ID code: '2P7D' 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 2 beta 41 47 44 66 C1' C A 3 beta 61 67 64 86 C1' C A 4 beta 81 87 84 106 C1' A A 5 beta 101 107 104 126 C1' C B 2 beta 121 127 124 146 C1' G B 3 beta 141 147 144 169 C1' G B 4 beta 164 170 167 192 C1' U B 5 beta 187 193 190 212 C1' G B 6 beta 207 213 210 235 C1' A B 7 beta 230 236 233 303 C1' A B 9 beta 298 304 301 325 C1' A B 10 beta 320 326 323 347 C1' G B 11 beta 342 348 345 370 C1' G B 12 beta 365 371 368 393 C1' G B 13 beta 388 394 391 430 C1' G C 15 beta 425 431 428 453 C1' G C 16 beta 448 454 451 476 C1' C C 17 beta 471 477 474 496 C1' A C 18 beta 491 497 494 518 C1' G C 19 beta 513 519 516 541 C1' A C 20 beta 536 542 539 563 C1' G C 21 beta 558 564 561 586 C1' A C 22 beta 581 587 584 608 C1' A C 23 beta 603 609 606 630 C1' A C 24 beta 625 631 628 652 C1' C C 25 beta 647 653 650 672 C1' A C 26 beta 667 673 670 694 C1' C C 27 beta 689 695 692 714 C1' A C 28 beta 709 715 712 736 C1' C C 29 beta 731 737 734 756 C1' G C 30 beta 751 757 754 779 C1' A C 31 beta 774 780 777 799 C1' U D 31 beta 794 800 797 819 C1' C D 32 beta 814 820 817 839 C1' G D 33 beta 834 840 837 862 C1' U D 34 beta 857 863 860 882 C1' G D 35 beta 877 883 880 905 C1' G D 36 beta 900 906 903 928 C1' U D 37 beta 923 929 926 948 C1' A D 38 beta 943 949 946 970 C1' C D 39 beta 965 971 968 990 C1' A D 40 beta 985 991 988 1012 C1' U D 41 beta 1007 1013 1010 1032 C1' U D 42 beta 1027 1033 1030 1052 C1' A D 43 beta 1047 1053 1050 1074 C1' C D 44 beta 1069 1075 1072 1094 C1' C D 45 beta 1089 1095 1092 1114 C1' U D 46 beta 1109 1115 1112 1134 C1' G D 47 beta 1129 1135 1132 1157 C1' C D 48 beta 1152 1158 1155 1177 C1' C D 49 beta 1172 1178 1175 1195 C1' G P 6 beta 1190 1196 1193 1218 C1' U P 7 beta 1213 1219 1216 1238 C1' C P 8 beta 1233 1239 1236 1258 C1' C P 9 beta 1253 1259 1256 1278 C1' A P 10 beta 1273 1279 1276 1300 C1' C P 11 beta 1295 1301 1298 1320 C1' C P 12 beta 1315 1321 1318 1340 C1' G P 13 beta 1335 1341 1338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 44 C2' C A 2 OK 46 42 45 64 C2' C A 3 OK 66 62 65 84 C2' C A 4 OK 86 82 85 104 C2' A A 5 OK 106 102 105 124 C2' C B 2 OK 126 122 125 144 C2' G B 3 OK 146 142 145 167 C2' G B 4 OK 169 165 168 190 C2' U B 5 OK 192 188 191 210 C2' G B 6 OK 212 208 211 233 C2' A B 7 OK 235 231 234 301 C2' A B 9 OK 303 299 302 323 C2' A B 10 OK 325 321 324 345 C2' G B 11 OK 347 343 346 368 C2' G B 12 OK 370 366 369 391 C2' G B 13 OK 393 389 392 428 C2' G C 15 OK 430 426 429 451 C2' G C 16 OK 453 449 452 474 C2' C C 17 OK 476 472 475 494 C2' A C 18 OK 496 492 495 516 C2' G C 19 OK 518 514 517 539 C2' A C 20 OK 541 537 540 561 C2' G C 21 OK 563 559 562 584 C2' A C 22 OK 586 582 585 606 C2' A C 23 OK 608 604 607 628 C2' A C 24 OK 630 626 629 650 C2' C C 25 OK 652 648 651 670 C2' A C 26 OK 672 668 671 692 C2' C C 27 OK 694 690 693 712 C2' A C 28 OK 714 710 713 734 C2' C C 29 OK 736 732 735 754 C2' G C 30 OK 756 752 755 777 C2' A C 31 OK 779 775 778 797 C2' U D 31 OK 799 795 