ID code: '2BCY' 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' MTU B 8 beta 420 422 432 447 C1' A B 9 beta 442 448 445 469 C1' A B 10 beta 464 470 467 491 C1' G B 11 beta 486 492 489 514 C1' G B 12 beta 509 515 512 537 C1' G B 13 beta 532 538 535 558 C1' G C 15 beta 553 559 556 581 C1' G C 16 beta 576 582 579 604 C1' C C 17 beta 599 605 602 624 C1' A C 18 beta 619 625 622 646 C1' G C 19 beta 641 647 644 669 C1' A C 20 beta 664 670 667 691 C1' G C 21 beta 686 692 689 714 C1' A C 22 beta 709 715 712 736 C1' A C 23 beta 731 737 734 758 C1' A C 24 beta 753 759 756 780 C1' C C 25 beta 775 781 778 800 C1' A C 26 beta 795 801 798 822 C1' C C 27 beta 817 823 820 842 C1' A C 28 beta 837 843 840 864 C1' C C 29 beta 859 865 862 884 C1' G C 30 beta 879 885 882 907 C1' A C 31 beta 902 908 905 927 C1' U D 31 beta 922 928 925 947 C1' C D 32 beta 942 948 945 967 C1' G D 33 beta 962 968 965 990 C1' U D 34 beta 985 991 988 1010 C1' G D 35 beta 1005 1011 1008 1033 C1' G D 36 beta 1028 1034 1031 1056 C1' U D 37 beta 1051 1057 1054 1076 C1' A D 38 beta 1071 1077 1074 1098 C1' C D 39 beta 1093 1099 1096 1118 C1' A D 40 beta 1113 1119 1116 1140 C1' U D 41 beta 1135 1141 1138 1160 C1' U D 42 beta 1155 1161 1158 1180 C1' A D 43 beta 1175 1181 1178 1202 C1' C D 44 beta 1197 1203 1200 1222 C1' C D 45 beta 1217 1223 1220 1242 C1' U D 46 beta 1237 1243 1240 1262 C1' G D 47 beta 1257 1263 1260 1285 C1' C D 48 beta 1280 1286 1283 1305 C1' C D 49 beta 1300 1306 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 403 399 402 432 C2' MTU B 8 OK 421 434 433 445 C2' A B 9 OK 447 443 446 467 C2' A B 10 OK 469 465 468 489 C2' G B 11 OK 491 487 490 512 C2' G B 12 OK 514 510 513 535 C2' G B 13 OK 537 533 536 556 C2' G C 15 OK 558 554 557 579 C2' G C 16 OK 581 577 580 602 C2' C C 17 OK 604 600 603 622 C2' A C 18 OK 624 620 623 644 C2' G C 19 OK 646 642 645 667 C2' A C 20 OK 669 665 668 689 C2' G C 21 OK 691 687 690 712 C2' A C 22 OK 714 710 713 734 C2' A C 23 OK 736 732 735 756 C2' A C 24 OK 758 754 757 778 C2' C C 25 OK 780 776 779 798 C2' A C 26 OK 800 796 799 820 C2' C C 27 OK 822 818 821 840 C2' A C 28 OK 842 838 841 862 C2' C C 29 OK 864 860 863 882 C2' G C 30 OK 884 880 883 905 C2' A C 31 OK 907 903 906 925 C2' U D 31 OK 927 923 926 945 C2' C D 32 OK 947 943 946 965 C2' G D 33 OK 967 963 966 988 C2' U D 34 OK 990 986 989 1008 C2' G D 35 OK 1010 1006 1009 1031 C2' G D 36 OK 1033 1029 1032 1054 C2' U D 37 OK 1056 1052 1055 1074 C2' A D 38 OK 1076 1072 1075 1096 C2' C D 39 OK 1098 1094 1097 1116 C2' A D 40 OK 1118 1114 1117 1138 C2' U D 41 OK 1140 1136 1139 1158 C2' U D 42 OK 1160 1156 1159 1178 C2' A D 43 OK 1180 1176 1179 1200 C2' C D 44 OK 1202 1198 1201 1220 C2' C D 45 OK 1222 1218 1221 1240 C2' U D 46 OK 1242 1238 1241 1260 C2' G D 47 OK 1262 1258 1261 1283 C2' C D 48 OK 1285 1281 1284 1303 C2' C D 49 OK 1305 1301 1304 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 397 400 401 434 C3' MTU B 8 OK 419 