ID code: '3GS1' 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 -4 beta 41 47 44 66 C1' C A -3 beta 61 67 64 86 C1' C A -2 beta 81 87 84 106 C1' A A -1 beta 101 107 104 128 C1' G A 1 beta 123 129 126 151 C1' U A 2 beta 146 152 149 171 C1' C A 3 beta 166 172 169 191 C1' C A 4 beta 186 192 189 211 C1' A A 5 beta 206 212 209 233 C1' C A 6 beta 228 234 231 253 C1' C A 7 beta 248 254 251 273 C1' G A 8 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 398 404 401 425 C1' G B 8 beta 420 426 423 448 C1' A B 9 beta 443 449 446 470 C1' A B 10 beta 465 471 468 492 C1' G B 11 beta 487 493 490 515 C1' G B 12 beta 510 516 513 538 C1' G B 13 beta 533 539 536 562 C1' G C 15 beta 557 563 560 585 C1' G C 16 beta 580 586 583 608 C1' C C 17 beta 603 609 606 628 C1' A C 18 beta 623 629 626 650 C1' G C 19 beta 645 651 648 673 C1' A C 20 beta 668 674 671 695 C1' G C 21 beta 690 696 693 718 C1' A C 22 beta 713 719 716 740 C1' A C 23 beta 735 741 738 762 C1' A C 24 beta 757 763 760 784 C1' C C 25 beta 779 785 782 804 C1' A C 26 beta 799 805 802 826 C1' C C 27 beta 821 827 824 846 C1' A C 28 beta 841 847 844 868 C1' C C 29 beta 863 869 866 888 C1' G C 30 beta 883 889 886 911 C1' A C 31 beta 906 912 909 931 C1' U D 31 beta 926 932 929 951 C1' C D 32 beta 946 952 949 971 C1' G D 33 beta 966 972 969 994 C1' U D 34 beta 989 995 992 1014 C1' G D 35 beta 1009 1015 1012 1037 C1' G D 36 beta 1032 1038 1035 1060 C1' U D 37 beta 1055 1061 1058 1080 C1' A D 38 beta 1075 1081 1078 1102 C1' C D 39 beta 1097 1103 1100 1122 C1' A D 40 beta 1117 1123 1120 1144 C1' U D 41 beta 1139 1145 1142 1164 C1' U D 42 beta 1159 1165 1162 1184 C1' A D 43 beta 1179 1185 1182 1206 C1' C D 44 beta 1201 1207 1204 1226 C1' C D 45 beta 1221 1227 1224 1246 C1' U D 46 beta 1241 1247 1244 1266 C1' G D 47 beta 1261 1267 1264 1289 C1' C D 48 beta 1284 1290 1287 1309 C1' C D 49 beta 1304 1310 1307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 44 C2' C A -4 OK 46 42 45 64 C2' C A -3 OK 66 62 65 84 C2' C A -2 OK 86 82 85 104 C2' A A -1 OK 106 102 105 126 C2' G A 1 OK 128 124 127 149 C2' U A 2 OK 151 147 150 169 C2' C A 3 OK 171 167 170 189 C2' C A 4 OK 191 187 190 209 C2' A A 5 OK 211 207 210 231 C2' C A 6 OK 233 229 232 251 C2' C A 7 OK 253 249 252 271 C2' G A 8 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 403 399 402 423 C2' G B 8 OK 425 421 424 446 C2' A B 9 OK 448 444 447 468 C2' A B 10 OK 470 466 469 490 C2' G B 11 OK 492 488 491 513 C2' G B 12 OK 515 511 514 536 C2' G B 13 OK 538 534 537 560 C2' G C 15 OK 562 558 561 583 C2' G C 16 OK 585 581 584 606 C2' C C 17 OK 608 604 607 626 C2' A C 18 OK 628 624 627 648 C2' G C 19 OK 650 646 649 671 C2' A C 20 OK 673 669 672 693 C2' G C 21 OK 695 691 694 716 C2' A C 22 OK 718 714 717 738 C2' A C 23 OK 740 736 739 760 C2' A C 24 OK 762 758 761 782 C2' C C 25 OK 784 780 783 802 C2' A