798 817 C2' C D 32 OK 819 815 818 837 C2' G D 33 OK 839 835 838 860 C2' U D 34 OK 862 858 861 880 C2' G D 35 OK 882 878 881 903 C2' G D 36 OK 905 901 904 926 C2' U D 37 OK 928 924 927 946 C2' A D 38 OK 948 944 947 968 C2' C D 39 OK 970 966 969 988 C2' A D 40 OK 990 986 989 1010 C2' U D 41 OK 1012 1008 1011 1030 C2' U D 42 OK 1032 1028 1031 1050 C2' A D 43 OK 1052 1048 1051 1072 C2' C D 44 OK 1074 1070 1073 1092 C2' C D 45 OK 1094 1090 1093 1112 C2' U D 46 OK 1114 1110 1113 1132 C2' G D 47 OK 1134 1130 1133 1155 C2' C D 48 OK 1157 1153 1156 1175 C2' C D 49 OK 1177 1173 1176 1193 C2' G P 6 OK 1195 1191 1194 1216 C2' U P 7 OK 1218 1214 1217 1236 C2' C P 8 OK 1238 1234 1237 1256 C2' C P 9 OK 1258 1254 1257 1276 C2' A P 10 OK 1278 1274 1277 1298 C2' C P 11 OK 1300 1296 1299 1318 C2' C P 12 OK 1320 1316 1319 1338 C2' G P 13 OK 1340 1336 1339 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 42 C3' C A 2 OK 40 43 44 62 C3' C A 3 OK 60 63 64 82 C3' C A 4 OK 80 83 84 102 C3' A A 5 OK 100 103 104 122 C3' C B 2 OK 120 123 124 142 C3' G B 3 OK 140 143 144 165 C3' G B 4 OK 163 166 167 188 C3' U B 5 OK 186 189 190 208 C3' G B 6 OK 206 209 210 231 C3' A B 7 OK 229 232 233 299 C3' A B 9 OK 297 300 301 321 C3' A B 10 OK 319 322 323 343 C3' G B 11 OK 341 344 345 366 C3' G B 12 OK 364 367 368 389 C3' G B 13 OK 387 390 391 426 C3' G C 15 OK 424 427 428 449 C3' G C 16 OK 447 450 451 472 C3' C C 17 OK 470 473 474 492 C3' A C 18 OK 490 493 494 514 C3' G C 19 OK 512 515 516 537 C3' A C 20 OK 535 538 539 559 C3' G C 21 OK 557 560 561 582 C3' A C 22 OK 580 583 584 604 C3' A C 23 OK 602 605 606 626 C3' A C 24 OK 624 627 628 648 C3' C C 25 OK 646 649 650 668 C3' A C 26 OK 666 669 670 690 C3' C C 27 OK 688 691 692 710 C3' A C 28 OK 708 711 712 732 C3' C C 29 OK 730 733 734 752 C3' G C 30 OK 750 753 754 775 C3' A C 31 OK 773 776 777 795 C3' U D 31 OK 793 796 797 815 C3' C D 32 OK 813 816 817 835 C3' G D 33 OK 833 836 837 858 C3' U D 34 OK 856 859 860 878 C3' G D 35 OK 876 879 880 901 C3' G D 36 OK 899 902 903 924 C3' U D 37 OK 922 925 926 944 C3' A D 38 OK 942 945 946 966 C3' C D 39 OK 964 967 968 986 C3' A D 40 OK 984 987 988 1008 C3' U D 41 OK 1006 1009 1010 1028 C3' U D 42 OK 1026 1029 1030 1048 C3' A D 43 OK 1046 1049 1050 1070 C3' C D 44 OK 1068 1071 1072 1090 C3' C D 45 OK 1088 1091 1092 1110 C3' U D 46 OK 1108 1111 1112 1130 C3' G D 47 OK 1128 1131 1132 1153 C3' C D 48 OK 1151 1154 1155 1173 C3' C D 49 OK 1171 1174 1175 1191 C3' G P 6 OK 1189 1192 1193 1214 C3' U P 7 OK 1212 1215 1216 1234 C3' C P 8 OK 1232 1235 1236 1254 C3' C P 9 OK 1252 1255 1256 1274 C3' A P 10 OK 1272 1275 1276 1296 C3' C P 11 OK 1294 1297 1298 1316 C3' C P 12 OK 1314 1317 1318 1336 C3' G P 13 OK 1334 1337 1338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 40 C4' C A 2 OK 42 39 41 60 C4' C A 3 OK 62 59 61 80 C4' C A 4 OK 82 79 81 100 C4' A A 5 OK 102 99 101 120 C4' C B 2 OK 122 119 121 140 C4' G B 3 OK 142 139 141 163 C4' G B 4 OK 165 162 164 186 C4' U B 5 OK 188 185 187 206 C4' G B 6 OK 208 