435 432 443 C3' A B 9 OK 441 444 445 465 C3' A B 10 OK 463 466 467 487 C3' G B 11 OK 485 488 489 510 C3' G B 12 OK 508 511 512 533 C3' G B 13 OK 531 534 535 554 C3' G C 15 OK 552 555 556 577 C3' G C 16 OK 575 578 579 600 C3' C C 17 OK 598 601 602 620 C3' A C 18 OK 618 621 622 642 C3' G C 19 OK 640 643 644 665 C3' A C 20 OK 663 666 667 687 C3' G C 21 OK 685 688 689 710 C3' A C 22 OK 708 711 712 732 C3' A C 23 OK 730 733 734 754 C3' A C 24 OK 752 755 756 776 C3' C C 25 OK 774 777 778 796 C3' A C 26 OK 794 797 798 818 C3' C C 27 OK 816 819 820 838 C3' A C 28 OK 836 839 840 860 C3' C C 29 OK 858 861 862 880 C3' G C 30 OK 878 881 882 903 C3' A C 31 OK 901 904 905 923 C3' U D 31 OK 921 924 925 943 C3' C D 32 OK 941 944 945 963 C3' G D 33 OK 961 964 965 986 C3' U D 34 OK 984 987 988 1006 C3' G D 35 OK 1004 1007 1008 1029 C3' G D 36 OK 1027 1030 1031 1052 C3' U D 37 OK 1050 1053 1054 1072 C3' A D 38 OK 1070 1073 1074 1094 C3' C D 39 OK 1092 1095 1096 1114 C3' A D 40 OK 1112 1115 1116 1136 C3' U D 41 OK 1134 1137 1138 1156 C3' U D 42 OK 1154 1157 1158 1176 C3' A D 43 OK 1174 1177 1178 1198 C3' C D 44 OK 1196 1199 1200 1218 C3' C D 45 OK 1216 1219 1220 1238 C3' U D 46 OK 1236 1239 1240 1258 C3' G D 47 OK 1256 1259 1260 1281 C3' C D 48 OK 1279 1282 1283 1301 C3' C D 49 OK 1299 1302 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' MTU B 8 OK 434 418 420 441 C4' A B 9 OK 443 440 442 463 C4' A B 10 OK 465 462 464 485 C4' G B 11 OK 487 484 486 508 C4' G B 12 OK 510 507 509 531 C4' G B 13 OK 533 530 532 552 C4' G C 15 OK 554 551 553 575 C4' G C 16 OK 577 574 576 598 C4' C C 17 OK 600 597 599 618 C4' A C 18 OK 620 617 619 640 C4' G C 19 OK 642 639 641 663 C4' A C 20 OK 665 662 664 685 C4' G C 21 OK 687 684 686 708 C4' A C 22 OK 710 707 709 730 C4' A C 23 OK 732 729 731 752 C4' A C 24 OK 754 751 753 774 C4' C C 25 OK 776 773 775 794 C4' A C 26 OK 796 793 795 816 C4' C C 27 OK 818 815 817 836 C4' A C 28 OK 838 835 837 858 C4' C C 29 OK 860 857 859 878 C4' G C 30 OK 880 877 879 901 C4' A C 31 OK 903 900 902 921 C4' U D 31 OK 923 920 922 941 C4' C D 32 OK 943 940 942 961 C4' G D 33 OK 963 960 962 984 C4' U D 34 OK 986 983 985 1004 C4' G D 35 OK 1006 1003 1005 1027 C4' G D 36 OK 1029 1026 1028 1050 C4' U D 37 OK 1052 1049 1051 1070 C4' A D 38 OK 1072 1069 1071 1092 C4' C D 39 OK 1094 1091 1093 1112 C4' A D 40 OK 1114 1111 1113 1134 C4' U D 41 OK 1136 1133 1135 1154 C4' U D 42 OK 1156 1153 1155 1174 C4' A D 43 OK 1176 1173 1175 1196 C4' C D 44 OK 1198 1195 1197 1216 C4' C D 45 OK 1218 1215 1217 1236 C4' U D 46 OK 1238 1235 1237 1256 C4' G D 47 OK 1258 1255 1257 1279 C4' C D 48 OK 1281 1278 1280 1299 C4' C D 49 OK 1301 1298 1300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' MTU B 8 417 419 440 C5' A B 9 439 441 462 C5' A B 10 461 463 484 C5' G B 11 483 485 507 C5' G B 12 506 508 530 C5' G B 13 529 531 551 C5' G C 15 550 552 574 C5' G C 16 573 575 597 C5' C C 17 596 598 617 C5' A C 18 616 618 639 