ID code: '3NJ7' 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 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' C A 3 beta 50 56 53 75 C1' A A 4 beta 70 76 73 97 C1' G A 5 beta 92 98 95 120 C1' C A 6 beta 115 121 118 140 C1' A A 7 beta 135 141 138 162 C1' G A 8 beta 157 163 160 185 C1' C A 9 beta 180 186 183 205 C1' C A 10 beta 200 206 203 223 C1' G B 1 beta 218 224 221 246 C1' G B 2 beta 241 247 244 269 C1' C B 3 beta 264 270 267 289 C1' A B 4 beta 284 290 287 311 C1' G B 5 beta 306 312 309 334 C1' C B 6 beta 329 335 332 354 C1' A B 7 beta 349 355 352 376 C1' G B 8 beta 371 377 374 399 C1' C B 9 beta 394 400 397 419 C1' C B 10 beta 414 420 417 437 C1' G C 1 beta 432 438 435 460 C1' G C 2 beta 455 461 458 483 C1' C C 3 beta 478 484 481 503 C1' A C 4 beta 498 504 501 525 C1' G C 5 beta 520 526 523 548 C1' C C 6 beta 543 549 546 568 C1' A C 7 beta 563 569 566 590 C1' G C 8 beta 585 591 588 613 C1' C C 9 beta 608 614 611 633 C1' C C 10 beta 628 634 631 651 C1' G D 1 beta 646 652 649 674 C1' G D 2 beta 669 675 672 697 C1' C D 3 beta 692 698 695 717 C1' A D 4 beta 712 718 715 739 C1' G D 5 beta 734 740 737 762 C1' C D 6 beta 757 763 760 782 C1' A D 7 beta 777 783 780 804 C1' G D 8 beta 799 805 802 827 C1' C D 9 beta 822 828 825 847 C1' C D 10 beta 842 848 845 865 C1' G E 1 beta 860 866 863 888 C1' G E 2 beta 883 889 886 911 C1' C E 3 beta 906 912 909 931 C1' A E 4 beta 926 932 929 953 C1' G E 5 beta 948 954 951 976 C1' C E 6 beta 971 977 974 996 C1' A E 7 beta 991 997 994 1018 C1' G E 8 beta 1013 1019 1016 1041 C1' C E 9 beta 1036 1042 1039 1061 C1' C E 10 beta 1056 1062 1059 1079 C1' G F 1 beta 1074 1080 1077 1102 C1' G F 2 beta 1097 1103 1100 1125 C1' C F 3 beta 1120 1126 1123 1145 C1' A F 4 beta 1140 1146 1143 1167 C1' G F 5 beta 1162 1168 1165 1190 C1' C F 6 beta 1185 1191 1188 1210 C1' A F 7 beta 1205 1211 1208 1232 C1' G F 8 beta 1227 1233 1230 1255 C1' C F 9 beta 1250 1256 1253 1275 C1' C F 10 beta 1270 1276 1273 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' C A 3 OK 55 51 54 73 C2' A A 4 OK 75 71 74 95 C2' G A 5 OK 97 93 96 118 C2' C A 6 OK 120 116 119 138 C2' A A 7 OK 140 136 139 160 C2' G A 8 OK 162 158 161 183 C2' C A 9 OK 185 181 184 203 C2' C A 10 OK 205 201 204 221 C2' G B 1 OK 223 219 222 244 C2' G B 2 OK 246 242 245 267 C2' C B 3 OK 269 265 268 287 C2' A B 4 OK 289 285 288 309 C2' G B 5 OK 311 307 310 332 C2' C B 6 OK 334 330 333 352 C2' A B 7 OK 354 350 353 374 C2' G B 8 OK 376 372 375 397 C2' C B 9 OK 399 395 398 417 C2' C B 10 OK 419 415 418 435 C2' G C 1 OK 437 433 436 458 C2' G C 2 OK 460 456 459 481 C2' C C 3 OK 483 479 482 501 C2' A C 4 OK 503 499 502 523 C2' G C 5 OK 525 521 524 546 C2' C C 6 OK 548 544 547 566 C2' A C 7 OK 568 564 567 588 C2' G C 8 OK 590 586 589 611 C2' C C 9 OK 613 609 612 631 C2' C C 10 OK 633 629 632 649 C2' G D 1 OK 651 647 650 