ID code: '2XNW' 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' --------------------------------------------------------------------------------- 12 C1' G A 16 beta 7 13 10 35 C1' A A 17 beta 30 36 33 57 C1' C A 18 beta 52 58 55 77 C1' A A 19 beta 72 78 75 99 C1' U A 20 beta 94 100 97 119 C1' A A 21 beta 114 120 117 141 C1' U A 22 beta 136 142 139 161 C1' A A 23 beta 156 162 159 183 C1' A A 24 beta 178 184 181 205 C1' U A 25 beta 200 206 203 225 C1' C A 26 beta 220 226 223 245 C1' G A 27 beta 240 246 243 268 C1' C A 28 beta 263 269 266 288 C1' G A 29 beta 283 289 286 311 C1' U A 30 beta 306 312 309 331 C1' G A 31 beta 326 332 329 354 C1' G A 32 beta 349 355 352 377 C1' A A 33 beta 372 378 375 399 C1' U A 34 beta 394 400 397 419 C1' A A 35 beta 414 420 417 441 C1' U A 36 beta 436 442 439 461 C1' G A 37 beta 456 462 459 484 C1' G A 38 beta 479 485 482 507 C1' C A 39 beta 502 508 505 527 C1' A A 40 beta 522 528 525 549 C1' C A 41 beta 544 550 547 569 C1' G A 42 beta 564 570 567 592 C1' C A 43 beta 587 593 590 612 C1' A A 44 beta 607 613 610 634 C1' A A 45 beta 629 635 632 656 C1' G A 46 beta 651 657 654 679 C1' U A 47 beta 674 680 677 699 C1' U A 48 beta 694 700 697 719 C1' U A 49 beta 714 720 717 739 C1' C A 50 beta 734 740 737 759 C1' U A 51 beta 754 760 757 779 C1' A A 52 beta 774 780 777 801 C1' C A 53 beta 796 802 799 821 C1' C A 54 beta 816 822 819 841 C1' G A 55 beta 836 842 839 864 C1' G A 56 beta 859 865 862 887 C1' G A 57 beta 882 888 885 910 C1' C A 58 beta 905 911 908 930 C1' A A 59 beta 925 931 928 952 C1' C A 60 beta 947 953 950 972 C1' C A 61 beta 967 973 970 992 C1' G A 62 beta 987 993 990 1015 C1' U A 63 beta 1010 1016 1013 1035 C1' A A 64 beta 1030 1036 1033 1057 C1' A A 65 beta 1052 1058 1055 1079 C1' A A 66 beta 1074 1080 1077 1101 C1' U A 67 beta 1096 1102 1099 1121 C1' G A 68 beta 1116 1122 1119 1144 C1' U A 69 beta 1139 1145 1142 1164 C1' C A 70 beta 1159 1165 1162 1184 C1' C A 71 beta 1179 1185 1182 1204 C1' G A 72 beta 1199 1205 1202 1227 C1' A A 73 beta 1222 1228 1225 1249 C1' U A 74 beta 1244 1250 1247 1269 C1' U A 75 beta 1264 1270 1267 1289 C1' A A 76 beta 1284 1290 1287 1311 C1' U A 77 beta 1306 1312 1309 1331 C1' G A 78 beta 1326 1332 1329 1354 C1' U A 79 beta 1349 1355 1352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 16 OK 12 8 11 33 C2' A A 17 OK 35 31 34 55 C2' C A 18 OK 57 53 56 75 C2' A A 19 OK 77 73 76 97 C2' U A 20 OK 99 95 98 117 C2' A A 21 OK 119 115 118 139 C2' U A 22 OK 141 137 140 159 C2' A A 23 OK 161 157 160 181 C2' A A 24 OK 183 179 182 203 C2' U A 25 OK 205 201 204 223 C2' C A 26 OK 225 221 224 243 C2' G A 27 OK 245 241 244 266 C2' C A 28 OK 268 264 267 286 C2' G A 29 OK 288 284 287 309 C2' U A 30 OK 311 307 310 329 C2' G A 31 OK 331 327 330 352 C2' G A 32 OK 354 350 353 375 C2' A A 33 OK 377 373 376 397 C2' U A 34 OK 399 395 398 417 C2' A A 35 OK 419 415 418 439 C2' U A 36 OK 441 437 440 459 C2' G A 37 OK 461 457 460 482 C2' G A 38 OK 484 480 483 505 C2' C A 39 OK 507 503 506 525 C2' A A 40 OK 527 523 526 547 C2' C A 41 OK 549 545 548 567 C2' G A 42 OK 569 565 568 590 C2' C A 43 OK 592 588 591 610 C2' A A 44 OK 612 608 611 632 C2' A A 45 OK 634 630 633 654 C2' G A 46 OK 656 652 655 677 C2' U A 47 OK 679 675 678 697 C2' U A 48 OK 699 695 698 717 C2' U A 49 OK 719 715 718 737 C2' C