ID code: '4PCO' 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' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' U A 10 alpha beta 296 317 302 299 330 C1' G B 1 alpha beta 325 348 331 328 365 C1' G B 2 alpha beta 360 383 366 363 399 C1' U B 3 alpha beta 394 414 400 397 429 C1' G B 4 alpha beta 424 447 430 427 463 C1' G B 5 alpha beta 458 481 464 461 497 C1' C B 6 alpha beta 492 512 498 495 528 C1' U B 7 alpha beta 523 543 529 526 558 C1' G B 8 alpha beta 553 576 559 556 592 C1' U B 9 alpha beta 587 607 593 590 622 C1' U B 10 alpha beta 617 638 623 620 651 C1' G C 1 alpha beta 646 669 652 649 686 C1' G C 2 alpha beta 681 704 687 684 720 C1' U C 3 alpha beta 715 735 721 718 750 C1' G C 4 alpha beta 745 768 751 748 784 C1' G C 5 alpha beta 779 802 785 782 818 C1' C C 6 alpha beta 813 833 819 816 849 C1' U C 7 alpha beta 844 864 850 847 879 C1' G C 8 alpha beta 874 897 880 877 913 C1' U C 9 alpha beta 908 928 914 911 943 C1' U C 10 beta 938 944 941 961 C1' G D 1 alpha beta 956 979 962 959 995 C1' G D 2 alpha beta 990 1013 996 993 1029 C1' U D 3 alpha beta 1024 1044 1030 1027 1059 C1' G D 4 alpha beta 1054 1077 1060 1057 1093 C1' G D 5 alpha beta 1088 1111 1094 1091 1127 C1' C D 6 alpha beta 1122 1142 1128 1125 1158 C1' U D 7 alpha beta 1153 1173 1159 1156 1188 C1' G D 8 alpha beta 1183 1206 1189 1186 1222 C1' U D 9 alpha beta 1217 1237 1223 1220 1252 C1' U D 10 alpha beta 1247 1268 1253 1250 1476 C1' G E 4 alpha beta 1471 1494 1477 1474 1510 C1' G E 5 alpha beta 1505 1528 1511 1508 1544 C1' C E 6 alpha beta 1539 1559 1545 1542 1575 C1' U E 7 alpha beta 1570 1590 1576 1573 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' G A 5 OK OK 142 138 158 141 174 C2' C A 6 OK OK 176 172 189 175 205 C2' U A 7 OK OK 207 203 220 206 235 C2' G A 8 OK OK 237 233 253 236 269 C2' U A 9 OK OK 271 267 284 270 299 C2' U A 10 OK OK 301 297 315 300 328 C2' G B 1 OK OK 330 326 346 329 363 C2' G B 2 OK OK 365 361 381 364 397 C2' U B 3 OK OK 399 395 412 398 427 C2' G B 4 OK OK 429 425 445 428 461 C2' G B 5 OK OK 463 459 479 462 495 C2' C B 6 OK OK 497 493 510 496 526 C2' U B 7 OK OK 528 524 541 527 556 C2' G B 8 OK OK 558 554 574 557 590 C2' U B 9 OK OK 592 588 605 591 620 C2' U B 10 OK OK 622 618 636 621 649 C2' G C 1 OK OK 651 647 667 650 684 C2' G C 2 OK OK 686 682 702 685 718 C2' U C 3 OK OK 720 716 733 719 748 C2' G C 4 OK OK 750 746 766 749 782 C2' G C 5 OK OK 784 780 800 783 816 C2' C C 6 OK OK 818 814 831 817 847 C2' U C 7 OK OK 849 845 862 848 877 C2' G C 8 OK OK 879 875 895 878 911 C2' U C 9 OK OK 913 909 926 912 941 C2' U C 10 OK 943 939 942 959 C2' G D 1 OK OK 961 957 977 960 993 C2' G D 2 OK OK 995 991 1011 994 1027 C2' U D 3 OK OK 1029 1025 1042 1028 1057 C2' G D 4 OK OK 1059 1055 1075 1058 1091 C2' G D 5 OK OK 1093 1089 1109 1092 1125 C2' C D 6 OK OK 1127 1123 1140 1126 1156 C2' U D 7 OK OK 1158 1154 1171 1157 1186 C2' G D 8 OK OK 1188 1184 1204 1187 1220 C2' U D 9 OK OK 1222 1218 1235 1221 1250 C2' U D 10 OK OK 1252 1248 1266 1251 1474 C2' G E 4 OK OK 1476 1472 1492 1475 1508 C2' G E 5 OK OK 1510 1506 1526 1509 1542 C2' C E 6 OK OK 1544 1540 1557 1543 1573 C2' U E 7 OK OK 1575 1571 1588 1574 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' G A 5 OK OK 136 157 139 140 172 C3' C A 6 OK OK 170 188 173 174 203 C3' U A 7 OK OK 201 