ID code: '1X9K' 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' U A 2 beta 4 10 7 29 C1' C A 3 beta 24 30 27 49 C1' G A 4 beta 44 50 47 72 C1' C A 5 beta 67 73 70 92 C1' A A 6 beta 87 93 90 114 C1' G A 7 beta 109 115 112 137 C1' U A 8 beta 132 138 135 157 C1' C A 9 beta 152 158 155 177 C1' C A 10 beta 172 178 175 197 C1' U A 11 beta 192 198 195 217 C1' A A 12 beta 212 218 215 239 C1' U A 13 beta 234 240 237 259 C1' U A 14 beta 254 260 257 277 C1' A B 2 beta 272 278 275 299 C1' A B 3 beta 294 300 297 321 C1' U B 4 beta 316 322 319 341 C1' A B 5 beta 336 342 339 363 C1' G B 6 beta 358 364 361 386 C1' A B 7 beta 381 387 384 408 C1' G B 8 beta 403 409 406 431 C1' A B 9 beta 426 432 429 453 C1' A B 10 beta 448 454 451 475 C1' G B 11 beta 470 476 473 498 C1' C B 12 beta 493 499 496 518 C1' G B 13 beta 513 519 516 541 C1' A B 14 beta 536 542 539 561 C1' G C 15 beta 556 562 559 584 C1' G C 16 beta 579 585 582 607 C1' C C 17 beta 602 608 605 627 C1' A C 18 beta 622 628 625 649 C1' G C 19 beta 644 650 647 672 C1' A C 20 beta 667 673 670 694 C1' G C 21 beta 689 695 692 717 C1' A C 22 beta 712 718 715 739 C1' A C 23 beta 734 740 737 761 C1' A C 24 beta 756 762 759 783 C1' C C 25 beta 778 784 781 803 C1' A C 26 beta 798 804 801 825 C1' C C 27 beta 820 826 823 845 C1' A C 28 beta 840 846 843 867 C1' C C 29 beta 862 868 865 887 C1' G C 30 beta 882 888 885 910 C1' A C 31 beta 905 911 908 930 C1' U D 31 beta 925 931 928 950 C1' C D 32 beta 945 951 948 970 C1' G D 33 beta 965 971 968 993 C1' U D 34 beta 988 994 991 1013 C1' G D 35 beta 1008 1014 1011 1036 C1' G D 36 beta 1031 1037 1034 1059 C1' U D 37 beta 1054 1060 1057 1079 C1' A D 38 beta 1074 1080 1077 1101 C1' C D 39 beta 1096 1102 1099 1121 C1' A D 40 beta 1116 1122 1119 1143 C1' U D 41 beta 1138 1144 1141 1163 C1' U D 42 beta 1158 1164 1161 1183 C1' A D 43 beta 1178 1184 1181 1205 C1' C D 44 beta 1200 1206 1203 1225 C1' C D 45 beta 1220 1226 1223 1245 C1' U D 46 beta 1240 1246 1243 1265 C1' G D 47 beta 1260 1266 1263 1288 C1' C D 48 beta 1283 1289 1286 1308 C1' C D 49 beta 1303 1309 1306 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 2 OK 9 5 8 27 C2' C A 3 OK 29 25 28 47 C2' G A 4 OK 49 45 48 70 C2' C A 5 OK 72 68 71 90 C2' A A 6 OK 92 88 91 112 C2' G A 7 OK 114 110 113 135 C2' U A 8 OK 137 133 136 155 C2' C A 9 OK 157 153 156 175 C2' C A 10 OK 177 173 176 195 C2' U A 11 OK 197 193 196 215 C2' A A 12 OK 217 213 216 237 C2' U A 13 OK 239 235 238 257 C2' U A 14 OK 259 255 258 275 C2' A B 2 OK 277 273 276 297 C2' A B 3 OK 299 295 298 319 C2' U B 4 OK 321 317 320 339 C2' A B 5 OK 341 337 340 361 C2' G B 6 OK 363 359 362 384 C2' A B 7 OK 386 382 385 406 C2' G B 8 OK 408 404 407 429 C2' A B 9 OK 431 427 430 451 C2' A B 10 OK 453 449 452 473 C2' G B 11 OK 475 471 474 496 C2' C B 12 OK 498 494 497 516 C2' G B 13 OK 518 514 517 539 C2' A B 14 OK 541 537 540 559 C2' G C 15 OK 561 557 560 582 C2' G C 16 OK 584 580 583 605 C2' C C 17 OK 607 603 606 625 C2' A C 18 OK 627 623 626 647 C2' G C 19 OK 649 645 648 670 C2' A C 20 OK 672 668 671 692 C2' G C 21 OK 694 690 693 715 C2' A C 22 OK 