C 26 OK 804 800 803 824 C2' C C 27 OK 826 822 825 844 C2' A C 28 OK 846 842 845 866 C2' C C 29 OK 868 864 867 886 C2' G C 30 OK 888 884 887 909 C2' A C 31 OK 911 907 910 929 C2' U D 31 OK 931 927 930 949 C2' C D 32 OK 951 947 950 969 C2' G D 33 OK 971 967 970 992 C2' U D 34 OK 994 990 993 1012 C2' G D 35 OK 1014 1010 1013 1035 C2' G D 36 OK 1037 1033 1036 1058 C2' U D 37 OK 1060 1056 1059 1078 C2' A D 38 OK 1080 1076 1079 1100 C2' C D 39 OK 1102 1098 1101 1120 C2' A D 40 OK 1122 1118 1121 1142 C2' U D 41 OK 1144 1140 1143 1162 C2' U D 42 OK 1164 1160 1163 1182 C2' A D 43 OK 1184 1180 1183 1204 C2' C D 44 OK 1206 1202 1205 1224 C2' C D 45 OK 1226 1222 1225 1244 C2' U D 46 OK 1246 1242 1245 1264 C2' G D 47 OK 1266 1262 1265 1287 C2' C D 48 OK 1289 1285 1288 1307 C2' C D 49 OK 1309 1305 1308 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 42 C3' C A -4 OK 40 43 44 62 C3' C A -3 OK 60 63 64 82 C3' C A -2 OK 80 83 84 102 C3' A A -1 OK 100 103 104 124 C3' G A 1 OK 122 125 126 147 C3' U A 2 OK 145 148 149 167 C3' C A 3 OK 165 168 169 187 C3' C A 4 OK 185 188 189 207 C3' A A 5 OK 205 208 209 229 C3' C A 6 OK 227 230 231 249 C3' C A 7 OK 247 250 251 269 C3' G A 8 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 397 400 401 421 C3' G B 8 OK 419 422 423 444 C3' A B 9 OK 442 445 446 466 C3' A B 10 OK 464 467 468 488 C3' G B 11 OK 486 489 490 511 C3' G B 12 OK 509 512 513 534 C3' G B 13 OK 532 535 536 558 C3' G C 15 OK 556 559 560 581 C3' G C 16 OK 579 582 583 604 C3' C C 17 OK 602 605 606 624 C3' A C 18 OK 622 625 626 646 C3' G C 19 OK 644 647 648 669 C3' A C 20 OK 667 670 671 691 C3' G C 21 OK 689 692 693 714 C3' A C 22 OK 712 715 716 736 C3' A C 23 OK 734 737 738 758 C3' A C 24 OK 756 759 760 780 C3' C C 25 OK 778 781 782 800 C3' A C 26 OK 798 801 802 822 C3' C C 27 OK 820 823 824 842 C3' A C 28 OK 840 843 844 864 C3' C C 29 OK 862 865 866 884 C3' G C 30 OK 882 885 886 907 C3' A C 31 OK 905 908 909 927 C3' U D 31 OK 925 928 929 947 C3' C D 32 OK 945 948 949 967 C3' G D 33 OK 965 968 969 990 C3' U D 34 OK 988 991 992 1010 C3' G D 35 OK 1008 1011 1012 1033 C3' G D 36 OK 1031 1034 1035 1056 C3' U D 37 OK 1054 1057 1058 1076 C3' A D 38 OK 1074 1077 1078 1098 C3' C D 39 OK 1096 1099 1100 1118 C3' A D 40 OK 1116 1119 1120 1140 C3' U D 41 OK 1138 1141 1142 1160 C3' U D 42 OK 1158 1161 1162 1180 C3' A D 43 OK 1178 1181 1182 1202 C3' C D 44 OK 1200 1203 1204 1222 C3' C D 45 OK 1220 1223 1224 1242 C3' U D 46 OK 1240 1243 1244 1262 C3' G D 47 OK 1260 1263 1264 1285 C3' C D 48 OK 1283 1286 1287 1305 C3' C D 49 OK 1303 1306 1307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 40 C4' C A -4 OK 42 39 41 60 C4' C A -3 OK 62 59 61 80 C4' C A -2 OK 82 79 81 100 C4' A A -1 OK 102 99 101 122 C4' G A 1 OK 124 121 123 145 C4' U A 2 OK 147 144 146 165 C4' C A 3 OK 167 164 166 185 C4' C A 4 OK 187 