ID code: '2N6X' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' A A 8 alpha beta 234 256 240 237 272 C1' C A 9 alpha beta 267 287 273 270 303 C1' G A 10 alpha beta 298 321 304 301 337 C1' U A 11 alpha beta 332 352 338 335 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' A A 14 alpha beta 429 451 435 432 467 C1' G A 15 alpha beta 462 485 468 465 501 C1' U A 16 alpha beta 496 516 502 499 531 C1' A A 17 alpha beta 526 548 532 529 564 C1' U A 18 alpha beta 559 579 565 562 594 C1' A A 19 alpha beta 589 611 595 592 627 C1' C A 20 alpha beta 622 642 628 625 658 C1' U A 21 alpha beta 653 673 659 656 688 C1' U A 22 alpha beta 683 703 689 686 718 C1' C A 23 alpha beta 713 733 719 716 749 C1' G A 24 alpha beta 744 767 750 747 783 C1' G A 25 alpha beta 778 801 784 781 817 C1' U A 26 alpha beta 812 832 818 815 847 C1' A A 27 alpha beta 842 864 848 845 880 C1' U A 28 alpha beta 875 895 881 878 910 C1' A A 29 alpha beta 905 927 911 908 943 C1' C A 30 alpha beta 938 958 944 941 974 C1' U A 31 alpha beta 969 989 975 972 1004 C1' U A 32 alpha beta 999 1019 1005 1002 1034 C1' A A 33 alpha beta 1029 1051 1035 1032 1067 C1' U A 34 alpha beta 1062 1082 1068 1065 1097 C1' A A 35 alpha beta 1092 1114 1098 1095 1130 C1' U A 36 alpha beta 1125 1145 1131 1128 1160 C1' A A 37 alpha beta 1155 1177 1161 1158 1193 C1' C A 38 alpha beta 1188 1208 1194 1191 1224 C1' U A 39 alpha beta 1219 1239 1225 1222 1254 C1' U A 40 alpha beta 1249 1269 1255 1252 1284 C1' A A 41 alpha beta 1279 1301 1285 1282 1317 C1' C A 42 alpha beta 1312 1332 1318 1315 1348 C1' C A 43 alpha beta 1343 1364 1349 1346 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' G A 6 OK OK 175 171 191 174 207 C2' U A 7 OK OK 209 205 222 208 237 C2' A A 8 OK OK 239 235 254 238 270 C2' C A 9 OK OK 272 268 285 271 301 C2' G A 10 OK OK 303 299 319 302 335 C2' U A 11 OK OK 337 333 350 336 365 C2' A A 12 OK OK 367 363 382 366 398 C2' G A 13 OK OK 400 396 416 399 432 C2' A A 14 OK OK 434 430 449 433 465 C2' G A 15 OK OK 467 463 483 466 499 C2' U A 16 OK OK 501 497 514 500 529 C2' A A 17 OK OK 531 527 546 530 562 C2' U A 18 OK OK 564 560 577 563 592 C2' A A 19 OK OK 594 590 609 593 625 C2' C A 20 OK OK 627 623 640 626 656 C2' U A 21 OK OK 658 654 671 657 686 C2' U A 22 OK OK 688 684 701 687 716 C2' C A 23 OK OK 718 714 731 717 747 C2' G A 24 OK OK 749 745 765 748 781 C2' G A 25 OK OK 783 779 799 782 815 C2' U A 26 OK OK 817 813 830 816 845 C2' A A 27 OK OK 847 843 862 846 878 C2' U A 28 OK OK 880 876 893 879 908 C2' A A 29 OK OK 910 906 925 909 941 C2' C A 30 OK OK 943 939 956 942 972 C2' U A 31 OK OK 974 970 987 973 1002 C2' U A 32 OK OK 1004 1000 1017 1003 1032 C2' A A 33 OK OK 1034 1030 1049 1033 1065 C2' U A 34 OK OK 1067 1063 1080 1066 1095 C2' A A 35 OK OK 1097 1093 1112 1096 1128 C2' U A 36 OK OK 1130 1126 1143 1129 1158 C2' A A 37 OK OK 1160 1156 1175 1159 1191 C2' C A 38 OK OK 1193 1189 1206 1192 1222 C2' U A 39 OK OK 1224 1220 1237 1223 1252 C2' U A 40 OK OK 1254 1250 1267 1253 1282 C2' A A 41 OK OK 1284 1280 1299 1283 1315 C2' C A 42 OK OK 1317 1313 1330 1316 1346 C2' C A 43 OK OK 1348 1344 1362 1347 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' G A 6 OK OK 169 190 172 173 205 C3' U A 7 OK OK 203 221 206 207 