ID code: '1MNX' 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 68 alpha beta 4 27 10 7 44 C1' G A 69 alpha beta 39 62 45 42 78 C1' G A 70 alpha beta 73 96 79 76 112 C1' U A 71 alpha beta 107 127 113 110 142 C1' G A 72 alpha beta 137 160 143 140 176 C1' A A 73 alpha beta 171 193 177 174 209 C1' C A 74 alpha beta 204 224 210 207 240 C1' G A 75 alpha beta 235 258 241 238 274 C1' A A 76 alpha beta 269 291 275 272 307 C1' U A 77 alpha beta 302 322 308 305 337 C1' A A 78 alpha beta 332 354 338 335 370 C1' C A 79 alpha beta 365 385 371 368 401 C1' U A 80 alpha beta 396 416 402 399 431 C1' G A 81 alpha beta 426 449 432 429 465 C1' U A 82 alpha beta 460 480 466 463 495 C1' A A 83 alpha beta 490 512 496 493 528 C1' G A 84 alpha beta 523 546 529 526 562 C1' G A 85 alpha beta 557 580 563 560 596 C1' C A 86 alpha beta 591 611 597 594 627 C1' G A 87 alpha beta 622 645 628 625 661 C1' A A 88 alpha beta 656 678 662 659 694 C1' G A 88 alpha beta 689 712 695 692 728 C1' A A 89 alpha beta 723 745 729 726 761 C1' G A 90 alpha beta 756 779 762 759 795 C1' C A 91 alpha beta 790 810 796 793 826 C1' C A 92 alpha beta 821 841 827 824 857 C1' U A 93 alpha beta 852 872 858 855 887 C1' G A 94 alpha beta 882 905 888 885 921 C1' C A 95 alpha beta 916 936 922 919 952 C1' G A 96 alpha beta 947 970 953 950 986 C1' G A 97 alpha beta 981 1004 987 984 1020 C1' A A 98 alpha beta 1015 1037 1021 1018 1053 C1' A A 99 alpha beta 1048 1070 1054 1051 1086 C1' A A 100 alpha beta 1081 1103 1087 1084 1119 C1' A A 101 alpha beta 1114 1136 1120 1117 1152 C1' A A 102 alpha beta 1147 1169 1153 1150 1185 C1' U A 103 alpha beta 1180 1200 1186 1183 1215 C1' A A 104 alpha beta 1210 1232 1216 1213 1248 C1' G A 105 alpha beta 1243 1266 1249 1246 1282 C1' C A 106 alpha beta 1277 1297 1283 1280 1313 C1' C A 107 alpha beta 1308 1328 1314 1311 1344 C1' C A 108 alpha beta 1339 1360 1345 1342 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 68 OK OK 9 5 25 8 42 C2' G A 69 OK OK 44 40 60 43 76 C2' G A 70 OK OK 78 74 94 77 110 C2' U A 71 OK OK 112 108 125 111 140 C2' G A 72 OK OK 142 138 158 141 174 C2' A A 73 OK OK 176 172 191 175 207 C2' C A 74 OK OK 209 205 222 208 238 C2' G A 75 OK OK 240 236 256 239 272 C2' A A 76 OK OK 274 270 289 273 305 C2' U A 77 OK OK 307 303 320 306 335 C2' A A 78 OK OK 337 333 352 336 368 C2' C A 79 OK OK 370 366 383 369 399 C2' U A 80 OK OK 401 397 414 400 429 C2' G A 81 OK OK 431 427 447 430 463 C2' U A 82 OK OK 465 461 478 464 493 C2' A A 83 OK OK 495 491 510 494 526 C2' G A 84 OK OK 528 524 544 527 560 C2' G A 85 OK OK 562 558 578 561 594 C2' C A 86 OK OK 596 592 609 595 625 C2' G A 87 OK OK 627 623 643 626 659 C2' A A 88 OK OK 661 657 676 660 692 C2' G A 88 OK OK 694 690 710 693 726 C2' A A 89 OK OK 728 724 743 727 759 C2' G A 90 OK OK 761 757 777 760 793 C2' C A 91 OK OK 795 791 808 794 824 C2' C A 92 OK OK 826 822 839 825 855 C2' U A 93 OK OK 857 853 870 856 885 C2' G A 94 OK OK 887 883 903 886 919 C2' C A 95 OK OK 921 917 934 920 950 C2' G A 96 OK OK 952 948 968 951 984 C2' G A 97 OK OK 986 982 1002 985 1018 C2' A A 98 OK OK 1020 1016 1035 1019 1051 C2' A A 99 OK OK 1053 1049 1068 1052 1084 C2' A A 100 OK OK 1086 1082 1101 1085 1117 C2' A A 101 OK OK 1119 1115 1134 1118 1150 C2' A A 102 OK OK 1152 1148 1167 1151 1183 C2' U A 103 OK OK 1185 1181 1198 1184 1213 C2' A A 104 OK OK 1215 1211 1230 1214 1246 C2' G A 105 OK OK 1248 1244 1264 1247 1280 C2' C A 106 OK OK 1282 1278 1295 1281 1311 C2' C A 107 OK OK 1313 1309 1326 1312 1342 C2' C A 108 OK OK 1344 1340 1358 1343 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 