184 186 205 C4' A A 5 OK 207 204 206 227 C4' C A 6 OK 229 226 228 247 C4' C A 7 OK 249 246 248 267 C4' G A 8 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' G B 8 OK 421 418 420 442 C4' A B 9 OK 444 441 443 464 C4' A B 10 OK 466 463 465 486 C4' G B 11 OK 488 485 487 509 C4' G B 12 OK 511 508 510 532 C4' G B 13 OK 534 531 533 556 C4' G C 15 OK 558 555 557 579 C4' G C 16 OK 581 578 580 602 C4' C C 17 OK 604 601 603 622 C4' A C 18 OK 624 621 623 644 C4' G C 19 OK 646 643 645 667 C4' A C 20 OK 669 666 668 689 C4' G C 21 OK 691 688 690 712 C4' A C 22 OK 714 711 713 734 C4' A C 23 OK 736 733 735 756 C4' A C 24 OK 758 755 757 778 C4' C C 25 OK 780 777 779 798 C4' A C 26 OK 800 797 799 820 C4' C C 27 OK 822 819 821 840 C4' A C 28 OK 842 839 841 862 C4' C C 29 OK 864 861 863 882 C4' G C 30 OK 884 881 883 905 C4' A C 31 OK 907 904 906 925 C4' U D 31 OK 927 924 926 945 C4' C D 32 OK 947 944 946 965 C4' G D 33 OK 967 964 966 988 C4' U D 34 OK 990 987 989 1008 C4' G D 35 OK 1010 1007 1009 1031 C4' G D 36 OK 1033 1030 1032 1054 C4' U D 37 OK 1056 1053 1055 1074 C4' A D 38 OK 1076 1073 1075 1096 C4' C D 39 OK 1098 1095 1097 1116 C4' A D 40 OK 1118 1115 1117 1138 C4' U D 41 OK 1140 1137 1139 1158 C4' U D 42 OK 1160 1157 1159 1178 C4' A D 43 OK 1180 1177 1179 1200 C4' C D 44 OK 1202 1199 1201 1220 C4' C D 45 OK 1222 1219 1221 1240 C4' U D 46 OK 1242 1239 1241 1260 C4' G D 47 OK 1262 1259 1261 1283 C4' C D 48 OK 1285 1282 1284 1303 C4' C D 49 OK 1305 1302 1304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 39 C5' C A -4 38 40 59 C5' C A -3 58 60 79 C5' C A -2 78 80 99 C5' A A -1 98 100 121 C5' G A 1 120 122 144 C5' U A 2 143 145 164 C5' C A 3 163 165 184 C5' C A 4 183 185 204 C5' A A 5 203 205 226 C5' C A 6 225 227 246 C5' C A 7 245 247 266 C5' G A 8 265 267 287 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' G B 8 417 419 441 C5' A B 9 440 442 463 C5' A B 10 462 464 485 C5' G B 11 484 486 508 C5' G B 12 507 509 531 C5' G B 13 530 532 555 C5' G C 15 554 556 578 C5' G C 16 577 579 601 C5' C C 17 600 602 621 C5' A C 18 620 622 643 C5' G C 19 642 644 666 C5' A C 20 665 667 688 C5' G C 21 687 689 711 C5' A C 22 710 712 733 C5' A C 23 732 734 755 C5' A C 24 754 756 777 C5' C C 25 776 778 797 C5' A C 26 796 798 819 C5' C C 27 818 820 839 C5' A C 28 838 840 861 C5' C C 29 860 862 881 C5' G C 30 880 882 904 C5' A C 31 903 905 924 C5' U D 31 923 925 944 C5' C D 32 943 945 964 C5' G D 33 963 965 987 C5' U D 34 986 988 1007 C5' G D 35 1006 1008 1030 C5' G D 36 1029 1031 1053 C5' U D 37 1052 1054 1073 C5' A D 38 1072 1074 1095 C5' C D 39 1094 1096 1115 C5' A D 40 1114 1116 1137 C5' U D 41 1136 1138 1157 C5' U D 42 1156 1158 1177 C5' A D 43 1176 1178 1199 C5' C D 44 1198 1200 1219 C5' C D 45 1218 1220 1239 C5' U D 46 1238 1240 1259 C5' G D 47 1258 1260 1282 C5' C D 48 1281 1283 1302 C5' C D 49 