28 OK 840 836 839 860 C2' C C 29 OK 862 858 861 880 C2' G C 30 OK 882 878 881 903 C2' A C 31 OK 905 901 904 923 C2' U D 31 OK 925 921 924 943 C2' C D 32 OK 945 941 944 963 C2' G D 33 OK 965 961 964 986 C2' U D 34 OK 988 984 987 1006 C2' G D 35 OK 1008 1004 1007 1029 C2' G D 36 OK 1031 1027 1030 1052 C2' U D 37 OK 1054 1050 1053 1072 C2' A D 38 OK 1074 1070 1073 1094 C2' C D 39 OK 1096 1092 1095 1114 C2' A D 40 OK 1116 1112 1115 1136 C2' U D 41 OK 1138 1134 1137 1156 C2' U D 42 OK 1158 1154 1157 1176 C2' A D 43 OK 1178 1174 1177 1198 C2' C D 44 OK 1200 1196 1199 1218 C2' C D 45 OK 1220 1216 1219 1238 C2' U D 46 OK 1240 1236 1239 1258 C2' G D 47 OK 1260 1256 1259 1281 C2' C D 48 OK 1283 1279 1282 1301 C2' C D 49 OK 1303 1299 1302 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U B 8 OK 419 422 423 441 C3' A B 9 OK 439 442 443 463 C3' A B 10 OK 461 464 465 485 C3' G B 11 OK 483 486 487 508 C3' G B 12 OK 506 509 510 531 C3' G B 13 OK 529 532 533 552 C3' G C 15 OK 550 553 554 575 C3' G C 16 OK 573 576 577 598 C3' C C 17 OK 596 599 600 618 C3' A C 18 OK 616 619 620 640 C3' G C 19 OK 638 641 642 663 C3' A C 20 OK 661 664 665 685 C3' G C 21 OK 683 686 687 708 C3' A C 22 OK 706 709 710 730 C3' A C 23 OK 728 731 732 752 C3' A C 24 OK 750 753 754 774 C3' C C 25 OK 772 775 776 794 C3' A C 26 OK 792 795 796 816 C3' C C 27 OK 814 817 818 836 C3' A C 28 OK 834 837 838 858 C3' C C 29 OK 856 859 860 878 C3' G C 30 OK 876 879 880 901 C3' A C 31 OK 899 902 903 921 C3' U D 31 OK 919 922 923 941 C3' C D 32 OK 939 942 943 961 C3' G D 33 OK 959 962 963 984 C3' U D 34 OK 982 985 986 1004 C3' G D 35 OK 1002 1005 1006 1027 C3' G D 36 OK 1025 1028 1029 1050 C3' U D 37 OK 1048 1051 1052 1070 C3' A D 38 OK 1068 1071 1072 1092 C3' C D 39 OK 1090 1093 1094 1112 C3' A D 40 OK 1110 1113 1114 1134 C3' U D 41 OK 1132 1135 1136 1154 C3' U D 42 OK 1152 1155 1156 1174 C3' A D 43 OK 1172 1175 1176 1196 C3' C D 44 OK 1194 1197 1198 1216 C3' C D 45 OK 1214 1217 1218 1236 C3' U D 46 OK 1234 1237 1238 1256 C3' G D 47 OK 1254 1257 1258 1279 C3' C D 48 OK 1277 1280 1281 1299 C3' C D 49 OK 1297 1300 1301 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U B 8 OK 421 418 420 439 C4' A B 9 OK 441 438 440 461 C4' A B 10 OK 463 460 462 483 C4' G B 11 OK 485 482 484 506 C4' G B 12 OK 508 505 507 529 C4' G B 13 OK 531 528 530 550 C4' G C 15 OK 552 549 551 573 C4' G C 16 OK 575 572 574 596 C4' C C 17 OK 598 595 597 616 C4' A C 18 OK 618 615 617 638 C4' G C 19 OK 640 637 639 661 C4' A C 20 OK 663 660 662 683 C4' G C 21 OK 685 682 684 706 C4' A C 22 OK 708 705 707 728 C4' A C 23 OK 730 727 729 750 C4' A C 24 OK 752 749 751 772 C4' C C 25 OK 774 771 773 792 C4' A C 26 OK 794 791 793 814 C4' C C 27 OK 816 813 815 834 C4' A C 28 OK 836 833 835 856 C4' C C 29 OK 858 855 857 876 C4' G C 30 OK 878 875 877 899 C4' A C 31 OK 901 898 900 919 C4' U D 31 OK 921 918 920 939 C4' C D 32 OK 941 938 940 959 C4' G D 33 OK 961 958 960 982 C4' U D 34 OK 984 981 983 1002 C4' G D 35 OK 1004 1001 1003 1025 C4' G D 36 OK 1027 1024 1026 1048 C4' U D 37 OK 1050 1047 1049 1068 C4' A D 38 OK 1070 1067 1069 1090 C4' C D 39 OK 1092 1089 1091 1110 C4' A D 40 OK 1112 1109 1111 1132 C4' U D 41 OK 1134 1131 1133 1152 C4' U D 42 OK 1154 1151 1153 1172 C4' A D 43 OK 1174 1171 1173 1194 C4' C D 44 OK 1196 1193 1195 1214 C4' C D 45 OK 1216 1213 1215 1234 C4' U D 46 OK 1236 1233 1235 1254 C4' G D 47 OK 1256 