205 207 229 C4' A B 7 OK 231 228 230 297 C4' A B 9 OK 299 296 298 319 C4' A B 10 OK 321 318 320 341 C4' G B 11 OK 343 340 342 364 C4' G B 12 OK 366 363 365 387 C4' G B 13 OK 389 386 388 424 C4' G C 15 OK 426 423 425 447 C4' G C 16 OK 449 446 448 470 C4' C C 17 OK 472 469 471 490 C4' A C 18 OK 492 489 491 512 C4' G C 19 OK 514 511 513 535 C4' A C 20 OK 537 534 536 557 C4' G C 21 OK 559 556 558 580 C4' A C 22 OK 582 579 581 602 C4' A C 23 OK 604 601 603 624 C4' A C 24 OK 626 623 625 646 C4' C C 25 OK 648 645 647 666 C4' A C 26 OK 668 665 667 688 C4' C C 27 OK 690 687 689 708 C4' A C 28 OK 710 707 709 730 C4' C C 29 OK 732 729 731 750 C4' G C 30 OK 752 749 751 773 C4' A C 31 OK 775 772 774 793 C4' U D 31 OK 795 792 794 813 C4' C D 32 OK 815 812 814 833 C4' G D 33 OK 835 832 834 856 C4' U D 34 OK 858 855 857 876 C4' G D 35 OK 878 875 877 899 C4' G D 36 OK 901 898 900 922 C4' U D 37 OK 924 921 923 942 C4' A D 38 OK 944 941 943 964 C4' C D 39 OK 966 963 965 984 C4' A D 40 OK 986 983 985 1006 C4' U D 41 OK 1008 1005 1007 1026 C4' U D 42 OK 1028 1025 1027 1046 C4' A D 43 OK 1048 1045 1047 1068 C4' C D 44 OK 1070 1067 1069 1088 C4' C D 45 OK 1090 1087 1089 1108 C4' U D 46 OK 1110 1107 1109 1128 C4' G D 47 OK 1130 1127 1129 1151 C4' C D 48 OK 1153 1150 1152 1171 C4' C D 49 OK 1173 1170 1172 1189 C4' G P 6 OK 1191 1188 1190 1212 C4' U P 7 OK 1214 1211 1213 1232 C4' C P 8 OK 1234 1231 1233 1252 C4' C P 9 OK 1254 1251 1253 1272 C4' A P 10 OK 1274 1271 1273 1294 C4' C P 11 OK 1296 1293 1295 1314 C4' C P 12 OK 1316 1313 1315 1334 C4' G P 13 OK 1336 1333 1335 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 39 C5' C A 2 38 40 59 C5' C A 3 58 60 79 C5' C A 4 78 80 99 C5' A A 5 98 100 119 C5' C B 2 118 120 139 C5' G B 3 138 140 162 C5' G B 4 161 163 185 C5' U B 5 184 186 205 C5' G B 6 204 206 228 C5' A B 7 227 229 296 C5' A B 9 295 297 318 C5' A B 10 317 319 340 C5' G B 11 339 341 363 C5' G B 12 362 364 386 C5' G B 13 385 387 423 C5' G C 15 422 424 446 C5' G C 16 445 447 469 C5' C C 17 468 470 489 C5' A C 18 488 490 511 C5' G C 19 510 512 534 C5' A C 20 533 535 556 C5' G C 21 555 557 579 C5' A C 22 578 580 601 C5' A C 23 600 602 623 C5' A C 24 622 624 645 C5' C C 25 644 646 665 C5' A C 26 664 666 687 C5' C C 27 686 688 707 C5' A C 28 706 708 729 C5' C C 29 728 730 749 C5' G C 30 748 750 772 C5' A C 31 771 773 792 C5' U D 31 791 793 812 C5' C D 32 811 813 832 C5' G D 33 831 833 855 C5' U D 34 854 856 875 C5' G D 35 874 876 898 C5' G D 36 897 899 921 C5' U D 37 920 922 941 C5' A D 38 940 942 963 C5' C D 39 962 964 983 C5' A D 40 982 984 1005 C5' U D 41 1004 1006 1025 C5' U D 42 1024 1026 1045 C5' A D 43 1044 1046 1067 C5' C D 44 1066 1068 1087 C5' C D 45 1086 1088 1107 C5' U D 46 1106 1108 1127 C5' G D 47 1126 1128 1150 C5' C D 48 1149 1151 1170 C5' C D 49 1169 1171 1188 C5' G P 6 1187 1189 1211 C5' U P 7 1210 1212 1231 C5' C P 8 1230 1232 1251 C5' C P 9 1250 1252 1271 C5' A P 10 1270 1272 1293 C5' C P 11 1292 1294 1313 C5' C P 12 1312 1314 1333 C5' G P 13 1332 