219 204 205 233 C3' G A 8 OK OK 231 252 234 235 267 C3' U A 9 OK OK 265 283 268 269 297 C3' U A 10 OK OK 295 313 298 299 326 C3' G B 1 OK OK 324 345 327 328 361 C3' G B 2 OK OK 359 380 362 363 395 C3' U B 3 OK OK 393 411 396 397 425 C3' G B 4 OK OK 423 444 426 427 459 C3' G B 5 OK OK 457 478 460 461 493 C3' C B 6 OK OK 491 509 494 495 524 C3' U B 7 OK OK 522 540 525 526 554 C3' G B 8 OK OK 552 573 555 556 588 C3' U B 9 OK OK 586 604 589 590 618 C3' U B 10 OK OK 616 634 619 620 647 C3' G C 1 OK OK 645 666 648 649 682 C3' G C 2 OK OK 680 701 683 684 716 C3' U C 3 OK OK 714 732 717 718 746 C3' G C 4 OK OK 744 765 747 748 780 C3' G C 5 OK OK 778 799 781 782 814 C3' C C 6 OK OK 812 830 815 816 845 C3' U C 7 OK OK 843 861 846 847 875 C3' G C 8 OK OK 873 894 876 877 909 C3' U C 9 OK OK 907 925 910 911 939 C3' U C 10 OK 937 940 941 957 C3' G D 1 OK OK 955 976 958 959 991 C3' G D 2 OK OK 989 1010 992 993 1025 C3' U D 3 OK OK 1023 1041 1026 1027 1055 C3' G D 4 OK OK 1053 1074 1056 1057 1089 C3' G D 5 OK OK 1087 1108 1090 1091 1123 C3' C D 6 OK OK 1121 1139 1124 1125 1154 C3' U D 7 OK OK 1152 1170 1155 1156 1184 C3' G D 8 OK OK 1182 1203 1185 1186 1218 C3' U D 9 OK OK 1216 1234 1219 1220 1248 C3' U D 10 OK OK 1246 1264 1249 1250 1472 C3' G E 4 OK OK 1470 1491 1473 1474 1506 C3' G E 5 OK OK 1504 1525 1507 1508 1540 C3' C E 6 OK OK 1538 1556 1541 1542 1571 C3' U E 7 OK OK 1569 1587 1572 1573 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' G A 5 OK OK 138 156 135 137 170 C4' C A 6 OK OK 172 187 169 171 201 C4' U A 7 OK OK 203 218 200 202 231 C4' G A 8 OK OK 233 251 230 232 265 C4' U A 9 OK OK 267 282 264 266 295 C4' U A 10 OK OK 297 312 294 296 324 C4' G B 1 OK OK 326 344 323 325 359 C4' G B 2 OK OK 361 379 358 360 393 C4' U B 3 OK OK 395 410 392 394 423 C4' G B 4 OK OK 425 443 422 424 457 C4' G B 5 OK OK 459 477 456 458 491 C4' C B 6 OK OK 493 508 490 492 522 C4' U B 7 OK OK 524 539 521 523 552 C4' G B 8 OK OK 554 572 551 553 586 C4' U B 9 OK OK 588 603 585 587 616 C4' U B 10 OK OK 618 633 615 617 645 C4' G C 1 OK OK 647 665 644 646 680 C4' G C 2 OK OK 682 700 679 681 714 C4' U C 3 OK OK 716 731 713 715 744 C4' G C 4 OK OK 746 764 743 745 778 C4' G C 5 OK OK 780 798 777 779 812 C4' C C 6 OK OK 814 829 811 813 843 C4' U C 7 OK OK 845 860 842 844 873 C4' G C 8 OK OK 875 893 872 874 907 C4' U C 9 OK OK 909 924 906 908 937 C4' U C 10 OK 939 936 938 955 C4' G D 1 OK OK 957 975 954 956 989 C4' G D 2 OK OK 991 1009 988 990 1023 C4' U D 3 OK OK 1025 1040 1022 1024 1053 C4' G D 4 OK OK 1055 1073 1052 1054 1087 C4' G D 5 OK OK 1089 1107 1086 1088 1121 C4' C D 6 OK OK 1123 1138 1120 1122 1152 C4' U D 7 OK OK 1154 1169 1151 1153 1182 C4' G D 8 OK OK 1184 1202 1181 1183 1216 C4' U D 9 OK OK 1218 1233 1215 1217 1246 C4' U D 10 OK OK 1248 1263 1245 1247 1470 C4' G E 4 OK OK 1472 1490 1469 1471 1504 C4' G E 5 OK OK 1506 1524 1503 1505 1538 C4' C E 6 OK OK 1540 1555 1537 1539 1569 C4' U E 7 OK OK 1571 1586 1568 1570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' G A 5 OK OK 134 154 155 136 169 C5' C A 6 OK OK 168 185 186 170 200 C5' U A 7 OK OK 199 216 217 201 230 C5' G A 8 OK OK 229 249 250 231 264 C5' U A 9 OK OK 263 280 281 265 294 C5' U A 10 OK OK 293 310 311 295 323 C5' G B 1 OK OK 322 342 343 324 358 C5' G B 2 OK OK 357 377 378 359 392 C5' U B 3 