ID code: '2FGP' 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 398 404 401 421 C1' N6G B 8 beta 420 422 433 448 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 533 539 536 559 C1' G C 15 beta 554 560 557 582 C1' G C 16 beta 577 583 580 605 C1' C C 17 beta 600 606 603 625 C1' A C 18 beta 620 626 623 647 C1' G C 19 beta 642 648 645 670 C1' A C 20 beta 665 671 668 692 C1' G C 21 beta 687 693 690 715 C1' A C 22 beta 710 716 713 737 C1' A C 23 beta 732 738 735 759 C1' A C 24 beta 754 760 757 781 C1' C C 25 beta 776 782 779 801 C1' A C 26 beta 796 802 799 823 C1' C C 27 beta 818 824 821 843 C1' A C 28 beta 838 844 841 865 C1' C C 29 beta 860 866 863 885 C1' G C 30 beta 880 886 883 908 C1' A C 31 beta 903 909 906 928 C1' U D 31 beta 923 929 926 948 C1' C D 32 beta 943 949 946 968 C1' G D 33 beta 963 969 966 991 C1' U D 34 beta 986 992 989 1011 C1' G D 35 beta 1006 1012 1009 1034 C1' G D 36 beta 1029 1035 1032 1057 C1' U D 37 beta 1052 1058 1055 1077 C1' A D 38 beta 1072 1078 1075 1099 C1' C D 39 beta 1094 1100 1097 1119 C1' A D 40 beta 1114 1120 1117 1141 C1' U D 41 beta 1136 1142 1139 1161 C1' U D 42 beta 1156 1162 1159 1181 C1' A D 43 beta 1176 1182 1179 1203 C1' C D 44 beta 1198 1204 1201 1223 C1' C D 45 beta 1218 1224 1221 1243 C1' U D 46 beta 1238 1244 1241 1263 C1' G D 47 beta 1258 1264 1261 1286 C1' C D 48 beta 1281 1287 1284 1306 C1' C D 49 beta 1301 1307 1304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 403 399 402 433 C2' N6G B 8 OK 421 435 434 446 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 538 534 537 557 C2' G C 15 OK 559 555 558 580 C2' G C 16 OK 582 578 581 603 C2' C C 17 OK 605 601 604 623 C2' A C 18 OK 625 621 624 645 C2' G C 19 OK 647 643 646 668 C2' A C 20 OK 670 666 669 690 C2' G C 21 OK 692 688 691 713 C2' A C 22 OK 715 711 714 735 C2' A C 23 OK 737 733 736 757 C2' A C 24 OK 759 755 758 779 C2' C C 25 OK 781 777 780 799 C2' A C 26 OK 801 797 800 821 C2' C C 27 OK 823 819 822 841 C2' A C 28 OK 843 839 842 863 C2' C C 29 OK 865 861 864 883 C2' G C 30 OK 885 881 884 906 C2' A C 31 OK 908 904 907 926 C2' U D 31 OK 928 924 927 946 C2' C D 32 OK 948 944 947 966 C2' G D 33 OK 968 964 967 989 C2' U D 34 OK 991 987 990 1009 C2' G D 35 OK 1011 1007 1010 1032 C2' G D 36 OK 1034 1030 1033 1055 C2' U D 37 OK 1057 1053 1056 1075 C2' A D 38 OK 1077 1073 1076 1097 C2' C D 39 OK 1099 1095 1098 1117 C2' A D 40 OK 1119 1115 1118 1139 C2' U D 41 OK 1141 1137 1140 1159 C2' U D 42 OK 1161 1157 1160 1179 C2' A D 43 OK 1181 1177 1180 1201 C2' C D 44 OK 1203 1199 1202 1221 C2' C D 45 OK 1223 1219 1222 1241 C2' U D 46 OK 1243 1239 1242 1261 C2' G D 47 OK 1263 1259 1262 1284 C2' C D 48 OK 1286 1282 1285 1304 C2' C D 49 OK 1306 1302 1305 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 397 400 401 435 C3' N6G