ID code: '2BJ2' 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' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' A A 9 alpha beta 269 291 275 272 307 C1' U A 10 alpha beta 302 322 308 305 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' G A 12 alpha beta 366 389 372 369 405 C1' U A 13 alpha beta 400 420 406 403 435 C1' U A 14 alpha beta 430 450 436 433 465 C1' C A 15 alpha beta 460 480 466 463 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' U A 17 alpha beta 525 545 531 528 560 C1' U A 18 alpha beta 555 575 561 558 590 C1' G A 19 alpha beta 585 608 591 588 624 C1' C A 20 alpha beta 619 639 625 622 655 C1' C A 21 alpha beta 650 671 656 653 685 C1' G B 1 alpha beta 680 703 686 683 720 C1' C B 2 alpha beta 715 735 721 718 751 C1' A B 3 alpha beta 746 768 752 749 784 C1' C B 4 alpha beta 779 799 785 782 815 C1' C B 5 alpha beta 810 830 816 813 846 C1' G B 6 alpha beta 841 864 847 844 880 C1' A B 7 alpha beta 875 897 881 878 913 C1' A B 8 alpha beta 908 930 914 911 946 C1' C B 9 alpha beta 941 961 947 944 977 C1' C B 10 alpha beta 972 992 978 975 1008 C1' A B 11 alpha beta 1003 1025 1009 1006 1041 C1' U B 12 alpha beta 1036 1056 1042 1039 1071 C1' C B 13 alpha beta 1066 1086 1072 1069 1102 C1' C B 14 alpha beta 1097 1117 1103 1100 1133 C1' G B 15 alpha beta 1128 1151 1134 1131 1167 C1' G B 16 alpha beta 1162 1185 1168 1165 1201 C1' U B 17 alpha beta 1196 1216 1202 1199 1231 C1' G B 18 alpha beta 1226 1249 1232 1229 1265 C1' C B 19 alpha beta 1260 1281 1266 1263 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' A A 5 OK OK 142 138 157 141 173 C2' C A 6 OK OK 175 171 188 174 204 C2' G A 7 OK OK 206 202 222 205 238 C2' G A 8 OK OK 240 236 256 239 272 C2' A A 9 OK OK 274 270 289 273 305 C2' U A 10 OK OK 307 303 320 306 335 C2' G A 11 OK OK 337 333 353 336 369 C2' G A 12 OK OK 371 367 387 370 403 C2' U A 13 OK OK 405 401 418 404 433 C2' U A 14 OK OK 435 431 448 434 463 C2' C A 15 OK OK 465 461 478 464 494 C2' G A 16 OK OK 496 492 512 495 528 C2' U A 17 OK OK 530 526 543 529 558 C2' U A 18 OK OK 560 556 573 559 588 C2' G A 19 OK OK 590 586 606 589 622 C2' C A 20 OK OK 624 620 637 623 653 C2' C A 21 OK OK 655 651 669 654 683 C2' G B 1 OK OK 685 681 701 684 718 C2' C B 2 OK OK 720 716 733 719 749 C2' A B 3 OK OK 751 747 766 750 782 C2' C B 4 OK OK 784 780 797 783 813 C2' C B 5 OK OK 815 811 828 814 844 C2' G B 6 OK OK 846 842 862 845 878 C2' A B 7 OK OK 880 876 895 879 911 C2' A B 8 OK OK 913 909 928 912 944 C2' C B 9 OK OK 946 942 959 945 975 C2' C B 10 OK OK 977 973 990 976 1006 C2' A B 11 OK OK 1008 1004 1023 1007 1039 C2' U B 12 OK OK 1041 1037 1054 1040 1069 C2' C B 13 OK OK 1071 1067 1084 1070 1100 C2' C B 14 OK OK 1102 1098 1115 1101 1131 C2' G B 15 OK OK 1133 1129 1149 1132 1165 C2' G B 16 OK OK 1167 1163 1183 1166 1199 C2' U B 17 OK OK 1201 1197 1214 1200 1229 C2' G B 18 OK OK 1231 1227 1247 1230 1263 C2' C B 19 OK OK 1265 1261 1279 1264 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' A A 5 OK OK 136 156 139 140 171 C3' C