OK OK 391 408 409 393 422 C5' G B 4 OK OK 421 441 442 423 456 C5' G B 5 OK OK 455 475 476 457 490 C5' C B 6 OK OK 489 506 507 491 521 C5' U B 7 OK OK 520 537 538 522 551 C5' G B 8 OK OK 550 570 571 552 585 C5' U B 9 OK OK 584 601 602 586 615 C5' U B 10 OK OK 614 631 632 616 644 C5' G C 1 OK OK 643 663 664 645 679 C5' G C 2 OK OK 678 698 699 680 713 C5' U C 3 OK OK 712 729 730 714 743 C5' G C 4 OK OK 742 762 763 744 777 C5' G C 5 OK OK 776 796 797 778 811 C5' C C 6 OK OK 810 827 828 812 842 C5' U C 7 OK OK 841 858 859 843 872 C5' G C 8 OK OK 871 891 892 873 906 C5' U C 9 OK OK 905 922 923 907 936 C5' U C 10 935 937 954 C5' G D 1 OK OK 953 973 974 955 988 C5' G D 2 OK OK 987 1007 1008 989 1022 C5' U D 3 OK OK 1021 1038 1039 1023 1052 C5' G D 4 OK OK 1051 1071 1072 1053 1086 C5' G D 5 OK OK 1085 1105 1106 1087 1120 C5' C D 6 OK OK 1119 1136 1137 1121 1151 C5' U D 7 OK OK 1150 1167 1168 1152 1181 C5' G D 8 OK OK 1180 1200 1201 1182 1215 C5' U D 9 OK OK 1214 1231 1232 1216 1245 C5' U D 10 OK OK 1244 1261 1262 1246 1469 C5' G E 4 OK OK 1468 1488 1489 1470 1503 C5' G E 5 OK OK 1502 1522 1523 1504 1537 C5' C E 6 OK OK 1536 1553 1554 1538 1568 C5' U E 7 OK OK 1567 1584 1585 1569 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P G A 5 distorted distorted 105 132 133 134 165 P C A 6 distorted distorted 139 166 167 168 196 P U A 7 distorted distorted 173 197 198 199 226 P G A 8 distorted distorted 204 227 228 229 260 P U A 9 distorted distorted 234 261 262 263 290 P U A 10 distorted distorted 268 291 292 293 354 P G B 2 distorted distorted 327 355 356 357 388 P U B 3 distorted distorted 362 389 390 391 418 P G B 4 distorted distorted 396 419 420 421 452 P G B 5 distorted distorted 426 453 454 455 486 P C B 6 distorted distorted 460 487 488 489 517 P U B 7 distorted distorted 494 518 519 520 547 P G B 8 distorted distorted 525 548 549 550 581 P U B 9 distorted distorted 555 582 583 584 611 P U B 10 distorted distorted 589 612 613 614 675 P G C 2 distorted distorted 648 676 677 678 709 P U C 3 distorted distorted 683 710 711 712 739 P G C 4 distorted distorted 717 740 741 742 773 P G C 5 distorted distorted 747 774 775 776 807 P C C 6 distorted distorted 781 808 809 810 838 P U C 7 distorted distorted 815 839 840 841 868 P G C 8 distorted distorted 846 869 870 871 902 P U C 9 distorted distorted 876 903 904 905 932 P U C 10 distorted distorted 910 933 934 935 984 P G D 2 distorted distorted 958 985 986 987 1018 P U D 3 distorted distorted 992 1019 1020 1021 1048 P G D 4 distorted distorted 1026 1049 1050 1051 1082 P G D 5 distorted distorted 1056 1083 1084 1085 1116 P C D 6 distorted distorted 1090 1117 1118 1119 1147 P U D 7 distorted distorted 1124 1148 1149 1150 1177 P G D 8 distorted distorted 1155 1178 1179 1180 1211 P U D 9 distorted distorted 1185 1212 1213 1214 1241 P U D 10 distorted distorted 1219 1242 1243 1244 1337 P G E 2 1338 P G E 2 1405 P U E 3 1406 P U E 3 1465 P G E 4 distorted distorted 1466 1467 1468 1499 P G E 5 distorted distorted 1473 1500 1501 1502 1533 P C E 6 distorted distorted 1507 1534 1535 1536 1564 P U E 7 distorted distorted 1541 1565 1566 1567 1594 P G E 8 1572 1595 P G E 8 1572 1662 P U E 9 1663 P U E 9 1722 P U E 10 1723 P U E 10 ---------------------------------------------------------------------------------