B 8 OK 419 436 433 444 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 532 535 536 555 C3' G C 15 OK 553 556 557 578 C3' G C 16 OK 576 579 580 601 C3' C C 17 OK 599 602 603 621 C3' A C 18 OK 619 622 623 643 C3' G C 19 OK 641 644 645 666 C3' A C 20 OK 664 667 668 688 C3' G C 21 OK 686 689 690 711 C3' A C 22 OK 709 712 713 733 C3' A C 23 OK 731 734 735 755 C3' A C 24 OK 753 756 757 777 C3' C C 25 OK 775 778 779 797 C3' A C 26 OK 795 798 799 819 C3' C C 27 OK 817 820 821 839 C3' A C 28 OK 837 840 841 861 C3' C C 29 OK 859 862 863 881 C3' G C 30 OK 879 882 883 904 C3' A C 31 OK 902 905 906 924 C3' U D 31 OK 922 925 926 944 C3' C D 32 OK 942 945 946 964 C3' G D 33 OK 962 965 966 987 C3' U D 34 OK 985 988 989 1007 C3' G D 35 OK 1005 1008 1009 1030 C3' G D 36 OK 1028 1031 1032 1053 C3' U D 37 OK 1051 1054 1055 1073 C3' A D 38 OK 1071 1074 1075 1095 C3' C D 39 OK 1093 1096 1097 1115 C3' A D 40 OK 1113 1116 1117 1137 C3' U D 41 OK 1135 1138 1139 1157 C3' U D 42 OK 1155 1158 1159 1177 C3' A D 43 OK 1175 1178 1179 1199 C3' C D 44 OK 1197 1200 1201 1219 C3' C D 45 OK 1217 1220 1221 1239 C3' U D 46 OK 1237 1240 1241 1259 C3' G D 47 OK 1257 1260 1261 1282 C3' C D 48 OK 1280 1283 1284 1302 C3' C D 49 OK 1300 1303 1304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' N6G B 8 OK 435 418 420 442 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 534 531 533 553 C4' G C 15 OK 555 552 554 576 C4' G C 16 OK 578 575 577 599 C4' C C 17 OK 601 598 600 619 C4' A C 18 OK 621 618 620 641 C4' G C 19 OK 643 640 642 664 C4' A C 20 OK 666 663 665 686 C4' G C 21 OK 688 685 687 709 C4' A C 22 OK 711 708 710 731 C4' A C 23 OK 733 730 732 753 C4' A C 24 OK 755 752 754 775 C4' C C 25 OK 777 774 776 795 C4' A C 26 OK 797 794 796 817 C4' C C 27 OK 819 816 818 837 C4' A C 28 OK 839 836 838 859 C4' C C 29 OK 861 858 860 879 C4' G C 30 OK 881 878 880 902 C4' A C 31 OK 904 901 903 922 C4' U D 31 OK 924 921 923 942 C4' C D 32 OK 944 941 943 962 C4' G D 33 OK 964 961 963 985 C4' U D 34 OK 987 984 986 1005 C4' G D 35 OK 1007 1004 1006 1028 C4' G D 36 OK 1030 1027 1029 1051 C4' U D 37 OK 1053 1050 1052 1071 C4' A D 38 OK 1073 1070 1072 1093 C4' C D 39 OK 1095 1092 1094 1113 C4' A D 40 OK 1115 1112 1114 1135 C4' U D 41 OK 1137 1134 1136 1155 C4' U D 42 OK 1157 1154 1156 1175 C4' A D 43 OK 1177 1174 1176 1197 C4' C D 44 OK 1199 1196 1198 1217 C4' C D 45 OK 1219 1216 1218 1237 C4' U D 46 OK 1239 1236 1238 1257 C4' G D 47 OK 1259 1256 1258 1280 C4' C D 48 OK 1282 1279 1281 1300 C4' C D 49 OK 1302 1299 1301 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' N6G 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 13 530 532 552 C5' G C 15 551 553 575 C5' G C 16 574 576 598 C5' C C 17 597 599 618 C5' A C 18 617 619 640 C5' G C 19 639 641 663 C5' A C 20 662 