ID code: '1WSU' 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 E 13 beta 4 10 7 32 C1' G E 14 beta 27 33 30 55 C1' C E 15 beta 50 56 53 75 C1' G E 16 beta 70 76 73 98 C1' U E 17 beta 93 99 96 118 C1' U E 18 beta 113 119 116 138 C1' G E 19 beta 133 139 136 161 C1' C E 20 beta 156 162 159 181 C1' C E 21 beta 176 182 179 201 C1' G E 22 beta 196 202 199 224 C1' G E 23 beta 219 225 222 247 C1' U E 24 beta 242 248 245 267 C1' C E 25 beta 262 268 265 284 C1' G E 27 beta 279 285 282 307 C1' G E 28 beta 302 308 305 330 C1' C E 29 beta 325 331 328 350 C1' A E 30 beta 345 351 348 372 C1' A E 31 beta 367 373 370 394 C1' C E 32 beta 389 395 392 414 C1' G E 33 beta 409 415 412 437 C1' C E 34 beta 432 438 435 457 C1' C E 35 beta 452 458 455 475 C1' G F 13 beta 470 476 473 498 C1' G F 14 beta 493 499 496 521 C1' C F 15 beta 516 522 519 541 C1' G F 16 beta 536 542 539 564 C1' U F 17 beta 559 565 562 584 C1' U F 18 beta 579 585 582 604 C1' G F 19 beta 599 605 602 627 C1' C F 20 beta 622 628 625 647 C1' C F 21 beta 642 648 645 667 C1' G F 22 beta 662 668 665 690 C1' G F 23 beta 685 691 688 713 C1' U F 24 beta 708 714 711 733 C1' C F 25 beta 728 734 731 750 C1' G F 27 beta 745 751 748 773 C1' G F 28 beta 768 774 771 796 C1' C F 29 beta 791 797 794 816 C1' A F 30 beta 811 817 814 838 C1' A F 31 beta 833 839 836 860 C1' C F 32 beta 855 861 858 880 C1' G F 33 beta 875 881 878 903 C1' C F 34 beta 898 904 901 923 C1' C F 35 beta 918 924 921 941 C1' G G 13 beta 936 942 939 964 C1' G G 14 beta 959 965 962 987 C1' C G 15 beta 982 988 985 1007 C1' G G 16 beta 1002 1008 1005 1030 C1' U G 17 beta 1025 1031 1028 1050 C1' U G 18 beta 1045 1051 1048 1070 C1' G G 19 beta 1065 1071 1068 1093 C1' C G 20 beta 1088 1094 1091 1113 C1' C G 21 beta 1108 1114 1111 1133 C1' G G 22 beta 1128 1134 1131 1156 C1' G G 23 beta 1151 1157 1154 1179 C1' U G 24 beta 1174 1180 1177 1196 C1' G G 27 beta 1191 1197 1194 1219 C1' G G 28 beta 1214 1220 1217 1242 C1' C G 29 beta 1237 1243 1240 1262 C1' A G 30 beta 1257 1263 1260 1284 C1' A G 31 beta 1279 1285 1282 1306 C1' C G 32 beta 1301 1307 1304 1326 C1' G G 33 beta 1321 1327 1324 1349 C1' C G 34 beta 1344 1350 1347 1369 C1' C G 35 beta 1364 1370 1367 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G E 13 OK 9 5 8 30 C2' G E 14 OK 32 28 31 53 C2' C E 15 OK 55 51 54 73 C2' G E 16 OK 75 71 74 96 C2' U E 17 OK 98 94 97 116 C2' U E 18 OK 118 114 117 136 C2' G E 19 OK 138 134 137 159 C2' C E 20 OK 161 157 160 179 C2' C E 21 OK 181 177 180 199 C2' G E 22 OK 201 197 200 222 C2' G E 23 OK 224 220 223 245 C2' U E 24 OK 247 243 246 265 C2' C E 25 OK 267 263 266 282 C2' G E 27 OK 284 280 283 305 C2' G E 28 OK 307 303 306 328 C2' C E 29 OK 330 326 329 348 C2' A E 30 OK 350 346 349 370 C2' A E 31 OK 372 368 371 392 C2' C E 32 OK 394 390 393 412 C2' G E 33 OK 414 410 413 435 C2' C E 34 OK 437 433 436 455 C2' C E 35 OK 457 453 456 473 C2' G F 13 OK 475 471 474 496 C2' G F 14 OK 498 494 497 519 C2' C F 15 OK 521 517 520 539 C2' G F 16 OK 541 537 540 562 C2' U F 17 OK 564 560 563 582 C2' U F 18 OK 584 580 583 602 C2' G F 19 OK 604 600 603 625 C2' C F 20 OK 627 623 626 645 C2' C F 21 OK 647 643 646 665 C2' G F 22 OK 667 663 666 688 C2' G F 23 OK 690 686 689 711 C2' U F 24 OK 713 709 712 731 C2' C F 