672 C2' G D 2 OK 674 670 673 695 C2' C D 3 OK 697 693 696 715 C2' A D 4 OK 717 713 716 737 C2' G D 5 OK 739 735 738 760 C2' C D 6 OK 762 758 761 780 C2' A D 7 OK 782 778 781 802 C2' G D 8 OK 804 800 803 825 C2' C D 9 OK 827 823 826 845 C2' C D 10 OK 847 843 846 863 C2' G E 1 OK 865 861 864 886 C2' G E 2 OK 888 884 887 909 C2' C E 3 OK 911 907 910 929 C2' A E 4 OK 931 927 930 951 C2' G E 5 OK 953 949 952 974 C2' C E 6 OK 976 972 975 994 C2' A E 7 OK 996 992 995 1016 C2' G E 8 OK 1018 1014 1017 1039 C2' C E 9 OK 1041 1037 1040 1059 C2' C E 10 OK 1061 1057 1060 1077 C2' G F 1 OK 1079 1075 1078 1100 C2' G F 2 OK 1102 1098 1101 1123 C2' C F 3 OK 1125 1121 1124 1143 C2' A F 4 OK 1145 1141 1144 1165 C2' G F 5 OK 1167 1163 1166 1188 C2' C F 6 OK 1190 1186 1189 1208 C2' A F 7 OK 1210 1206 1209 1230 C2' G F 8 OK 1232 1228 1231 1253 C2' C F 9 OK 1255 1251 1254 1273 C2' C F 10 OK 1275 1271 1274 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' C A 3 OK 49 52 53 71 C3' A A 4 OK 69 72 73 93 C3' G A 5 OK 91 94 95 116 C3' C A 6 OK 114 117 118 136 C3' A A 7 OK 134 137 138 158 C3' G A 8 OK 156 159 160 181 C3' C A 9 OK 179 182 183 201 C3' C A 10 OK 199 202 203 219 C3' G B 1 OK 217 220 221 242 C3' G B 2 OK 240 243 244 265 C3' C B 3 OK 263 266 267 285 C3' A B 4 OK 283 286 287 307 C3' G B 5 OK 305 308 309 330 C3' C B 6 OK 328 331 332 350 C3' A B 7 OK 348 351 352 372 C3' G B 8 OK 370 373 374 395 C3' C B 9 OK 393 396 397 415 C3' C B 10 OK 413 416 417 433 C3' G C 1 OK 431 434 435 456 C3' G C 2 OK 454 457 458 479 C3' C C 3 OK 477 480 481 499 C3' A C 4 OK 497 500 501 521 C3' G C 5 OK 519 522 523 544 C3' C C 6 OK 542 545 546 564 C3' A C 7 OK 562 565 566 586 C3' G C 8 OK 584 587 588 609 C3' C C 9 OK 607 610 611 629 C3' C C 10 OK 627 630 631 647 C3' G D 1 OK 645 648 649 670 C3' G D 2 OK 668 671 672 693 C3' C D 3 OK 691 694 695 713 C3' A D 4 OK 711 714 715 735 C3' G D 5 OK 733 736 737 758 C3' C D 6 OK 756 759 760 778 C3' A D 7 OK 776 779 780 800 C3' G D 8 OK 798 801 802 823 C3' C D 9 OK 821 824 825 843 C3' C D 10 OK 841 844 845 861 C3' G E 1 OK 859 862 863 884 C3' G E 2 OK 882 885 886 907 C3' C E 3 OK 905 908 909 927 C3' A E 4 OK 925 928 929 949 C3' G E 5 OK 947 950 951 972 C3' C E 6 OK 970 973 974 992 C3' A E 7 OK 990 993 994 1014 C3' G E 8 OK 1012 1015 1016 1037 C3' C E 9 OK 1035 1038 1039 1057 C3' C E 10 OK 1055 1058 1059 1075 C3' G F 1 OK 1073 1076 1077 1098 C3' G F 2 OK 1096 1099 1100 1121 C3' C F 3 OK 1119 1122 1123 1141 C3' A F 4 OK 1139 1142 1143 1163 C3' G F 5 OK 1161 1164 1165 1186 C3' C F 6 OK 1184 1187 1188 1206 C3' A F 7 OK 1204 1207 1208 1228 C3' G F 8 OK 1226 1229 1230 1251 C3' C F 9 OK 1249 1252 1253 1271 C3' C F 10 OK 1269 1272 1273 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' C A 3 OK 51 48 50 69 C4' A A 4 OK 71 68 70 91 C4' G A 5 OK 93 90 92 114 C4' C A 6 OK 116 113 115 134 C4' A A 7 OK 136 