A 6 OK OK 169 187 172 173 202 C3' G A 7 OK OK 200 221 203 204 236 C3' G A 8 OK OK 234 255 237 238 270 C3' A A 9 OK OK 268 288 271 272 303 C3' U A 10 OK OK 301 319 304 305 333 C3' G A 11 OK OK 331 352 334 335 367 C3' G A 12 OK OK 365 386 368 369 401 C3' U A 13 OK OK 399 417 402 403 431 C3' U A 14 OK OK 429 447 432 433 461 C3' C A 15 OK OK 459 477 462 463 492 C3' G A 16 OK OK 490 511 493 494 526 C3' U A 17 OK OK 524 542 527 528 556 C3' U A 18 OK OK 554 572 557 558 586 C3' G A 19 OK OK 584 605 587 588 620 C3' C A 20 OK OK 618 636 621 622 651 C3' C A 21 OK OK 649 667 652 653 681 C3' G B 1 OK OK 679 700 682 683 716 C3' C B 2 OK OK 714 732 717 718 747 C3' A B 3 OK OK 745 765 748 749 780 C3' C B 4 OK OK 778 796 781 782 811 C3' C B 5 OK OK 809 827 812 813 842 C3' G B 6 OK OK 840 861 843 844 876 C3' A B 7 OK OK 874 894 877 878 909 C3' A B 8 OK OK 907 927 910 911 942 C3' C B 9 OK OK 940 958 943 944 973 C3' C B 10 OK OK 971 989 974 975 1004 C3' A B 11 OK OK 1002 1022 1005 1006 1037 C3' U B 12 OK OK 1035 1053 1038 1039 1067 C3' C B 13 OK OK 1065 1083 1068 1069 1098 C3' C B 14 OK OK 1096 1114 1099 1100 1129 C3' G B 15 OK OK 1127 1148 1130 1131 1163 C3' G B 16 OK OK 1161 1182 1164 1165 1197 C3' U B 17 OK OK 1195 1213 1198 1199 1227 C3' G B 18 OK OK 1225 1246 1228 1229 1261 C3' C B 19 OK OK 1259 1277 1262 1263 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' A A 5 OK OK 138 155 135 137 169 C4' C A 6 OK OK 171 186 168 170 200 C4' G A 7 OK OK 202 220 199 201 234 C4' G A 8 OK OK 236 254 233 235 268 C4' A A 9 OK OK 270 287 267 269 301 C4' U A 10 OK OK 303 318 300 302 331 C4' G A 11 OK OK 333 351 330 332 365 C4' G A 12 OK OK 367 385 364 366 399 C4' U A 13 OK OK 401 416 398 400 429 C4' U A 14 OK OK 431 446 428 430 459 C4' C A 15 OK OK 461 476 458 460 490 C4' G A 16 OK OK 492 510 489 491 524 C4' U A 17 OK OK 526 541 523 525 554 C4' U A 18 OK OK 556 571 553 555 584 C4' G A 19 OK OK 586 604 583 585 618 C4' C A 20 OK OK 620 635 617 619 649 C4' C A 21 OK OK 651 666 648 650 679 C4' G B 1 OK OK 681 699 678 680 714 C4' C B 2 OK OK 716 731 713 715 745 C4' A B 3 OK OK 747 764 744 746 778 C4' C B 4 OK OK 780 795 777 779 809 C4' C B 5 OK OK 811 826 808 810 840 C4' G B 6 OK OK 842 860 839 841 874 C4' A B 7 OK OK 876 893 873 875 907 C4' A B 8 OK OK 909 926 906 908 940 C4' C B 9 OK OK 942 957 939 941 971 C4' C B 10 OK OK 973 988 970 972 1002 C4' A B 11 OK OK 1004 1021 1001 1003 1035 C4' U B 12 OK OK 1037 1052 1034 1036 1065 C4' C B 13 OK OK 1067 1082 1064 1066 1096 C4' C B 14 OK OK 1098 1113 1095 1097 1127 C4' G B 15 OK OK 1129 1147 1126 1128 1161 C4' G B 16 OK OK 1163 1181 1160 1162 1195 C4' U B 17 OK OK 1197 1212 1194 1196 1225 C4' G B 18 OK OK 1227 1245 1224 1226 1259 C4' C B 19 OK OK 1261 1276 1258 1260 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' A A 5 OK OK 134 153 154 136 168 C5' C A 6 OK OK 167 184 185 169 199 C5' G A 7 OK OK 198 218 219 200 233 C5' G A 8 OK OK 232 252 253 234 267 C5' A A 9 OK OK 266 285 286 268 300 C5' U A 10 OK OK 299 316 317 301 330 C5' G A 