1253 1255 1277 C4' C D 48 OK 1279 1276 1278 1297 C4' C D 49 OK 1299 1296 1298 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U B 8 417 419 438 C5' A B 9 437 439 460 C5' A B 10 459 461 482 C5' G B 11 481 483 505 C5' G B 12 504 506 528 C5' G B 13 527 529 549 C5' G C 15 548 550 572 C5' G C 16 571 573 595 C5' C C 17 594 596 615 C5' A C 18 614 616 637 C5' G C 19 636 638 660 C5' A C 20 659 661 682 C5' G C 21 681 683 705 C5' A C 22 704 706 727 C5' A C 23 726 728 749 C5' A C 24 748 750 771 C5' C C 25 770 772 791 C5' A C 26 790 792 813 C5' C C 27 812 814 833 C5' A C 28 832 834 855 C5' C C 29 854 856 875 C5' G C 30 874 876 898 C5' A C 31 897 899 918 C5' U D 31 917 919 938 C5' C D 32 937 939 958 C5' G D 33 957 959 981 C5' U D 34 980 982 1001 C5' G D 35 1000 1002 1024 C5' G D 36 1023 1025 1047 C5' U D 37 1046 1048 1067 C5' A D 38 1066 1068 1089 C5' C D 39 1088 1090 1109 C5' A D 40 1108 1110 1131 C5' U D 41 1130 1132 1151 C5' U D 42 1150 1152 1171 C5' A D 43 1170 1172 1193 C5' C D 44 1192 1194 1213 C5' C D 45 1212 1214 1233 C5' U D 46 1232 1234 1253 C5' G D 47 1252 1254 1276 C5' C D 48 1275 1277 1296 C5' C D 49 1295 1297 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 distorted distorted 103 118 119 120 140 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 U B 8 distorted distorted 400 415 416 417 434 P A B 9 distorted distorted 422 435 436 437 456 P A B 10 distorted distorted 442 457 458 459 478 P G B 11 distorted distorted 464 479 480 481 501 P G B 12 distorted distorted 486 502 503 504 524 P G B 13 distorted distorted 509 525 526 527 568 P G C 16 distorted distorted 553 569 570 571 591 P C C 17 distorted distorted 576 592 593 594 611 P A C 18 distorted distorted 599 612 613 614 633 P G C 19 distorted distorted 619 634 635 636 656 P A C 20 distorted distorted 641 657 658 659 678 P G C 21 distorted distorted 664 679 680 681 701 P A C 22 distorted distorted 686 702 703 704 723 P A C 23 distorted distorted 709 724 725 726 745 P A C 24 distorted distorted 731 746 747 748 767 P C C 25 distorted distorted 753 768 769 770 787 P A C 26 distorted distorted 775 788 789 790 809 P C C 27 distorted distorted 795 810 811 812 829 P A C 28 distorted distorted 817 830 831 832 851 P C C 29 distorted distorted 837 852 853 854 871 P G C 30 distorted distorted 859 872 873 874 894 P A C 31 distorted distorted 879 895 896 897 934 P C D 32 distorted distorted 922 935 936 937 954 P G D 33 distorted distorted 942 955 956 957 977 P U D 34 distorted distorted 962 978 979 980 997 P G D 35 distorted distorted 985 998 999 1000 1020 P G D 36 distorted distorted 1005 1021 1022 1023 1043 P U D 37 distorted distorted 1028 1044 1045 1046 1063 P A D 38 distorted distorted 1051 1064 1065 1066 1085 P C D 39 distorted distorted 1071 1086 1087 1088 1105 P A D 40 distorted distorted 1093 1106 1107 1108 1127 P U D 41 distorted distorted 1113 1128 1129 1130 1147 P U D 42 distorted distorted 1135 1148 1149 1150 1167 P A D 43 distorted distorted 1155 1168 1169 1170 1189 P C D 44 distorted distorted 1175 1190 1191 1192 1209 P C D 45 distorted distorted 1197 1210 1211 1212 1229 P U D 46 distorted distorted 1217 1230 1231 1232 1249 P G D 47 distorted distorted 1237 1250 1251 1252 1272 P C D 48 distorted distorted 1257 1273 1274 1275 1292 P C D 49 distorted distorted 1280 1293 1294 1295 ---------------------------------------------------------------------------------