133 135 156 C4' G A 8 OK 158 155 157 179 C4' C A 9 OK 181 178 180 199 C4' C A 10 OK 201 198 200 217 C4' G B 1 OK 219 216 218 240 C4' G B 2 OK 242 239 241 263 C4' C B 3 OK 265 262 264 283 C4' A B 4 OK 285 282 284 305 C4' G B 5 OK 307 304 306 328 C4' C B 6 OK 330 327 329 348 C4' A B 7 OK 350 347 349 370 C4' G B 8 OK 372 369 371 393 C4' C B 9 OK 395 392 394 413 C4' C B 10 OK 415 412 414 431 C4' G C 1 OK 433 430 432 454 C4' G C 2 OK 456 453 455 477 C4' C C 3 OK 479 476 478 497 C4' A C 4 OK 499 496 498 519 C4' G C 5 OK 521 518 520 542 C4' C C 6 OK 544 541 543 562 C4' A C 7 OK 564 561 563 584 C4' G C 8 OK 586 583 585 607 C4' C C 9 OK 609 606 608 627 C4' C C 10 OK 629 626 628 645 C4' G D 1 OK 647 644 646 668 C4' G D 2 OK 670 667 669 691 C4' C D 3 OK 693 690 692 711 C4' A D 4 OK 713 710 712 733 C4' G D 5 OK 735 732 734 756 C4' C D 6 OK 758 755 757 776 C4' A D 7 OK 778 775 777 798 C4' G D 8 OK 800 797 799 821 C4' C D 9 OK 823 820 822 841 C4' C D 10 OK 843 840 842 859 C4' G E 1 OK 861 858 860 882 C4' G E 2 OK 884 881 883 905 C4' C E 3 OK 907 904 906 925 C4' A E 4 OK 927 924 926 947 C4' G E 5 OK 949 946 948 970 C4' C E 6 OK 972 969 971 990 C4' A E 7 OK 992 989 991 1012 C4' G E 8 OK 1014 1011 1013 1035 C4' C E 9 OK 1037 1034 1036 1055 C4' C E 10 OK 1057 1054 1056 1073 C4' G F 1 OK 1075 1072 1074 1096 C4' G F 2 OK 1098 1095 1097 1119 C4' C F 3 OK 1121 1118 1120 1139 C4' A F 4 OK 1141 1138 1140 1161 C4' G F 5 OK 1163 1160 1162 1184 C4' C F 6 OK 1186 1183 1185 1204 C4' A F 7 OK 1206 1203 1205 1226 C4' G F 8 OK 1228 1225 1227 1249 C4' C F 9 OK 1251 1248 1250 1269 C4' C F 10 OK 1271 1268 1270 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' C A 3 47 49 68 C5' A A 4 67 69 90 C5' G A 5 89 91 113 C5' C A 6 112 114 133 C5' A A 7 132 134 155 C5' G A 8 154 156 178 C5' C A 9 177 179 198 C5' C A 10 197 199 216 C5' G B 1 215 217 239 C5' G B 2 238 240 262 C5' C B 3 261 263 282 C5' A B 4 281 283 304 C5' G B 5 303 305 327 C5' C B 6 326 328 347 C5' A B 7 346 348 369 C5' G B 8 368 370 392 C5' C B 9 391 393 412 C5' C B 10 411 413 430 C5' G C 1 429 431 453 C5' G C 2 452 454 476 C5' C C 3 475 477 496 C5' A C 4 495 497 518 C5' G C 5 517 519 541 C5' C C 6 540 542 561 C5' A C 7 560 562 583 C5' G C 8 582 584 606 C5' C C 9 605 607 626 C5' C C 10 625 627 644 C5' G D 1 643 645 667 C5' G D 2 666 668 690 C5' C D 3 689 691 710 C5' A D 4 709 711 732 C5' G D 5 731 733 755 C5' C D 6 754 756 775 C5' A D 7 774 776 797 C5' G D 8 796 798 820 C5' C D 9 819 821 840 C5' C D 10 839 841 858 C5' G E 1 857 859 881 C5' G E 2 880 882 904 C5' C E 3 903 905 924 C5' A E 4 923 925 946 C5' G E 5 945 947 969 C5' C E 6 968 970 989 C5' A E 7 988 990 1011 C5' G E 8 1010 1012 1034 C5' C E 9 1033 1035 1054 C5' C E 10 1053 1055 1072 C5' G F 1 1071 1073 1095 C5' G F 2 1094 1096 1118 C5' C F 3 1117 1119 1138 C5' A F 4 1137 1139 1160 C5' G F 5 1159 1161 1183 