68 OK OK 3 24 6 7 40 C3' G A 69 OK OK 38 59 41 42 74 C3' G A 70 OK OK 72 93 75 76 108 C3' U A 71 OK OK 106 124 109 110 138 C3' G A 72 OK OK 136 157 139 140 172 C3' A A 73 OK OK 170 190 173 174 205 C3' C A 74 OK OK 203 221 206 207 236 C3' G A 75 OK OK 234 255 237 238 270 C3' A A 76 OK OK 268 288 271 272 303 C3' U A 77 OK OK 301 319 304 305 333 C3' A A 78 OK OK 331 351 334 335 366 C3' C A 79 OK OK 364 382 367 368 397 C3' U A 80 OK OK 395 413 398 399 427 C3' G A 81 OK OK 425 446 428 429 461 C3' U A 82 OK OK 459 477 462 463 491 C3' A A 83 OK OK 489 509 492 493 524 C3' G A 84 OK OK 522 543 525 526 558 C3' G A 85 OK OK 556 577 559 560 592 C3' C A 86 OK OK 590 608 593 594 623 C3' G A 87 OK OK 621 642 624 625 657 C3' A A 88 OK OK 655 675 658 659 690 C3' G A 88 OK OK 688 709 691 692 724 C3' A A 89 OK OK 722 742 725 726 757 C3' G A 90 OK OK 755 776 758 759 791 C3' C A 91 OK OK 789 807 792 793 822 C3' C A 92 OK OK 820 838 823 824 853 C3' U A 93 OK OK 851 869 854 855 883 C3' G A 94 OK OK 881 902 884 885 917 C3' C A 95 OK OK 915 933 918 919 948 C3' G A 96 OK OK 946 967 949 950 982 C3' G A 97 OK OK 980 1001 983 984 1016 C3' A A 98 OK OK 1014 1034 1017 1018 1049 C3' A A 99 OK OK 1047 1067 1050 1051 1082 C3' A A 100 OK OK 1080 1100 1083 1084 1115 C3' A A 101 OK OK 1113 1133 1116 1117 1148 C3' A A 102 OK OK 1146 1166 1149 1150 1181 C3' U A 103 OK OK 1179 1197 1182 1183 1211 C3' A A 104 OK OK 1209 1229 1212 1213 1244 C3' G A 105 OK OK 1242 1263 1245 1246 1278 C3' C A 106 OK OK 1276 1294 1279 1280 1309 C3' C A 107 OK OK 1307 1325 1310 1311 1340 C3' C A 108 OK OK 1338 1356 1341 1342 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 68 OK OK 5 23 2 4 38 C4' G A 69 OK OK 40 58 37 39 72 C4' G A 70 OK OK 74 92 71 73 106 C4' U A 71 OK OK 108 123 105 107 136 C4' G A 72 OK OK 138 156 135 137 170 C4' A A 73 OK OK 172 189 169 171 203 C4' C A 74 OK OK 205 220 202 204 234 C4' G A 75 OK OK 236 254 233 235 268 C4' A A 76 OK OK 270 287 267 269 301 C4' U A 77 OK OK 303 318 300 302 331 C4' A A 78 OK OK 333 350 330 332 364 C4' C A 79 OK OK 366 381 363 365 395 C4' U A 80 OK OK 397 412 394 396 425 C4' G A 81 OK OK 427 445 424 426 459 C4' U A 82 OK OK 461 476 458 460 489 C4' A A 83 OK OK 491 508 488 490 522 C4' G A 84 OK OK 524 542 521 523 556 C4' G A 85 OK OK 558 576 555 557 590 C4' C A 86 OK OK 592 607 589 591 621 C4' G A 87 OK OK 623 641 620 622 655 C4' A A 88 OK OK 657 674 654 656 688 C4' G A 88 OK OK 690 708 687 689 722 C4' A A 89 OK OK 724 741 721 723 755 C4' G A 90 OK OK 757 775 754 756 789 C4' C A 91 OK OK 791 806 788 790 820 C4' C A 92 OK OK 822 837 819 821 851 C4' U A 93 OK OK 853 868 850 852 881 C4' G A 94 OK OK 883 901 880 882 915 C4' C A 95 OK OK 917 932 914 916 946 C4' G A 96 OK OK 948 966 945 947 980 C4' G A 97 OK OK 982 1000 979 981 1014 C4' A A 98 OK OK 1016 1033 1013 1015 1047 C4' A A 99 OK OK 1049 1066 1046 1048 1080 C4' A A 100 OK OK 1082 1099 1079 1081 1113 C4' A A 101 OK OK 1115 1132 1112 1114 1146 C4' A A 102 OK OK 1148 1165 1145 1147 1179 C4' U A 103 OK OK 1181 1196 1178 1180 1209 C4' A A 104 OK OK 1211 1228 1208 1210 1242 C4' G A 105 OK OK 1244 1262 1241 1243 1276 C4' C A 106 OK OK 1278 1293 1275 1277 1307 C4' C A 107 OK OK 1309 1324 1306 1308 1338 C4' C A 108 OK OK 1340 1355 1337 1339 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 68 OK OK 1 21 22 3 37 C5' G A 69 OK OK 36 56 57 38 71 C5' G A 70 OK OK 70 90 91 72 105 C5' U A 71 OK OK 104 121 122 106 135 C5' G A 72 OK OK 134 154 155 136 169 C5' A A 73 OK OK 168 187 188 170 202 C5' C A 74 OK OK 201 218 219 203 