25 OK 733 729 732 748 C2' G F 27 OK 750 746 749 771 C2' G F 28 OK 773 769 772 794 C2' C F 29 OK 796 792 795 814 C2' A F 30 OK 816 812 815 836 C2' A F 31 OK 838 834 837 858 C2' C F 32 OK 860 856 859 878 C2' G F 33 OK 880 876 879 901 C2' C F 34 OK 903 899 902 921 C2' C F 35 OK 923 919 922 939 C2' G G 13 OK 941 937 940 962 C2' G G 14 OK 964 960 963 985 C2' C G 15 OK 987 983 986 1005 C2' G G 16 OK 1007 1003 1006 1028 C2' U G 17 OK 1030 1026 1029 1048 C2' U G 18 OK 1050 1046 1049 1068 C2' G G 19 OK 1070 1066 1069 1091 C2' C G 20 OK 1093 1089 1092 1111 C2' C G 21 OK 1113 1109 1112 1131 C2' G G 22 OK 1133 1129 1132 1154 C2' G G 23 OK 1156 1152 1155 1177 C2' U G 24 OK 1179 1175 1178 1194 C2' G G 27 OK 1196 1192 1195 1217 C2' G G 28 OK 1219 1215 1218 1240 C2' C G 29 OK 1242 1238 1241 1260 C2' A G 30 OK 1262 1258 1261 1282 C2' A G 31 OK 1284 1280 1283 1304 C2' C G 32 OK 1306 1302 1305 1324 C2' G G 33 OK 1326 1322 1325 1347 C2' C G 34 OK 1349 1345 1348 1367 C2' C G 35 OK 1369 1365 1368 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G E 13 OK 3 6 7 28 C3' G E 14 OK 26 29 30 51 C3' C E 15 OK 49 52 53 71 C3' G E 16 OK 69 72 73 94 C3' U E 17 OK 92 95 96 114 C3' U E 18 OK 112 115 116 134 C3' G E 19 OK 132 135 136 157 C3' C E 20 OK 155 158 159 177 C3' C E 21 OK 175 178 179 197 C3' G E 22 OK 195 198 199 220 C3' G E 23 OK 218 221 222 243 C3' U E 24 OK 241 244 245 263 C3' C E 25 OK 261 264 265 280 C3' G E 27 OK 278 281 282 303 C3' G E 28 OK 301 304 305 326 C3' C E 29 OK 324 327 328 346 C3' A E 30 OK 344 347 348 368 C3' A E 31 OK 366 369 370 390 C3' C E 32 OK 388 391 392 410 C3' G E 33 OK 408 411 412 433 C3' C E 34 OK 431 434 435 453 C3' C E 35 OK 451 454 455 471 C3' G F 13 OK 469 472 473 494 C3' G F 14 OK 492 495 496 517 C3' C F 15 OK 515 518 519 537 C3' G F 16 OK 535 538 539 560 C3' U F 17 OK 558 561 562 580 C3' U F 18 OK 578 581 582 600 C3' G F 19 OK 598 601 602 623 C3' C F 20 OK 621 624 625 643 C3' C F 21 OK 641 644 645 663 C3' G F 22 OK 661 664 665 686 C3' G F 23 OK 684 687 688 709 C3' U F 24 OK 707 710 711 729 C3' C F 25 OK 727 730 731 746 C3' G F 27 OK 744 747 748 769 C3' G F 28 OK 767 770 771 792 C3' C F 29 OK 790 793 794 812 C3' A F 30 OK 810 813 814 834 C3' A F 31 OK 832 835 836 856 C3' C F 32 OK 854 857 858 876 C3' G F 33 OK 874 877 878 899 C3' C F 34 OK 897 900 901 919 C3' C F 35 OK 917 920 921 937 C3' G G 13 OK 935 938 939 960 C3' G G 14 OK 958 961 962 983 C3' C G 15 OK 981 984 985 1003 C3' G G 16 OK 1001 1004 1005 1026 C3' U G 17 OK 1024 1027 1028 1046 C3' U G 18 OK 1044 1047 1048 1066 C3' G G 19 OK 1064 1067 1068 1089 C3' C G 20 OK 1087 1090 1091 1109 C3' C G 21 OK 1107 1110 1111 1129 C3' G G 22 OK 1127 1130 1131 1152 C3' G G 23 OK 1150 1153 1154 1175 C3' U G 24 OK 1173 1176 1177 1192 C3' G G 27 OK 1190 1193 1194 1215 C3' G G 28 OK 1213 1216 1217 1238 C3' C G 29 OK 1236 1239 1240 1258 C3' A G 30 OK 1256 1259 1260 1280 C3' A G 31 OK 1278 1281 1282 1302 C3' C G 32 OK 1300 1303 1304 1322 C3' G G 33 OK 1320 1323 1324 1345 C3' C G 34 OK 1343 1346 1347 1365 C3' C G 35 OK 1363 1366 1367 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G E 13 OK 5 2 4 26 C4' G E 14 OK 28 25 27 49 C4' C E 15 OK 51 48 50 69 C4' G E 16 OK 71 68 70 92 C4' U E 17 OK 94 91 93 112 C4' U E 18 OK 114 111 113 132 