A 50 OK 739 735 738 757 C2' U A 51 OK 759 755 758 777 C2' A A 52 OK 779 775 778 799 C2' C A 53 OK 801 797 800 819 C2' C A 54 OK 821 817 820 839 C2' G A 55 OK 841 837 840 862 C2' G A 56 OK 864 860 863 885 C2' G A 57 OK 887 883 886 908 C2' C A 58 OK 910 906 909 928 C2' A A 59 OK 930 926 929 950 C2' C A 60 OK 952 948 951 970 C2' C A 61 OK 972 968 971 990 C2' G A 62 OK 992 988 991 1013 C2' U A 63 OK 1015 1011 1014 1033 C2' A A 64 OK 1035 1031 1034 1055 C2' A A 65 OK 1057 1053 1056 1077 C2' A A 66 OK 1079 1075 1078 1099 C2' U A 67 OK 1101 1097 1100 1119 C2' G A 68 OK 1121 1117 1120 1142 C2' U A 69 OK 1144 1140 1143 1162 C2' C A 70 OK 1164 1160 1163 1182 C2' C A 71 OK 1184 1180 1183 1202 C2' G A 72 OK 1204 1200 1203 1225 C2' A A 73 OK 1227 1223 1226 1247 C2' U A 74 OK 1249 1245 1248 1267 C2' U A 75 OK 1269 1265 1268 1287 C2' A A 76 OK 1289 1285 1288 1309 C2' U A 77 OK 1311 1307 1310 1329 C2' G A 78 OK 1331 1327 1330 1352 C2' U A 79 OK 1354 1350 1353 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 16 OK 6 9 10 31 C3' A A 17 OK 29 32 33 53 C3' C A 18 OK 51 54 55 73 C3' A A 19 OK 71 74 75 95 C3' U A 20 OK 93 96 97 115 C3' A A 21 OK 113 116 117 137 C3' U A 22 OK 135 138 139 157 C3' A A 23 OK 155 158 159 179 C3' A A 24 OK 177 180 181 201 C3' U A 25 OK 199 202 203 221 C3' C A 26 OK 219 222 223 241 C3' G A 27 OK 239 242 243 264 C3' C A 28 OK 262 265 266 284 C3' G A 29 OK 282 285 286 307 C3' U A 30 OK 305 308 309 327 C3' G A 31 OK 325 328 329 350 C3' G A 32 OK 348 351 352 373 C3' A A 33 OK 371 374 375 395 C3' U A 34 OK 393 396 397 415 C3' A A 35 OK 413 416 417 437 C3' U A 36 OK 435 438 439 457 C3' G A 37 OK 455 458 459 480 C3' G A 38 OK 478 481 482 503 C3' C A 39 OK 501 504 505 523 C3' A A 40 OK 521 524 525 545 C3' C A 41 OK 543 546 547 565 C3' G A 42 OK 563 566 567 588 C3' C A 43 OK 586 589 590 608 C3' A A 44 OK 606 609 610 630 C3' A A 45 OK 628 631 632 652 C3' G A 46 OK 650 653 654 675 C3' U A 47 OK 673 676 677 695 C3' U A 48 OK 693 696 697 715 C3' U A 49 OK 713 716 717 735 C3' C A 50 OK 733 736 737 755 C3' U A 51 OK 753 756 757 775 C3' A A 52 OK 773 776 777 797 C3' C A 53 OK 795 798 799 817 C3' C A 54 OK 815 818 819 837 C3' G A 55 OK 835 838 839 860 C3' G A 56 OK 858 861 862 883 C3' G A 57 OK 881 884 885 906 C3' C A 58 OK 904 907 908 926 C3' A A 59 OK 924 927 928 948 C3' C A 60 OK 946 949 950 968 C3' C A 61 OK 966 969 970 988 C3' G A 62 OK 986 989 990 1011 C3' U A 63 OK 1009 1012 1013 1031 C3' A A 64 OK 1029 1032 1033 1053 C3' A A 65 OK 1051 1054 1055 1075 C3' A A 66 OK 1073 1076 1077 1097 C3' U A 67 OK 1095 1098 1099 1117 C3' G A 68 OK 1115 1118 1119 1140 C3' U A 69 OK 1138 1141 1142 1160 C3' C A 70 OK 1158 1161 1162 1180 C3' C A 71 OK 1178 1181 1182 1200 C3' G A 72 OK 1198 1201 1202 1223 C3' A A 73 OK 1221 1224 1225 1245 C3' U A 74 OK 1243 1246 1247 1265 C3' U A 75 OK 1263 1266 1267 1285 C3' A A 76 OK 1283 1286 1287 1307 C3' U A 77 OK 1305 1308 1309 1327 C3' G A 78 OK 1325 1328 1329 1350 C3' U A 79 OK 1348 1351 1352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 16 OK 8 5 7 29 C4' A A 17 OK 31 28 30 51 C4' C A 18 OK 53 50 52 71 C4' A A 19 OK 73 70 72 93 C4' U A 20 OK 95 92 94 113 C4' A A 21 OK 115 112 114 135 C4' U A 22 OK 137 134 136 155 C4' A A 23 OK 157 154 156 177 C4' A A 24 OK 179 176 178 199 C4' U A 25 OK 201 198 200 219 C4' C