1301 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 35 P C A -4 distorted distorted 36 37 38 55 P C A -3 distorted distorted 43 56 57 58 75 P C A -2 distorted distorted 63 76 77 78 95 P A A -1 distorted distorted 83 96 97 98 117 P G A 1 distorted distorted 103 118 119 120 140 P U A 2 distorted distorted 125 141 142 143 160 P C A 3 distorted distorted 148 161 162 163 180 P C A 4 distorted distorted 168 181 182 183 200 P A A 5 distorted distorted 188 201 202 203 222 P C A 6 distorted distorted 208 223 224 225 242 P C A 7 distorted distorted 230 243 244 245 262 P G A 8 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 G B 8 distorted distorted 400 415 416 417 437 P A B 9 distorted distorted 422 438 439 440 459 P A B 10 distorted distorted 445 460 461 462 481 P G B 11 distorted distorted 467 482 483 484 504 P G B 12 distorted distorted 489 505 506 507 527 P G B 13 distorted distorted 512 528 529 530 551 P G C 15 OK OK 1350 552 553 554 574 P G C 16 distorted distorted 559 575 576 577 597 P C C 17 distorted distorted 582 598 599 600 617 P A C 18 distorted distorted 605 618 619 620 639 P G C 19 distorted distorted 625 640 641 642 662 P A C 20 distorted distorted 647 663 664 665 684 P G C 21 distorted distorted 670 685 686 687 707 P A C 22 distorted distorted 692 708 709 710 729 P A C 23 distorted distorted 715 730 731 732 751 P A C 24 distorted distorted 737 752 753 754 773 P C C 25 distorted distorted 759 774 775 776 793 P A C 26 distorted distorted 781 794 795 796 815 P C C 27 distorted distorted 801 816 817 818 835 P A C 28 distorted distorted 823 836 837 838 857 P C C 29 distorted distorted 843 858 859 860 877 P G C 30 distorted distorted 865 878 879 880 900 P A C 31 distorted distorted 885 901 902 903 940 P C D 32 distorted distorted 928 941 942 943 960 P G D 33 distorted distorted 948 961 962 963 983 P U D 34 distorted distorted 968 984 985 986 1003 P G D 35 distorted distorted 991 1004 1005 1006 1026 P G D 36 distorted distorted 1011 1027 1028 1029 1049 P U D 37 distorted distorted 1034 1050 1051 1052 1069 P A D 38 distorted distorted 1057 1070 1071 1072 1091 P C D 39 distorted distorted 1077 1092 1093 1094 1111 P A D 40 distorted distorted 1099 1112 1113 1114 1133 P U D 41 distorted distorted 1119 1134 1135 1136 1153 P U D 42 distorted distorted 1141 1154 1155 1156 1173 P A D 43 distorted distorted 1161 1174 1175 1176 1195 P C D 44 distorted distorted 1181 1196 1197 1198 1215 P C D 45 distorted distorted 1203 1216 1217 1218 1235 P U D 46 distorted distorted 1223 1236 1237 1238 1255 P G D 47 distorted distorted 1243 1256 1257 1258 1278 P C D 48 distorted distorted 1263 1279 1280 1281 1298 P C D 49 distorted distorted 1286 1299 1300 1301 1338 P S9L C 14 distorted distorted 535 1339 1340 1341 ---------------------------------------------------------------------------------