C4' G E 19 OK 134 131 133 155 C4' C E 20 OK 157 154 156 175 C4' C E 21 OK 177 174 176 195 C4' G E 22 OK 197 194 196 218 C4' G E 23 OK 220 217 219 241 C4' U E 24 OK 243 240 242 261 C4' C E 25 OK 263 260 262 278 C4' G E 27 OK 280 277 279 301 C4' G E 28 OK 303 300 302 324 C4' C E 29 OK 326 323 325 344 C4' A E 30 OK 346 343 345 366 C4' A E 31 OK 368 365 367 388 C4' C E 32 OK 390 387 389 408 C4' G E 33 OK 410 407 409 431 C4' C E 34 OK 433 430 432 451 C4' C E 35 OK 453 450 452 469 C4' G F 13 OK 471 468 470 492 C4' G F 14 OK 494 491 493 515 C4' C F 15 OK 517 514 516 535 C4' G F 16 OK 537 534 536 558 C4' U F 17 OK 560 557 559 578 C4' U F 18 OK 580 577 579 598 C4' G F 19 OK 600 597 599 621 C4' C F 20 OK 623 620 622 641 C4' C F 21 OK 643 640 642 661 C4' G F 22 OK 663 660 662 684 C4' G F 23 OK 686 683 685 707 C4' U F 24 OK 709 706 708 727 C4' C F 25 OK 729 726 728 744 C4' G F 27 OK 746 743 745 767 C4' G F 28 OK 769 766 768 790 C4' C F 29 OK 792 789 791 810 C4' A F 30 OK 812 809 811 832 C4' A F 31 OK 834 831 833 854 C4' C F 32 OK 856 853 855 874 C4' G F 33 OK 876 873 875 897 C4' C F 34 OK 899 896 898 917 C4' C F 35 OK 919 916 918 935 C4' G G 13 OK 937 934 936 958 C4' G G 14 OK 960 957 959 981 C4' C G 15 OK 983 980 982 1001 C4' G G 16 OK 1003 1000 1002 1024 C4' U G 17 OK 1026 1023 1025 1044 C4' U G 18 OK 1046 1043 1045 1064 C4' G G 19 OK 1066 1063 1065 1087 C4' C G 20 OK 1089 1086 1088 1107 C4' C G 21 OK 1109 1106 1108 1127 C4' G G 22 OK 1129 1126 1128 1150 C4' G G 23 OK 1152 1149 1151 1173 C4' U G 24 OK 1175 1172 1174 1190 C4' G G 27 OK 1192 1189 1191 1213 C4' G G 28 OK 1215 1212 1214 1236 C4' C G 29 OK 1238 1235 1237 1256 C4' A G 30 OK 1258 1255 1257 1278 C4' A G 31 OK 1280 1277 1279 1300 C4' C G 32 OK 1302 1299 1301 1320 C4' G G 33 OK 1322 1319 1321 1343 C4' C G 34 OK 1345 1342 1344 1363 C4' C G 35 OK 1365 1362 1364 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G E 13 1 3 25 C5' G E 14 24 26 48 C5' C E 15 47 49 68 C5' G E 16 67 69 91 C5' U E 17 90 92 111 C5' U E 18 110 112 131 C5' G E 19 130 132 154 C5' C E 20 153 155 174 C5' C E 21 173 175 194 C5' G E 22 193 195 217 C5' G E 23 216 218 240 C5' U E 24 239 241 260 C5' C E 25 259 261 277 C5' G E 27 276 278 300 C5' G E 28 299 301 323 C5' C E 29 322 324 343 C5' A E 30 342 344 365 C5' A E 31 364 366 387 C5' C E 32 386 388 407 C5' G E 33 406 408 430 C5' C E 34 429 431 450 C5' C E 35 449 451 468 C5' G F 13 467 469 491 C5' G F 14 490 492 514 C5' C F 15 513 515 534 C5' G F 16 533 535 557 C5' U F 17 556 558 577 C5' U F 18 576 578 597 C5' G F 19 596 598 620 C5' C F 20 619 621 640 C5' C F 21 639 641 660 C5' G F 22 659 661 683 C5' G F 23 682 684 706 C5' U F 24 705 707 726 C5' C F 25 725 727 743 C5' G F 27 742 744 766 C5' G F 28 765 767 789 C5' C F 29 788 790 809 C5' A F 30 808 810 831 C5' A F 31 830 832 853 C5' C F 32 852 854 873 C5' G F 33 872 874 896 C5' C F 34 895 897 916 C5' C F 35 915 917 934 C5' G G 13 933 935 957 C5' G G 14 956 958 980 C5' C G 15 979 981 1000 C5' G G 16 999 1001 1023 C5' U G 17 1022 1024 1043 C5' U G 18 1042 1044 1063 C5' G G 19 1062 1064 1086 C5' C G 20 1085 1087 1106 C5' C G 21 1105 1107 1126 C5' G G 22 1125 1127 1149 C5' G G 23 1148 1150 1172 C5' U G 24 1171 1173 1189 C5' G G 27 1188 1190 1212 C5' G G 28 1211 1213 1235 C5' C G 29 