235 C3' A A 8 OK OK 233 253 236 237 268 C3' C A 9 OK OK 266 284 269 270 299 C3' G A 10 OK OK 297 318 300 301 333 C3' U A 11 OK OK 331 349 334 335 363 C3' A A 12 OK OK 361 381 364 365 396 C3' G A 13 OK OK 394 415 397 398 430 C3' A A 14 OK OK 428 448 431 432 463 C3' G A 15 OK OK 461 482 464 465 497 C3' U A 16 OK OK 495 513 498 499 527 C3' A A 17 OK OK 525 545 528 529 560 C3' U A 18 OK OK 558 576 561 562 590 C3' A A 19 OK OK 588 608 591 592 623 C3' C A 20 OK OK 621 639 624 625 654 C3' U A 21 OK OK 652 670 655 656 684 C3' U A 22 OK OK 682 700 685 686 714 C3' C A 23 OK OK 712 730 715 716 745 C3' G A 24 OK OK 743 764 746 747 779 C3' G A 25 OK OK 777 798 780 781 813 C3' U A 26 OK OK 811 829 814 815 843 C3' A A 27 OK OK 841 861 844 845 876 C3' U A 28 OK OK 874 892 877 878 906 C3' A A 29 OK OK 904 924 907 908 939 C3' C A 30 OK OK 937 955 940 941 970 C3' U A 31 OK OK 968 986 971 972 1000 C3' U A 32 OK OK 998 1016 1001 1002 1030 C3' A A 33 OK OK 1028 1048 1031 1032 1063 C3' U A 34 OK OK 1061 1079 1064 1065 1093 C3' A A 35 OK OK 1091 1111 1094 1095 1126 C3' U A 36 OK OK 1124 1142 1127 1128 1156 C3' A A 37 OK OK 1154 1174 1157 1158 1189 C3' C A 38 OK OK 1187 1205 1190 1191 1220 C3' U A 39 OK OK 1218 1236 1221 1222 1250 C3' U A 40 OK OK 1248 1266 1251 1252 1280 C3' A A 41 OK OK 1278 1298 1281 1282 1313 C3' C A 42 OK OK 1311 1329 1314 1315 1344 C3' C A 43 OK OK 1342 1360 1345 1346 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' G A 6 OK OK 171 189 168 170 203 C4' U A 7 OK OK 205 220 202 204 233 C4' A A 8 OK OK 235 252 232 234 266 C4' C A 9 OK OK 268 283 265 267 297 C4' G A 10 OK OK 299 317 296 298 331 C4' U A 11 OK OK 333 348 330 332 361 C4' A A 12 OK OK 363 380 360 362 394 C4' G A 13 OK OK 396 414 393 395 428 C4' A A 14 OK OK 430 447 427 429 461 C4' G A 15 OK OK 463 481 460 462 495 C4' U A 16 OK OK 497 512 494 496 525 C4' A A 17 OK OK 527 544 524 526 558 C4' U A 18 OK OK 560 575 557 559 588 C4' A A 19 OK OK 590 607 587 589 621 C4' C A 20 OK OK 623 638 620 622 652 C4' U A 21 OK OK 654 669 651 653 682 C4' U A 22 OK OK 684 699 681 683 712 C4' C A 23 OK OK 714 729 711 713 743 C4' G A 24 OK OK 745 763 742 744 777 C4' G A 25 OK OK 779 797 776 778 811 C4' U A 26 OK OK 813 828 810 812 841 C4' A A 27 OK OK 843 860 840 842 874 C4' U A 28 OK OK 876 891 873 875 904 C4' A A 29 OK OK 906 923 903 905 937 C4' C A 30 OK OK 939 954 936 938 968 C4' U A 31 OK OK 970 985 967 969 998 C4' U A 32 OK OK 1000 1015 997 999 1028 C4' A A 33 OK OK 1030 1047 1027 1029 1061 C4' U A 34 OK OK 1063 1078 1060 1062 1091 C4' A A 35 OK OK 1093 1110 1090 1092 1124 C4' U A 36 OK OK 1126 1141 1123 1125 1154 C4' A A 37 OK OK 1156 1173 1153 1155 1187 C4' C A 38 OK OK 1189 1204 1186 1188 1218 C4' U A 39 OK OK 1220 1235 1217 1219 1248 C4' U A 40 OK OK 1250 1265 1247 1249 1278 C4' A A 41 OK OK 1280 1297 1277 1279 1311 C4' C A 42 OK OK 1313 1328 1310 1312 1342 C4' C A 43 OK OK 1344 1359 1341 1343 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' G A 6 OK OK 167 187 188 169 202 C5' U A 7 OK OK 201 218 219 203 232 C5' A A 8 OK OK 231 250 251 233 265 C5' C A 9 OK OK 264 281 282 266 296 C5' G A 10 OK OK 295 315 316 297 330 C5' U A 11 OK OK 329 346 347 331 360 C5' A A 12 OK OK 359 378 379 361 393 C5' G A 13 OK OK 392 