1334 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 35 P C A 2 distorted distorted 36 37 38 55 P C A 3 distorted distorted 43 56 57 58 75 P C A 4 distorted distorted 63 76 77 78 95 P A A 5 distorted distorted 83 96 97 98 135 P G B 3 distorted distorted 123 136 137 138 158 P G B 4 distorted distorted 143 159 160 161 181 P U B 5 distorted distorted 166 182 183 184 201 P G B 6 distorted distorted 189 202 203 204 224 P A B 7 distorted distorted 209 225 226 227 246 P G B 8 232 247 P G B 8 232 292 P A B 9 distorted distorted 293 294 295 314 P A B 10 distorted distorted 300 315 316 317 336 P G B 11 distorted distorted 322 337 338 339 359 P G B 12 distorted distorted 344 360 361 362 382 P G B 13 distorted distorted 367 383 384 385 405 P S9L B 14 distorted distorted 390 406 407 408 419 P G C 15 distorted distorted 417 420 421 422 442 P G C 16 distorted distorted 427 443 444 445 465 P C C 17 distorted distorted 450 466 467 468 485 P A C 18 distorted distorted 473 486 487 488 507 P G C 19 distorted distorted 493 508 509 510 530 P A C 20 distorted distorted 515 531 532 533 552 P G C 21 distorted distorted 538 553 554 555 575 P A C 22 distorted distorted 560 576 577 578 597 P A C 23 distorted distorted 583 598 599 600 619 P A C 24 distorted distorted 605 620 621 622 641 P C C 25 distorted distorted 627 642 643 644 661 P A C 26 distorted distorted 649 662 663 664 683 P C C 27 distorted distorted 669 684 685 686 703 P A C 28 distorted distorted 691 704 705 706 725 P C C 29 distorted distorted 711 726 727 728 745 P G C 30 distorted distorted 733 746 747 748 768 P A C 31 distorted distorted 753 769 770 771 808 P C D 32 distorted distorted 796 809 810 811 828 P G D 33 distorted distorted 816 829 830 831 851 P U D 34 distorted distorted 836 852 853 854 871 P G D 35 distorted distorted 859 872 873 874 894 P G D 36 distorted distorted 879 895 896 897 917 P U D 37 distorted distorted 902 918 919 920 937 P A D 38 distorted distorted 925 938 939 940 959 P C D 39 distorted distorted 945 960 961 962 979 P A D 40 distorted distorted 967 980 981 982 1001 P U D 41 distorted distorted 987 1002 1003 1004 1021 P U D 42 distorted distorted 1009 1022 1023 1024 1041 P A D 43 distorted distorted 1029 1042 1043 1044 1063 P C D 44 distorted distorted 1049 1064 1065 1066 1083 P C D 45 distorted distorted 1071 1084 1085 1086 1103 P U D 46 distorted distorted 1091 1104 1105 1106 1123 P G D 47 distorted distorted 1111 1124 1125 1126 1146 P C D 48 distorted distorted 1131 1147 1148 1149 1166 P C D 49 distorted distorted 1154 1167 1168 1169 1207 P U P 7 distorted distorted 1192 1208 1209 1210 1227 P C P 8 distorted distorted 1215 1228 1229 1230 1247 P C P 9 distorted distorted 1235 1248 1249 1250 1267 P A P 10 distorted distorted 1255 1268 1269 1270 1289 P C P 11 distorted distorted 1275 1290 1291 1292 1309 P C P 12 distorted distorted 1297 1310 1311 1312 1329 P G P 13 distorted distorted 1317 1330 1331 1332 ---------------------------------------------------------------------------------