1234 1236 1255 C5' A G 30 1254 1256 1277 C5' A G 31 1276 1278 1299 C5' C G 32 1298 1300 1319 C5' G G 33 1318 1320 1342 C5' C G 34 1341 1343 1362 C5' C G 35 1361 1363 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G E 14 distorted distorted 6 22 23 24 44 P C E 15 distorted distorted 29 45 46 47 64 P G E 16 distorted distorted 52 65 66 67 87 P U E 17 distorted distorted 72 88 89 90 107 P U E 18 distorted distorted 95 108 109 110 127 P G E 19 distorted distorted 115 128 129 130 150 P C E 20 distorted distorted 135 151 152 153 170 P C E 21 distorted distorted 158 171 172 173 190 P G E 22 distorted distorted 178 191 192 193 213 P G E 23 distorted distorted 198 214 215 216 236 P U E 24 distorted distorted 221 237 238 239 256 P C E 25 distorted distorted 244 257 258 259 296 P G E 28 distorted distorted 281 297 298 299 319 P C E 29 distorted distorted 304 320 321 322 339 P A E 30 distorted distorted 327 340 341 342 361 P A E 31 distorted distorted 347 362 363 364 383 P C E 32 distorted distorted 369 384 385 386 403 P G E 33 distorted distorted 391 404 405 406 426 P C E 34 distorted distorted 411 427 428 429 446 P C E 35 distorted distorted 434 447 448 449 487 P G F 14 distorted distorted 472 488 489 490 510 P C F 15 distorted distorted 495 511 512 513 530 P G F 16 distorted distorted 518 531 532 533 553 P U F 17 distorted distorted 538 554 555 556 573 P U F 18 distorted distorted 561 574 575 576 593 P G F 19 distorted distorted 581 594 595 596 616 P C F 20 distorted distorted 601 617 618 619 636 P C F 21 distorted distorted 624 637 638 639 656 P G F 22 distorted distorted 644 657 658 659 679 P G F 23 distorted distorted 664 680 681 682 702 P U F 24 distorted distorted 687 703 704 705 722 P C F 25 distorted distorted 710 723 724 725 762 P G F 28 distorted distorted 747 763 764 765 785 P C F 29 distorted distorted 770 786 787 788 805 P A F 30 distorted distorted 793 806 807 808 827 P A F 31 distorted distorted 813 828 829 830 849 P C F 32 distorted distorted 835 850 851 852 869 P G F 33 distorted distorted 857 870 871 872 892 P C F 34 distorted distorted 877 893 894 895 912 P C F 35 distorted distorted 900 913 914 915 953 P G G 14 distorted distorted 938 954 955 956 976 P C G 15 distorted distorted 961 977 978 979 996 P G G 16 distorted distorted 984 997 998 999 1019 P U G 17 distorted distorted 1004 1020 1021 1022 1039 P U G 18 distorted distorted 1027 1040 1041 1042 1059 P G G 19 distorted distorted 1047 1060 1061 1062 1082 P C G 20 distorted distorted 1067 1083 1084 1085 1102 P C G 21 distorted distorted 1090 1103 1104 1105 1122 P G G 22 distorted distorted 1110 1123 1124 1125 1145 P G G 23 distorted distorted 1130 1146 1147 1148 1168 P U G 24 distorted distorted 1153 1169 1170 1171 1208 P G G 28 distorted distorted 1193 1209 1210 1211 1231 P C G 29 distorted distorted 1216 1232 1233 1234 1251 P A G 30 distorted distorted 1239 1252 1253 1254 1273 P A G 31 distorted distorted 1259 1274 1275 1276 1295 P C G 32 distorted distorted 1281 1296 1297 1298 1315 P G G 33 distorted distorted 1303 1316 1317 1318 1338 P C G 34 distorted distorted 1323 1339 1340 1341 1358 P C G 35 distorted distorted 1346 1359 1360 1361 ---------------------------------------------------------------------------------