233 C5' G A 75 OK OK 232 252 253 234 267 C5' A A 76 OK OK 266 285 286 268 300 C5' U A 77 OK OK 299 316 317 301 330 C5' A A 78 OK OK 329 348 349 331 363 C5' C A 79 OK OK 362 379 380 364 394 C5' U A 80 OK OK 393 410 411 395 424 C5' G A 81 OK OK 423 443 444 425 458 C5' U A 82 OK OK 457 474 475 459 488 C5' A A 83 OK OK 487 506 507 489 521 C5' G A 84 OK OK 520 540 541 522 555 C5' G A 85 OK OK 554 574 575 556 589 C5' C A 86 OK OK 588 605 606 590 620 C5' G A 87 OK OK 619 639 640 621 654 C5' A A 88 OK OK 653 672 673 655 687 C5' G A 88 OK OK 686 706 707 688 721 C5' A A 89 OK OK 720 739 740 722 754 C5' G A 90 OK OK 753 773 774 755 788 C5' C A 91 OK OK 787 804 805 789 819 C5' C A 92 OK OK 818 835 836 820 850 C5' U A 93 OK OK 849 866 867 851 880 C5' G A 94 OK OK 879 899 900 881 914 C5' C A 95 OK OK 913 930 931 915 945 C5' G A 96 OK OK 944 964 965 946 979 C5' G A 97 OK OK 978 998 999 980 1013 C5' A A 98 OK OK 1012 1031 1032 1014 1046 C5' A A 99 OK OK 1045 1064 1065 1047 1079 C5' A A 100 OK OK 1078 1097 1098 1080 1112 C5' A A 101 OK OK 1111 1130 1131 1113 1145 C5' A A 102 OK OK 1144 1163 1164 1146 1178 C5' U A 103 OK OK 1177 1194 1195 1179 1208 C5' A A 104 OK OK 1207 1226 1227 1209 1241 C5' G A 105 OK OK 1240 1260 1261 1242 1275 C5' C A 106 OK OK 1274 1291 1292 1276 1306 C5' C A 107 OK OK 1305 1322 1323 1307 1337 C5' C A 108 OK OK 1336 1353 1354 1338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 69 distorted distorted 6 34 35 36 67 P G A 70 distorted distorted 41 68 69 70 101 P U A 71 distorted distorted 75 102 103 104 131 P G A 72 distorted distorted 109 132 133 134 165 P A A 73 distorted distorted 139 166 167 168 198 P C A 74 distorted distorted 173 199 200 201 229 P G A 75 distorted distorted 206 230 231 232 263 P A A 76 distorted distorted 237 264 265 266 296 P U A 77 distorted distorted 271 297 298 299 326 P A A 78 distorted distorted 304 327 328 329 359 P C A 79 distorted distorted 334 360 361 362 390 P U A 80 distorted distorted 367 391 392 393 420 P G A 81 distorted distorted 398 421 422 423 454 P U A 82 distorted distorted 428 455 456 457 484 P A A 83 distorted distorted 462 485 486 487 517 P G A 84 distorted distorted 492 518 519 520 551 P G A 85 distorted distorted 525 552 553 554 585 P C A 86 distorted distorted 559 586 587 588 616 P G A 87 distorted distorted 593 617 618 619 650 P A A 88 distorted distorted 624 651 652 653 683 P G A 88 distorted distorted 658 684 685 686 717 P A A 89 distorted distorted 691 718 719 720 750 P G A 90 distorted distorted 725 751 752 753 784 P C A 91 distorted distorted 758 785 786 787 815 P C A 92 distorted distorted 792 816 817 818 846 P U A 93 distorted distorted 823 847 848 849 876 P G A 94 distorted distorted 854 877 878 879 910 P C A 95 distorted distorted 884 911 912 913 941 P G A 96 distorted distorted 918 942 943 944 975 P G A 97 distorted distorted 949 976 977 978 1009 P A A 98 distorted distorted 983 1010 1011 1012 1042 P A A 99 distorted distorted 1017 1043 1044 1045 1075 P A A 100 distorted distorted 1050 1076 1077 1078 1108 P A A 101 distorted distorted 1083 1109 1110 1111 1141 P A A 102 distorted distorted 1116 1142 1143 1144 1174 P U A 103 distorted distorted 1149 1175 1176 1177 1204 P A A 104 distorted distorted 1182 1205 1206 1207 1237 P G A 105 distorted distorted 1212 1238 1239 1240 1271 P C A 106 distorted distorted 1245 1272 1273 1274 1302 P C A 107 distorted distorted 1279 1303 1304 1305 1333 P C A 108 distorted distorted 1310 1334 1335 1336 ---------------------------------------------------------------------------------