717 713 716 737 C2' A C 23 OK 739 735 738 759 C2' A C 24 OK 761 757 760 781 C2' C C 25 OK 783 779 782 801 C2' A C 26 OK 803 799 802 823 C2' C C 27 OK 825 821 824 843 C2' A C 28 OK 845 841 844 865 C2' C C 29 OK 867 863 866 885 C2' G C 30 OK 887 883 886 908 C2' A C 31 OK 910 906 909 928 C2' U D 31 OK 930 926 929 948 C2' C D 32 OK 950 946 949 968 C2' G D 33 OK 970 966 969 991 C2' U D 34 OK 993 989 992 1011 C2' G D 35 OK 1013 1009 1012 1034 C2' G D 36 OK 1036 1032 1035 1057 C2' U D 37 OK 1059 1055 1058 1077 C2' A D 38 OK 1079 1075 1078 1099 C2' C D 39 OK 1101 1097 1100 1119 C2' A D 40 OK 1121 1117 1120 1141 C2' U D 41 OK 1143 1139 1142 1161 C2' U D 42 OK 1163 1159 1162 1181 C2' A D 43 OK 1183 1179 1182 1203 C2' C D 44 OK 1205 1201 1204 1223 C2' C D 45 OK 1225 1221 1224 1243 C2' U D 46 OK 1245 1241 1244 1263 C2' G D 47 OK 1265 1261 1264 1286 C2' C D 48 OK 1288 1284 1287 1306 C2' C D 49 OK 1308 1304 1307 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 2 OK 3 6 7 25 C3' C A 3 OK 23 26 27 45 C3' G A 4 OK 43 46 47 68 C3' C A 5 OK 66 69 70 88 C3' A A 6 OK 86 89 90 110 C3' G A 7 OK 108 111 112 133 C3' U A 8 OK 131 134 135 153 C3' C A 9 OK 151 154 155 173 C3' C A 10 OK 171 174 175 193 C3' U A 11 OK 191 194 195 213 C3' A A 12 OK 211 214 215 235 C3' U A 13 OK 233 236 237 255 C3' U A 14 OK 253 256 257 273 C3' A B 2 OK 271 274 275 295 C3' A B 3 OK 293 296 297 317 C3' U B 4 OK 315 318 319 337 C3' A B 5 OK 335 338 339 359 C3' G B 6 OK 357 360 361 382 C3' A B 7 OK 380 383 384 404 C3' G B 8 OK 402 405 406 427 C3' A B 9 OK 425 428 429 449 C3' A B 10 OK 447 450 451 471 C3' G B 11 OK 469 472 473 494 C3' C B 12 OK 492 495 496 514 C3' G B 13 OK 512 515 516 537 C3' A B 14 OK 535 538 539 557 C3' G C 15 OK 555 558 559 580 C3' G C 16 OK 578 581 582 603 C3' C C 17 OK 601 604 605 623 C3' A C 18 OK 621 624 625 645 C3' G C 19 OK 643 646 647 668 C3' A C 20 OK 666 669 670 690 C3' G C 21 OK 688 691 692 713 C3' A C 22 OK 711 714 715 735 C3' A C 23 OK 733 736 737 757 C3' A C 24 OK 755 758 759 779 C3' C C 25 OK 777 780 781 799 C3' A C 26 OK 797 800 801 821 C3' C C 27 OK 819 822 823 841 C3' A C 28 OK 839 842 843 863 C3' C C 29 OK 861 864 865 883 C3' G C 30 OK 881 884 885 906 C3' A C 31 OK 904 907 908 926 C3' U D 31 OK 924 927 928 946 C3' C D 32 OK 944 947 948 966 C3' G D 33 OK 964 967 968 989 C3' U D 34 OK 987 990 991 1009 C3' G D 35 OK 1007 1010 1011 1032 C3' G D 36 OK 1030 1033 1034 1055 C3' U D 37 OK 1053 1056 1057 1075 C3' A D 38 OK 1073 1076 1077 1097 C3' C D 39 OK 1095 1098 1099 1117 C3' A D 40 OK 1115 1118 1119 1139 C3' U D 41 OK 1137 1140 1141 1159 C3' U D 42 OK 1157 1160 1161 1179 C3' A D 43 OK 1177 1180 1181 1201 C3' C D 44 OK 1199 1202 1203 1221 C3' C D 45 OK 1219 1222 1223 1241 C3' U D 46 OK 1239 1242 1243 1261 C3' G D 47 OK 1259 1262 1263 1284 C3' C D 48 OK 1282 1285 1286 1304 C3' C D 49 OK 1302 1305 1306 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 2 OK 5 2 4 23 C4' C A 3 OK 25 22 24 43 C4' G A 4 OK 45 42 44 66 C4' C A 5 OK 68 65 67 86 C4' A A 6 OK 88 85 87 108 C4' G A 7 OK 110 107 109 131 C4' U A 8 OK 133 130 132 151 C4' C A 9 OK 153 