C5' G C 19 638 640 662 C5' A C 20 661 663 684 C5' G C 21 683 685 707 C5' A C 22 706 708 729 C5' A C 23 728 730 751 C5' A C 24 750 752 773 C5' C C 25 772 774 793 C5' A C 26 792 794 815 C5' C C 27 814 816 835 C5' A C 28 834 836 857 C5' C C 29 856 858 877 C5' G C 30 876 878 900 C5' A C 31 899 901 920 C5' U D 31 919 921 940 C5' C D 32 939 941 960 C5' G D 33 959 961 983 C5' U D 34 982 984 1003 C5' G D 35 1002 1004 1026 C5' G D 36 1025 1027 1049 C5' U D 37 1048 1050 1069 C5' A D 38 1068 1070 1091 C5' C D 39 1090 1092 1111 C5' A D 40 1110 1112 1133 C5' U D 41 1132 1134 1153 C5' U D 42 1152 1154 1173 C5' A D 43 1172 1174 1195 C5' C D 44 1194 1196 1215 C5' C D 45 1214 1216 1235 C5' U D 46 1234 1236 1255 C5' G D 47 1254 1256 1278 C5' C D 48 1277 1279 1298 C5' C D 49 1297 1299 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 MTU B 8 distorted distorted 400 415 416 417 436 P A B 9 distorted distorted 435 437 438 439 458 P A B 10 distorted distorted 444 459 460 461 480 P G B 11 distorted distorted 466 481 482 483 503 P G B 12 distorted distorted 488 504 505 506 526 P G B 13 distorted distorted 511 527 528 529 570 P G C 16 distorted distorted 555 571 572 573 593 P C C 17 distorted distorted 578 594 595 596 613 P A C 18 distorted distorted 601 614 615 616 635 P G C 19 distorted distorted 621 636 637 638 658 P A C 20 distorted distorted 643 659 660 661 680 P G C 21 distorted distorted 666 681 682 683 703 P A C 22 distorted distorted 688 704 705 706 725 P A C 23 distorted distorted 711 726 727 728 747 P A C 24 distorted distorted 733 748 749 750 769 P C C 25 distorted distorted 755 770 771 772 789 P A C 26 distorted distorted 777 790 791 792 811 P C C 27 distorted distorted 797 812 813 814 831 P A C 28 distorted distorted 819 832 833 834 853 P C C 29 distorted distorted 839 854 855 856 873 P G C 30 distorted distorted 861 874 875 876 896 P A C 31 distorted distorted 881 897 898 899 936 P C D 32 distorted distorted 924 937 938 939 956 P G D 33 distorted distorted 944 957 958 959 979 P U D 34 distorted distorted 964 980 981 982 999 P G D 35 distorted distorted 987 1000 1001 1002 1022 P G D 36 distorted distorted 1007 1023 1024 1025 1045 P U D 37 distorted distorted 1030 1046 1047 1048 1065 P A D 38 distorted distorted 1053 1066 1067 1068 1087 P C D 39 distorted distorted 1073 1088 1089 1090 1107 P A D 40 distorted distorted 1095 1108 1109 1110 1129 P U D 41 distorted distorted 1115 1130 1131 1132 1149 P U D 42 distorted distorted 1137 1150 1151 1152 1169 P A D 43 distorted distorted 1157 1170 1171 1172 1191 P C D 44 distorted distorted 1177 1192 1193 1194 1211 P C D 45 distorted distorted 1199 1212 1213 1214 1231 P U D 46 distorted distorted 1219 1232 1233 1234 1251 P G D 47 distorted distorted 1239 1252 1253 1254 1274 P C D 48 distorted distorted 1259 1275 1276 1277 1294 P C D 49 distorted distorted 1282 1295 1296 1297 ---------------------------------------------------------------------------------