ID code: '2M18' 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' G A 3 alpha beta 73 96 79 76 112 C1' U A 4 alpha beta 107 127 113 110 142 C1' U A 5 alpha beta 137 157 143 140 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' U A 10 alpha beta 302 323 308 305 336 C1' G B 11 alpha beta 331 354 337 334 371 C1' G B 12 alpha beta 366 389 372 369 405 C1' G B 13 alpha beta 400 423 406 403 439 C1' U B 14 alpha beta 434 454 440 437 469 C1' U B 15 alpha beta 464 484 470 467 499 C1' A B 16 alpha beta 494 516 500 497 532 C1' G B 17 alpha beta 527 550 533 530 566 C1' G B 18 alpha beta 561 584 567 564 600 C1' G B 19 alpha beta 595 618 601 598 634 C1' U B 20 alpha beta 629 650 635 632 663 C1' G C 21 alpha beta 658 681 664 661 698 C1' G C 22 alpha beta 693 716 699 696 732 C1' G C 23 alpha beta 727 750 733 730 766 C1' U C 24 alpha beta 761 781 767 764 796 C1' U C 25 alpha beta 791 811 797 794 826 C1' A C 26 alpha beta 821 843 827 824 859 C1' G C 27 alpha beta 854 877 860 857 893 C1' G C 28 alpha beta 888 911 894 891 927 C1' G C 29 alpha beta 922 945 928 925 961 C1' U C 30 alpha beta 956 977 962 959 990 C1' G D 31 alpha beta 985 1008 991 988 1025 C1' G D 32 alpha beta 1020 1043 1026 1023 1059 C1' G D 33 alpha beta 1054 1077 1060 1057 1093 C1' U D 34 alpha beta 1088 1108 1094 1091 1123 C1' U D 35 alpha beta 1118 1138 1124 1121 1153 C1' A D 36 alpha beta 1148 1170 1154 1151 1186 C1' G D 37 alpha beta 1181 1204 1187 1184 1220 C1' G D 38 alpha beta 1215 1238 1221 1218 1254 C1' G D 39 alpha beta 1249 1272 1255 1252 1288 C1' U D 40 alpha beta 1283 1304 1289 1286 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' U A 4 OK OK 112 108 125 111 140 C2' U A 5 OK OK 142 138 155 141 170 C2' A A 6 OK OK 172 168 187 171 203 C2' G A 7 OK OK 205 201 221 204 237 C2' G A 8 OK OK 239 235 255 238 271 C2' G A 9 OK OK 273 269 289 272 305 C2' U A 10 OK OK 307 303 321 306 334 C2' G B 11 OK OK 336 332 352 335 369 C2' G B 12 OK OK 371 367 387 370 403 C2' G B 13 OK OK 405 401 421 404 437 C2' U B 14 OK OK 439 435 452 438 467 C2' U B 15 OK OK 469 465 482 468 497 C2' A B 16 OK OK 499 495 514 498 530 C2' G B 17 OK OK 532 528 548 531 564 C2' G B 18 OK OK 566 562 582 565 598 C2' G B 19 OK OK 600 596 616 599 632 C2' U B 20 OK OK 634 630 648 633 661 C2' G C 21 OK OK 663 659 679 662 696 C2' G C 22 OK OK 698 694 714 697 730 C2' G C 23 OK OK 732 728 748 731 764 C2' U C 24 OK OK 766 762 779 765 794 C2' U C 25 OK OK 796 792 809 795 824 C2' A C 26 OK OK 826 822 841 825 857 C2' G C 27 OK OK 859 855 875 858 891 C2' G C 28 OK OK 893 889 909 892 925 C2' G C 29 OK OK 927 923 943 926 959 C2' U C 30 OK OK 961 957 975 960 988 C2' G D 31 OK OK 990 986 1006 989 1023 C2' G D 32 OK OK 1025 1021 1041 1024 1057 C2' G D 33 OK OK 1059 1055 1075 1058 1091 C2' U D 34 OK OK 1093 1089 1106 1092 1121 C2' U D 35 OK OK 1123 1119 1136 1122 1151 C2' A D 36 OK OK 1153 1149 1168 1152 1184 C2' G D 37 OK OK 1186 1182 1202 1185 1218 C2' G D 38 OK OK 1220 1216 1236 1219 1252 C2' G D 39 OK OK 1254 1250 1270 1253 1286 C2' U D 40 OK OK 1288 1284 1302 1287 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' U