664 685 C5' G C 21 684 686 708 C5' A C 22 707 709 730 C5' A C 23 729 731 752 C5' A C 24 751 753 774 C5' C C 25 773 775 794 C5' A C 26 793 795 816 C5' C C 27 815 817 836 C5' A C 28 835 837 858 C5' C C 29 857 859 878 C5' G C 30 877 879 901 C5' A C 31 900 902 921 C5' U D 31 920 922 941 C5' C D 32 940 942 961 C5' G D 33 960 962 984 C5' U D 34 983 985 1004 C5' G D 35 1003 1005 1027 C5' G D 36 1026 1028 1050 C5' U D 37 1049 1051 1070 C5' A D 38 1069 1071 1092 C5' C D 39 1091 1093 1112 C5' A D 40 1111 1113 1134 C5' U D 41 1133 1135 1154 C5' U D 42 1153 1155 1174 C5' A D 43 1173 1175 1196 C5' C D 44 1195 1197 1216 C5' C D 45 1215 1217 1236 C5' U D 46 1235 1237 1256 C5' G D 47 1255 1257 1279 C5' C D 48 1278 1280 1299 C5' C D 49 1298 1300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 N6G B 8 distorted distorted 400 415 416 417 437 P A B 9 distorted distorted 436 438 439 440 459 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 512 528 529 530 571 P G C 16 distorted distorted 556 572 573 574 594 P C C 17 distorted distorted 579 595 596 597 614 P A C 18 distorted distorted 602 615 616 617 636 P G C 19 distorted distorted 622 637 638 639 659 P A C 20 distorted distorted 644 660 661 662 681 P G C 21 distorted distorted 667 682 683 684 704 P A C 22 distorted distorted 689 705 706 707 726 P A C 23 distorted distorted 712 727 728 729 748 P A C 24 distorted distorted 734 749 750 751 770 P C C 25 distorted distorted 756 771 772 773 790 P A C 26 distorted distorted 778 791 792 793 812 P C C 27 distorted distorted 798 813 814 815 832 P A C 28 distorted distorted 820 833 834 835 854 P C C 29 distorted distorted 840 855 856 857 874 P G C 30 distorted distorted 862 875 876 877 897 P A C 31 distorted distorted 882 898 899 900 937 P C D 32 distorted distorted 925 938 939 940 957 P G D 33 distorted distorted 945 958 959 960 980 P U D 34 distorted distorted 965 981 982 983 1000 P G D 35 distorted distorted 988 1001 1002 1003 1023 P G D 36 distorted distorted 1008 1024 1025 1026 1046 P U D 37 distorted distorted 1031 1047 1048 1049 1066 P A D 38 distorted distorted 1054 1067 1068 1069 1088 P C D 39 distorted distorted 1074 1089 1090 1091 1108 P A D 40 distorted distorted 1096 1109 1110 1111 1130 P U D 41 distorted distorted 1116 1131 1132 1133 1150 P U D 42 distorted distorted 1138 1151 1152 1153 1170 P A D 43 distorted distorted 1158 1171 1172 1173 1192 P C D 44 distorted distorted 1178 1193 1194 1195 1212 P C D 45 distorted distorted 1200 1213 1214 1215 1232 P U D 46 distorted distorted 1220 1233 1234 1235 1252 P G D 47 distorted distorted 1240 1253 1254 1255 1275 P C D 48 distorted distorted 1260 1276 1277 1278 1295 P C D 49 distorted distorted 1283 1296 1297 1298 ---------------------------------------------------------------------------------