150 152 171 C4' C A 10 OK 173 170 172 191 C4' U A 11 OK 193 190 192 211 C4' A A 12 OK 213 210 212 233 C4' U A 13 OK 235 232 234 253 C4' U A 14 OK 255 252 254 271 C4' A B 2 OK 273 270 272 293 C4' A B 3 OK 295 292 294 315 C4' U B 4 OK 317 314 316 335 C4' A B 5 OK 337 334 336 357 C4' G B 6 OK 359 356 358 380 C4' A B 7 OK 382 379 381 402 C4' G B 8 OK 404 401 403 425 C4' A B 9 OK 427 424 426 447 C4' A B 10 OK 449 446 448 469 C4' G B 11 OK 471 468 470 492 C4' C B 12 OK 494 491 493 512 C4' G B 13 OK 514 511 513 535 C4' A B 14 OK 537 534 536 555 C4' G C 15 OK 557 554 556 578 C4' G C 16 OK 580 577 579 601 C4' C C 17 OK 603 600 602 621 C4' A C 18 OK 623 620 622 643 C4' G C 19 OK 645 642 644 666 C4' A C 20 OK 668 665 667 688 C4' G C 21 OK 690 687 689 711 C4' A C 22 OK 713 710 712 733 C4' A C 23 OK 735 732 734 755 C4' A C 24 OK 757 754 756 777 C4' C C 25 OK 779 776 778 797 C4' A C 26 OK 799 796 798 819 C4' C C 27 OK 821 818 820 839 C4' A C 28 OK 841 838 840 861 C4' C C 29 OK 863 860 862 881 C4' G C 30 OK 883 880 882 904 C4' A C 31 OK 906 903 905 924 C4' U D 31 OK 926 923 925 944 C4' C D 32 OK 946 943 945 964 C4' G D 33 OK 966 963 965 987 C4' U D 34 OK 989 986 988 1007 C4' G D 35 OK 1009 1006 1008 1030 C4' G D 36 OK 1032 1029 1031 1053 C4' U D 37 OK 1055 1052 1054 1073 C4' A D 38 OK 1075 1072 1074 1095 C4' C D 39 OK 1097 1094 1096 1115 C4' A D 40 OK 1117 1114 1116 1137 C4' U D 41 OK 1139 1136 1138 1157 C4' U D 42 OK 1159 1156 1158 1177 C4' A D 43 OK 1179 1176 1178 1199 C4' C D 44 OK 1201 1198 1200 1219 C4' C D 45 OK 1221 1218 1220 1239 C4' U D 46 OK 1241 1238 1240 1259 C4' G D 47 OK 1261 1258 1260 1282 C4' C D 48 OK 1284 1281 1283 1302 C4' C D 49 OK 1304 1301 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 2 1 3 22 C5' C A 3 21 23 42 C5' G A 4 41 43 65 C5' C A 5 64 66 85 C5' A A 6 84 86 107 C5' G A 7 106 108 130 C5' U A 8 129 131 150 C5' C A 9 149 151 170 C5' C A 10 169 171 190 C5' U A 11 189 191 210 C5' A A 12 209 211 232 C5' U A 13 231 233 252 C5' U A 14 251 253 270 C5' A B 2 269 271 292 C5' A B 3 291 293 314 C5' U B 4 313 315 334 C5' A B 5 333 335 356 C5' G B 6 355 357 379 C5' A B 7 378 380 401 C5' G B 8 400 402 424 C5' A B 9 423 425 446 C5' A B 10 445 447 468 C5' G B 11 467 469 491 C5' C B 12 490 492 511 C5' G B 13 510 512 534 C5' A B 14 533 535 554 C5' G C 15 553 555 577 C5' G C 16 576 578 600 C5' C C 17 599 601 620 C5' A C 18 619 621 642 C5' G C 19 641 643 665 C5' A C 20 664 666 687 C5' G C 21 686 688 710 C5' A C 22 709 711 732 C5' A C 23 731 733 754 C5' A C 24 753 755 776 C5' C C 25 775 777 796 C5' A C 26 795 797 818 C5' C C 27 817 819 838 C5' A C 28 837 839 860 C5' C C 29 859 861 880 C5' G C 30 879 881 903 C5' A C 31 902 904 923 C5' U D 31 922 924 943 C5' C D 32 942 944 963 C5' G D 33 962 964 986 C5' U D 34 985 987 1006 C5' G D 35 1005 1007 1029 C5' G D 36 1028 1030 1052 C5' U D 37 1051 1053 1072 C5' A D 38 1071 1073 1094 C5' C D 39 1093 1095 1114 C5' A D 40 1113 1115 1136 C5' U D 41 1135 1137 1156 C5' U D 42 1155 1157 1176 C5' A D 43 1175 1177 1198 C5' C D 44 1197 1199 1218 C5' C D 45 1217 1219 1238 C5' U D 46 1237 1239 