412 413 394 427 C5' A A 14 OK OK 426 445 446 428 460 C5' G A 15 OK OK 459 479 480 461 494 C5' U A 16 OK OK 493 510 511 495 524 C5' A A 17 OK OK 523 542 543 525 557 C5' U A 18 OK OK 556 573 574 558 587 C5' A A 19 OK OK 586 605 606 588 620 C5' C A 20 OK OK 619 636 637 621 651 C5' U A 21 OK OK 650 667 668 652 681 C5' U A 22 OK OK 680 697 698 682 711 C5' C A 23 OK OK 710 727 728 712 742 C5' G A 24 OK OK 741 761 762 743 776 C5' G A 25 OK OK 775 795 796 777 810 C5' U A 26 OK OK 809 826 827 811 840 C5' A A 27 OK OK 839 858 859 841 873 C5' U A 28 OK OK 872 889 890 874 903 C5' A A 29 OK OK 902 921 922 904 936 C5' C A 30 OK OK 935 952 953 937 967 C5' U A 31 OK OK 966 983 984 968 997 C5' U A 32 OK OK 996 1013 1014 998 1027 C5' A A 33 OK OK 1026 1045 1046 1028 1060 C5' U A 34 OK OK 1059 1076 1077 1061 1090 C5' A A 35 OK OK 1089 1108 1109 1091 1123 C5' U A 36 OK OK 1122 1139 1140 1124 1153 C5' A A 37 OK OK 1152 1171 1172 1154 1186 C5' C A 38 OK OK 1185 1202 1203 1187 1217 C5' U A 39 OK OK 1216 1233 1234 1218 1247 C5' U A 40 OK OK 1246 1263 1264 1248 1277 C5' A A 41 OK OK 1276 1295 1296 1278 1310 C5' C A 42 OK OK 1309 1326 1327 1311 1341 C5' C A 43 OK OK 1340 1357 1358 1342 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P G A 6 distorted distorted 139 165 166 167 198 P U A 7 distorted distorted 172 199 200 201 228 P A A 8 distorted distorted 206 229 230 231 261 P C A 9 distorted distorted 236 262 263 264 292 P G A 10 distorted distorted 269 293 294 295 326 P U A 11 distorted distorted 300 327 328 329 356 P A A 12 distorted distorted 334 357 358 359 389 P G A 13 distorted distorted 364 390 391 392 423 P A A 14 distorted distorted 397 424 425 426 456 P G A 15 distorted distorted 431 457 458 459 490 P U A 16 distorted distorted 464 491 492 493 520 P A A 17 distorted distorted 498 521 522 523 553 P U A 18 distorted distorted 528 554 555 556 583 P A A 19 distorted distorted 561 584 585 586 616 P C A 20 distorted distorted 591 617 618 619 647 P U A 21 distorted distorted 624 648 649 650 677 P U A 22 distorted distorted 655 678 679 680 707 P C A 23 distorted distorted 685 708 709 710 738 P G A 24 distorted distorted 715 739 740 741 772 P G A 25 distorted distorted 746 773 774 775 806 P U A 26 distorted distorted 780 807 808 809 836 P A A 27 distorted distorted 814 837 838 839 869 P U A 28 distorted distorted 844 870 871 872 899 P A A 29 distorted distorted 877 900 901 902 932 P C A 30 distorted distorted 907 933 934 935 963 P U A 31 distorted distorted 940 964 965 966 993 P U A 32 distorted distorted 971 994 995 996 1023 P A A 33 distorted distorted 1001 1024 1025 1026 1056 P U A 34 distorted distorted 1031 1057 1058 1059 1086 P A A 35 distorted distorted 1064 1087 1088 1089 1119 P U A 36 distorted distorted 1094 1120 1121 1122 1149 P A A 37 distorted distorted 1127 1150 1151 1152 1182 P C A 38 distorted distorted 1157 1183 1184 1185 1213 P U A 39 distorted distorted 1190 1214 1215 1216 1243 P U A 40 distorted distorted 1221 1244 1245 1246 1273 P A A 41 distorted distorted 1251 1274 1275 1276 1306 P C A 42 distorted distorted 1281 1307 1308 1309 1337 P C A 43 distorted distorted 1314 1338 1339 1340 ---------------------------------------------------------------------------------