A 26 OK 221 218 220 239 C4' G A 27 OK 241 238 240 262 C4' C A 28 OK 264 261 263 282 C4' G A 29 OK 284 281 283 305 C4' U A 30 OK 307 304 306 325 C4' G A 31 OK 327 324 326 348 C4' G A 32 OK 350 347 349 371 C4' A A 33 OK 373 370 372 393 C4' U A 34 OK 395 392 394 413 C4' A A 35 OK 415 412 414 435 C4' U A 36 OK 437 434 436 455 C4' G A 37 OK 457 454 456 478 C4' G A 38 OK 480 477 479 501 C4' C A 39 OK 503 500 502 521 C4' A A 40 OK 523 520 522 543 C4' C A 41 OK 545 542 544 563 C4' G A 42 OK 565 562 564 586 C4' C A 43 OK 588 585 587 606 C4' A A 44 OK 608 605 607 628 C4' A A 45 OK 630 627 629 650 C4' G A 46 OK 652 649 651 673 C4' U A 47 OK 675 672 674 693 C4' U A 48 OK 695 692 694 713 C4' U A 49 OK 715 712 714 733 C4' C A 50 OK 735 732 734 753 C4' U A 51 OK 755 752 754 773 C4' A A 52 OK 775 772 774 795 C4' C A 53 OK 797 794 796 815 C4' C A 54 OK 817 814 816 835 C4' G A 55 OK 837 834 836 858 C4' G A 56 OK 860 857 859 881 C4' G A 57 OK 883 880 882 904 C4' C A 58 OK 906 903 905 924 C4' A A 59 OK 926 923 925 946 C4' C A 60 OK 948 945 947 966 C4' C A 61 OK 968 965 967 986 C4' G A 62 OK 988 985 987 1009 C4' U A 63 OK 1011 1008 1010 1029 C4' A A 64 OK 1031 1028 1030 1051 C4' A A 65 OK 1053 1050 1052 1073 C4' A A 66 OK 1075 1072 1074 1095 C4' U A 67 OK 1097 1094 1096 1115 C4' G A 68 OK 1117 1114 1116 1138 C4' U A 69 OK 1140 1137 1139 1158 C4' C A 70 OK 1160 1157 1159 1178 C4' C A 71 OK 1180 1177 1179 1198 C4' G A 72 OK 1200 1197 1199 1221 C4' A A 73 OK 1223 1220 1222 1243 C4' U A 74 OK 1245 1242 1244 1263 C4' U A 75 OK 1265 1262 1264 1283 C4' A A 76 OK 1285 1282 1284 1305 C4' U A 77 OK 1307 1304 1306 1325 C4' G A 78 OK 1327 1324 1326 1348 C4' U A 79 OK 1350 1347 1349 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 16 4 6 28 C5' A A 17 27 29 50 C5' C A 18 49 51 70 C5' A A 19 69 71 92 C5' U A 20 91 93 112 C5' A A 21 111 113 134 C5' U A 22 133 135 154 C5' A A 23 153 155 176 C5' A A 24 175 177 198 C5' U A 25 197 199 218 C5' C A 26 217 219 238 C5' G A 27 237 239 261 C5' C A 28 260 262 281 C5' G A 29 280 282 304 C5' U A 30 303 305 324 C5' G A 31 323 325 347 C5' G A 32 346 348 370 C5' A A 33 369 371 392 C5' U A 34 391 393 412 C5' A A 35 411 413 434 C5' U A 36 433 435 454 C5' G A 37 453 455 477 C5' G A 38 476 478 500 C5' C A 39 499 501 520 C5' A A 40 519 521 542 C5' C A 41 541 543 562 C5' G A 42 561 563 585 C5' C A 43 584 586 605 C5' A A 44 604 606 627 C5' A A 45 626 628 649 C5' G A 46 648 650 672 C5' U A 47 671 673 692 C5' U A 48 691 693 712 C5' U A 49 711 713 732 C5' C A 50 731 733 752 C5' U A 51 751 753 772 C5' A A 52 771 773 794 C5' C A 53 793 795 814 C5' C A 54 813 815 834 C5' G A 55 833 835 857 C5' G A 56 856 858 880 C5' G A 57 879 881 903 C5' C A 58 902 904 923 C5' A A 59 922 924 945 C5' C A 60 944 946 965 C5' C A 61 964 966 985 C5' G A 62 984 986 1008 C5' U A 63 1007 1009 1028 C5' A A 64 1027 1029 1050 C5' A A 65 1049 1051 1072 C5' A A 66 1071 1073 1094 C5' U A 67 1093 1095 1114 C5' G A 68 1113 1115 1137 C5' U A 69 1136 1138 1157 C5' C A 70 1156 1158 1177 C5' C A 71 1176 1178 1197 C5' G A 72 1196 1198 1220 C5' A A 73 1219 1221 1242 C5' U A 74 1241 1243 1262 C5' U A 75 1261 1263 1282 C5' A A 76 1281 1283 1304 C5' U A 77 1303 1305 1324 C5' G A 78 1323 1325 1347 C5' U A 79 1346 1348 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 16 distorted