1258 C5' G D 47 1257 1259 1281 C5' C D 48 1280 1282 1301 C5' C D 49 1300 1302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 3 distorted distorted 6 19 20 21 38 P G A 4 distorted distorted 26 39 40 41 61 P C A 5 distorted distorted 46 62 63 64 81 P A A 6 distorted distorted 69 82 83 84 103 P G A 7 distorted distorted 89 104 105 106 126 P U A 8 distorted distorted 111 127 128 129 146 P C A 9 distorted distorted 134 147 148 149 166 P C A 10 distorted distorted 154 167 168 169 186 P U A 11 distorted distorted 174 187 188 189 206 P A A 12 distorted distorted 194 207 208 209 228 P U A 13 distorted distorted 214 229 230 231 248 P U A 14 distorted distorted 236 249 250 251 288 P A B 3 distorted distorted 274 289 290 291 310 P U B 4 distorted distorted 296 311 312 313 330 P A B 5 distorted distorted 318 331 332 333 352 P G B 6 distorted distorted 338 353 354 355 375 P A B 7 distorted distorted 360 376 377 378 397 P G B 8 distorted distorted 383 398 399 400 420 P A B 9 distorted distorted 405 421 422 423 442 P A B 10 distorted distorted 428 443 444 445 464 P G B 11 distorted distorted 450 465 466 467 487 P C B 12 distorted distorted 472 488 489 490 507 P G B 13 distorted distorted 495 508 509 510 530 P A B 14 distorted distorted 515 531 532 533 573 P G C 16 distorted distorted 558 574 575 576 596 P C C 17 distorted distorted 581 597 598 599 616 P A C 18 distorted distorted 604 617 618 619 638 P G C 19 distorted distorted 624 639 640 641 661 P A C 20 distorted distorted 646 662 663 664 683 P G C 21 distorted distorted 669 684 685 686 706 P A C 22 distorted distorted 691 707 708 709 728 P A C 23 distorted distorted 714 729 730 731 750 P A C 24 distorted distorted 736 751 752 753 772 P C C 25 distorted distorted 758 773 774 775 792 P A C 26 distorted distorted 780 793 794 795 814 P C C 27 distorted distorted 800 815 816 817 834 P A C 28 distorted distorted 822 835 836 837 856 P C C 29 distorted distorted 842 857 858 859 876 P G C 30 distorted distorted 864 877 878 879 899 P A C 31 distorted distorted 884 900 901 902 939 P C D 32 distorted distorted 927 940 941 942 959 P G D 33 distorted distorted 947 960 961 962 982 P U D 34 distorted distorted 967 983 984 985 1002 P G D 35 distorted distorted 990 1003 1004 1005 1025 P G D 36 distorted distorted 1010 1026 1027 1028 1048 P U D 37 distorted distorted 1033 1049 1050 1051 1068 P A D 38 distorted distorted 1056 1069 1070 1071 1090 P C D 39 distorted distorted 1076 1091 1092 1093 1110 P A D 40 distorted distorted 1098 1111 1112 1113 1132 P U D 41 distorted distorted 1118 1133 1134 1135 1152 P U D 42 distorted distorted 1140 1153 1154 1155 1172 P A D 43 distorted distorted 1160 1173 1174 1175 1194 P C D 44 distorted distorted 1180 1195 1196 1197 1214 P C D 45 distorted distorted 1202 1215 1216 1217 1234 P U D 46 distorted distorted 1222 1235 1236 1237 1254 P G D 47 distorted distorted 1242 1255 1256 1257 1277 P C D 48 distorted distorted 1262 1278 1279 1280 1297 P C D 49 distorted distorted 1285 1298 1299 1300 ---------------------------------------------------------------------------------