A 4 OK OK 106 124 109 110 138 C3' U A 5 OK OK 136 154 139 140 168 C3' A A 6 OK OK 166 186 169 170 201 C3' G A 7 OK OK 199 220 202 203 235 C3' G A 8 OK OK 233 254 236 237 269 C3' G A 9 OK OK 267 288 270 271 303 C3' U A 10 OK OK 301 319 304 305 332 C3' G B 11 OK OK 330 351 333 334 367 C3' G B 12 OK OK 365 386 368 369 401 C3' G B 13 OK OK 399 420 402 403 435 C3' U B 14 OK OK 433 451 436 437 465 C3' U B 15 OK OK 463 481 466 467 495 C3' A B 16 OK OK 493 513 496 497 528 C3' G B 17 OK OK 526 547 529 530 562 C3' G B 18 OK OK 560 581 563 564 596 C3' G B 19 OK OK 594 615 597 598 630 C3' U B 20 OK OK 628 646 631 632 659 C3' G C 21 OK OK 657 678 660 661 694 C3' G C 22 OK OK 692 713 695 696 728 C3' G C 23 OK OK 726 747 729 730 762 C3' U C 24 OK OK 760 778 763 764 792 C3' U C 25 OK OK 790 808 793 794 822 C3' A C 26 OK OK 820 840 823 824 855 C3' G C 27 OK OK 853 874 856 857 889 C3' G C 28 OK OK 887 908 890 891 923 C3' G C 29 OK OK 921 942 924 925 957 C3' U C 30 OK OK 955 973 958 959 986 C3' G D 31 OK OK 984 1005 987 988 1021 C3' G D 32 OK OK 1019 1040 1022 1023 1055 C3' G D 33 OK OK 1053 1074 1056 1057 1089 C3' U D 34 OK OK 1087 1105 1090 1091 1119 C3' U D 35 OK OK 1117 1135 1120 1121 1149 C3' A D 36 OK OK 1147 1167 1150 1151 1182 C3' G D 37 OK OK 1180 1201 1183 1184 1216 C3' G D 38 OK OK 1214 1235 1217 1218 1250 C3' G D 39 OK OK 1248 1269 1251 1252 1284 C3' U D 40 OK OK 1282 1300 1285 1286 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' U A 4 OK OK 108 123 105 107 136 C4' U A 5 OK OK 138 153 135 137 166 C4' A A 6 OK OK 168 185 165 167 199 C4' G A 7 OK OK 201 219 198 200 233 C4' G A 8 OK OK 235 253 232 234 267 C4' G A 9 OK OK 269 287 266 268 301 C4' U A 10 OK OK 303 318 300 302 330 C4' G B 11 OK OK 332 350 329 331 365 C4' G B 12 OK OK 367 385 364 366 399 C4' G B 13 OK OK 401 419 398 400 433 C4' U B 14 OK OK 435 450 432 434 463 C4' U B 15 OK OK 465 480 462 464 493 C4' A B 16 OK OK 495 512 492 494 526 C4' G B 17 OK OK 528 546 525 527 560 C4' G B 18 OK OK 562 580 559 561 594 C4' G B 19 OK OK 596 614 593 595 628 C4' U B 20 OK OK 630 645 627 629 657 C4' G C 21 OK OK 659 677 656 658 692 C4' G C 22 OK OK 694 712 691 693 726 C4' G C 23 OK OK 728 746 725 727 760 C4' U C 24 OK OK 762 777 759 761 790 C4' U C 25 OK OK 792 807 789 791 820 C4' A C 26 OK OK 822 839 819 821 853 C4' G C 27 OK OK 855 873 852 854 887 C4' G C 28 OK OK 889 907 886 888 921 C4' G C 29 OK OK 923 941 920 922 955 C4' U C 30 OK OK 957 972 954 956 984 C4' G D 31 OK OK 986 1004 983 985 1019 C4' G D 32 OK OK 1021 1039 1018 1020 1053 C4' G D 33 OK OK 1055 1073 1052 1054 1087 C4' U D 34 OK OK 1089 1104 1086 1088 1117 C4' U D 35 OK OK 1119 1134 1116 1118 1147 C4' A D 36 OK OK 1149 1166 1146 1148 1180 C4' G D 37 OK OK 1182 1200 1179 1181 1214 C4' G D 38 OK OK 1216 1234 1213 1215 1248 C4' G D 39 OK OK 1250 1268 1247 1249 1282 C4' U D 40 OK OK 1284 1299 1281 1283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' U A 4 OK OK 104 121 122 106 135 C5' U A 5 OK OK 134 151 152 136 165 C5' A A 6 OK OK 164 183 184 166 198 C5' G A 7 OK OK 197 217 218 199 232 C5' G A 8 OK OK 