11 OK OK 329 349 350 331 364 C5' G A 12 OK OK 363 383 384 365 398 C5' U A 13 OK OK 397 414 415 399 428 C5' U A 14 OK OK 427 444 445 429 458 C5' C A 15 OK OK 457 474 475 459 489 C5' G A 16 OK OK 488 508 509 490 523 C5' U A 17 OK OK 522 539 540 524 553 C5' U A 18 OK OK 552 569 570 554 583 C5' G A 19 OK OK 582 602 603 584 617 C5' C A 20 OK OK 616 633 634 618 648 C5' C A 21 OK OK 647 664 665 649 678 C5' G B 1 OK OK 677 697 698 679 713 C5' C B 2 OK OK 712 729 730 714 744 C5' A B 3 OK OK 743 762 763 745 777 C5' C B 4 OK OK 776 793 794 778 808 C5' C B 5 OK OK 807 824 825 809 839 C5' G B 6 OK OK 838 858 859 840 873 C5' A B 7 OK OK 872 891 892 874 906 C5' A B 8 OK OK 905 924 925 907 939 C5' C B 9 OK OK 938 955 956 940 970 C5' C B 10 OK OK 969 986 987 971 1001 C5' A B 11 OK OK 1000 1019 1020 1002 1034 C5' U B 12 OK OK 1033 1050 1051 1035 1064 C5' C B 13 OK OK 1063 1080 1081 1065 1095 C5' C B 14 OK OK 1094 1111 1112 1096 1126 C5' G B 15 OK OK 1125 1145 1146 1127 1160 C5' G B 16 OK OK 1159 1179 1180 1161 1194 C5' U B 17 OK OK 1193 1210 1211 1195 1224 C5' G B 18 OK OK 1223 1243 1244 1225 1258 C5' C B 19 OK OK 1257 1274 1275 1259 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P A A 5 distorted distorted 106 132 133 134 164 P C A 6 distorted distorted 139 165 166 167 195 P G A 7 distorted distorted 172 196 197 198 229 P G A 8 distorted distorted 203 230 231 232 263 P A A 9 distorted distorted 237 264 265 266 296 P U A 10 distorted distorted 271 297 298 299 326 P G A 11 distorted distorted 304 327 328 329 360 P G A 12 distorted distorted 334 361 362 363 394 P U A 13 distorted distorted 368 395 396 397 424 P U A 14 distorted distorted 402 425 426 427 454 P C A 15 distorted distorted 432 455 456 457 485 P G A 16 distorted distorted 462 486 487 488 519 P U A 17 distorted distorted 493 520 521 522 549 P U A 18 distorted distorted 527 550 551 552 579 P G A 19 distorted distorted 557 580 581 582 613 P C A 20 distorted distorted 587 614 615 616 644 P C A 21 distorted distorted 621 645 646 647 709 P C B 2 distorted distorted 682 710 711 712 740 P A B 3 distorted distorted 717 741 742 743 773 P C B 4 distorted distorted 748 774 775 776 804 P C B 5 distorted distorted 781 805 806 807 835 P G B 6 distorted distorted 812 836 837 838 869 P A B 7 distorted distorted 843 870 871 872 902 P A B 8 distorted distorted 877 903 904 905 935 P C B 9 distorted distorted 910 936 937 938 966 P C B 10 distorted distorted 943 967 968 969 997 P A B 11 distorted distorted 974 998 999 1000 1030 P U B 12 distorted distorted 1005 1031 1032 1033 1060 P C B 13 distorted distorted 1038 1061 1062 1063 1091 P C B 14 distorted distorted 1068 1092 1093 1094 1122 P G B 15 distorted distorted 1099 1123 1124 1125 1156 P G B 16 distorted distorted 1130 1157 1158 1159 1190 P U B 17 distorted distorted 1164 1191 1192 1193 1220 P G B 18 distorted distorted 1198 1221 1222 1223 1254 P C B 19 distorted distorted 1228 1255 1256 1257 ---------------------------------------------------------------------------------