C5' C F 6 1182 1184 1203 C5' A F 7 1202 1204 1225 C5' G F 8 1224 1226 1248 C5' C F 9 1247 1249 1268 C5' C F 10 1267 1269 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P C A 3 distorted distorted 29 45 46 47 64 P A A 4 distorted distorted 52 65 66 67 86 P G A 5 distorted distorted 72 87 88 89 109 P C A 6 distorted distorted 94 110 111 112 129 P A A 7 distorted distorted 117 130 131 132 151 P G A 8 distorted distorted 137 152 153 154 174 P C A 9 distorted distorted 159 175 176 177 194 P C A 10 distorted distorted 182 195 196 197 235 P G B 2 distorted distorted 220 236 237 238 258 P C B 3 distorted distorted 243 259 260 261 278 P A B 4 distorted distorted 266 279 280 281 300 P G B 5 distorted distorted 286 301 302 303 323 P C B 6 distorted distorted 308 324 325 326 343 P A B 7 distorted distorted 331 344 345 346 365 P G B 8 distorted distorted 351 366 367 368 388 P C B 9 distorted distorted 373 389 390 391 408 P C B 10 distorted distorted 396 409 410 411 449 P G C 2 distorted distorted 434 450 451 452 472 P C C 3 distorted distorted 457 473 474 475 492 P A C 4 distorted distorted 480 493 494 495 514 P G C 5 distorted distorted 500 515 516 517 537 P C C 6 distorted distorted 522 538 539 540 557 P A C 7 distorted distorted 545 558 559 560 579 P G C 8 distorted distorted 565 580 581 582 602 P C C 9 distorted distorted 587 603 604 605 622 P C C 10 distorted distorted 610 623 624 625 663 P G D 2 distorted distorted 648 664 665 666 686 P C D 3 distorted distorted 671 687 688 689 706 P A D 4 distorted distorted 694 707 708 709 728 P G D 5 distorted distorted 714 729 730 731 751 P C D 6 distorted distorted 736 752 753 754 771 P A D 7 distorted distorted 759 772 773 774 793 P G D 8 distorted distorted 779 794 795 796 816 P C D 9 distorted distorted 801 817 818 819 836 P C D 10 distorted distorted 824 837 838 839 877 P G E 2 distorted distorted 862 878 879 880 900 P C E 3 distorted distorted 885 901 902 903 920 P A E 4 distorted distorted 908 921 922 923 942 P G E 5 distorted distorted 928 943 944 945 965 P C E 6 distorted distorted 950 966 967 968 985 P A E 7 distorted distorted 973 986 987 988 1007 P G E 8 distorted distorted 993 1008 1009 1010 1030 P C E 9 distorted distorted 1015 1031 1032 1033 1050 P C E 10 distorted distorted 1038 1051 1052 1053 1091 P G F 2 distorted distorted 1076 1092 1093 1094 1114 P C F 3 distorted distorted 1099 1115 1116 1117 1134 P A F 4 distorted distorted 1122 1135 1136 1137 1156 P G F 5 distorted distorted 1142 1157 1158 1159 1179 P C F 6 distorted distorted 1164 1180 1181 1182 1199 P A F 7 distorted distorted 1187 1200 1201 1202 1221 P G F 8 distorted distorted 1207 1222 1223 1224 1244 P C F 9 distorted distorted 1229 1245 1246 1247 1264 P C F 10 distorted distorted 1252 1265 1266 1267 ---------------------------------------------------------------------------------