231 251 252 233 266 C5' G A 9 OK OK 265 285 286 267 300 C5' U A 10 OK OK 299 316 317 301 329 C5' G B 11 OK OK 328 348 349 330 364 C5' G B 12 OK OK 363 383 384 365 398 C5' G B 13 OK OK 397 417 418 399 432 C5' U B 14 OK OK 431 448 449 433 462 C5' U B 15 OK OK 461 478 479 463 492 C5' A B 16 OK OK 491 510 511 493 525 C5' G B 17 OK OK 524 544 545 526 559 C5' G B 18 OK OK 558 578 579 560 593 C5' G B 19 OK OK 592 612 613 594 627 C5' U B 20 OK OK 626 643 644 628 656 C5' G C 21 OK OK 655 675 676 657 691 C5' G C 22 OK OK 690 710 711 692 725 C5' G C 23 OK OK 724 744 745 726 759 C5' U C 24 OK OK 758 775 776 760 789 C5' U C 25 OK OK 788 805 806 790 819 C5' A C 26 OK OK 818 837 838 820 852 C5' G C 27 OK OK 851 871 872 853 886 C5' G C 28 OK OK 885 905 906 887 920 C5' G C 29 OK OK 919 939 940 921 954 C5' U C 30 OK OK 953 970 971 955 983 C5' G D 31 OK OK 982 1002 1003 984 1018 C5' G D 32 OK OK 1017 1037 1038 1019 1052 C5' G D 33 OK OK 1051 1071 1072 1053 1086 C5' U D 34 OK OK 1085 1102 1103 1087 1116 C5' U D 35 OK OK 1115 1132 1133 1117 1146 C5' A D 36 OK OK 1145 1164 1165 1147 1179 C5' G D 37 OK OK 1178 1198 1199 1180 1213 C5' G D 38 OK OK 1212 1232 1233 1214 1247 C5' G D 39 OK OK 1246 1266 1267 1248 1281 C5' U D 40 OK OK 1280 1297 1298 1282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P U A 4 distorted distorted 75 102 103 104 131 P U A 5 distorted distorted 109 132 133 134 161 P A A 6 distorted distorted 139 162 163 164 194 P G A 7 distorted distorted 169 195 196 197 228 P G A 8 distorted distorted 202 229 230 231 262 P G A 9 distorted distorted 236 263 264 265 296 P U A 10 distorted distorted 270 297 298 299 360 P G B 12 distorted distorted 333 361 362 363 394 P G B 13 distorted distorted 368 395 396 397 428 P U B 14 distorted distorted 402 429 430 431 458 P U B 15 distorted distorted 436 459 460 461 488 P A B 16 distorted distorted 466 489 490 491 521 P G B 17 distorted distorted 496 522 523 524 555 P G B 18 distorted distorted 529 556 557 558 589 P G B 19 distorted distorted 563 590 591 592 623 P U B 20 distorted distorted 597 624 625 626 687 P G C 22 distorted distorted 660 688 689 690 721 P G C 23 distorted distorted 695 722 723 724 755 P U C 24 distorted distorted 729 756 757 758 785 P U C 25 distorted distorted 763 786 787 788 815 P A C 26 distorted distorted 793 816 817 818 848 P G C 27 distorted distorted 823 849 850 851 882 P G C 28 distorted distorted 856 883 884 885 916 P G C 29 distorted distorted 890 917 918 919 950 P U C 30 distorted distorted 924 951 952 953 1014 P G D 32 distorted distorted 987 1015 1016 1017 1048 P G D 33 distorted distorted 1022 1049 1050 1051 1082 P U D 34 distorted distorted 1056 1083 1084 1085 1112 P U D 35 distorted distorted 1090 1113 1114 1115 1142 P A D 36 distorted distorted 1120 1143 1144 1145 1175 P G D 37 distorted distorted 1150 1176 1177 1178 1209 P G D 38 distorted distorted 1183 1210 1211 1212 1243 P G D 39 distorted distorted 1217 1244 1245 1246 1277 P U D 40 distorted distorted 1251 1278 1279 1280 ---------------------------------------------------------------------------------