distorted 2 3 4 24 P A A 17 distorted distorted 9 25 26 27 46 P C A 18 distorted distorted 32 47 48 49 66 P A A 19 distorted distorted 54 67 68 69 88 P U A 20 distorted distorted 74 89 90 91 108 P A A 21 distorted distorted 96 109 110 111 130 P U A 22 distorted distorted 116 131 132 133 150 P A A 23 distorted distorted 138 151 152 153 172 P A A 24 distorted distorted 158 173 174 175 194 P U A 25 distorted distorted 180 195 196 197 214 P C A 26 distorted distorted 202 215 216 217 234 P G A 27 distorted distorted 222 235 236 237 257 P C A 28 distorted distorted 242 258 259 260 277 P G A 29 distorted distorted 265 278 279 280 300 P U A 30 distorted distorted 285 301 302 303 320 P G A 31 distorted distorted 308 321 322 323 343 P G A 32 distorted distorted 328 344 345 346 366 P A A 33 distorted distorted 351 367 368 369 388 P U A 34 distorted distorted 374 389 390 391 408 P A A 35 distorted distorted 396 409 410 411 430 P U A 36 distorted distorted 416 431 432 433 450 P G A 37 distorted distorted 438 451 452 453 473 P G A 38 distorted distorted 458 474 475 476 496 P C A 39 distorted distorted 481 497 498 499 516 P A A 40 distorted distorted 504 517 518 519 538 P C A 41 distorted distorted 524 539 540 541 558 P G A 42 distorted distorted 546 559 560 561 581 P C A 43 distorted distorted 566 582 583 584 601 P A A 44 distorted distorted 589 602 603 604 623 P A A 45 distorted distorted 609 624 625 626 645 P G A 46 distorted distorted 631 646 647 648 668 P U A 47 distorted distorted 653 669 670 671 688 P U A 48 distorted distorted 676 689 690 691 708 P U A 49 distorted distorted 696 709 710 711 728 P C A 50 distorted distorted 716 729 730 731 748 P U A 51 distorted distorted 736 749 750 751 768 P A A 52 distorted distorted 756 769 770 771 790 P C A 53 distorted distorted 776 791 792 793 810 P C A 54 distorted distorted 798 811 812 813 830 P G A 55 distorted distorted 818 831 832 833 853 P G A 56 distorted distorted 838 854 855 856 876 P G A 57 distorted distorted 861 877 878 879 899 P C A 58 distorted distorted 884 900 901 902 919 P A A 59 distorted distorted 907 920 921 922 941 P C A 60 distorted distorted 927 942 943 944 961 P C A 61 distorted distorted 949 962 963 964 981 P G A 62 distorted distorted 969 982 983 984 1004 P U A 63 distorted distorted 989 1005 1006 1007 1024 P A A 64 distorted distorted 1012 1025 1026 1027 1046 P A A 65 distorted distorted 1032 1047 1048 1049 1068 P A A 66 distorted distorted 1054 1069 1070 1071 1090 P U A 67 distorted distorted 1076 1091 1092 1093 1110 P G A 68 distorted distorted 1098 1111 1112 1113 1133 P U A 69 distorted distorted 1118 1134 1135 1136 1153 P C A 70 distorted distorted 1141 1154 1155 1156 1173 P C A 71 distorted distorted 1161 1174 1175 1176 1193 P G A 72 distorted distorted 1181 1194 1195 1196 1216 P A A 73 distorted distorted 1201 1217 1218 1219 1238 P U A 74 distorted distorted 1224 1239 1240 1241 1258 P U A 75 distorted distorted 1246 1259 1260 1261 1278 P A A 76 distorted distorted 1266 1279 1280 1281 1300 P U A 77 distorted distorted 1286 1301 1302 1303 1320 P G A 78 distorted distorted 1308 1321 1322 1323 1343 P U A 79 distorted distorted 1328 1344 1345 1346 1363 P C A 80 distorted distorted 1351 1364 1365 1366 ---------------------------------------------------------------------------------