ID code: '5FJ0' 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' G A 4 beta 70 76 73 98 C1' A A 5 beta 93 99 96 120 C1' A A 6 beta 115 121 118 142 C1' G A 7 beta 137 143 140 165 C1' A A 8 beta 160 166 163 187 C1' A A 9 beta 182 188 185 209 C1' C A 10 beta 204 210 207 229 C1' C A 11 beta 224 230 227 249 C1' G A 12 beta 244 250 247 272 C1' G A 13 beta 267 273 270 295 C1' G A 14 beta 290 296 293 318 C1' G A 15 beta 313 319 316 341 C1' A A 16 beta 336 342 339 363 C1' G A 17 beta 358 364 361 386 C1' C A 18 beta 381 387 384 406 C1' C A 19 beta 401 407 404 424 C1' G B 1 beta 419 425 422 447 C1' G B 2 beta 442 448 445 470 C1' C B 3 beta 465 471 468 490 C1' G B 4 beta 485 491 488 513 C1' A B 5 beta 508 514 511 535 C1' A B 6 beta 530 536 533 557 C1' G B 7 beta 552 558 555 580 C1' A B 8 beta 575 581 578 602 C1' A B 9 beta 597 603 600 624 C1' C B 10 beta 619 625 622 644 C1' C B 11 beta 639 645 642 664 C1' G B 12 beta 659 665 662 687 C1' G B 13 beta 682 688 685 710 C1' G B 14 beta 705 711 708 733 C1' G B 15 beta 728 734 731 756 C1' A B 16 beta 751 757 754 778 C1' G B 17 beta 773 779 776 801 C1' C B 18 beta 796 802 799 821 C1' C B 19 beta 816 822 819 839 C1' G C 1 beta 834 840 837 862 C1' G C 2 beta 857 863 860 885 C1' C C 3 beta 880 886 883 905 C1' G C 4 beta 900 906 903 928 C1' A C 5 beta 923 929 926 950 C1' A C 6 beta 945 951 948 972 C1' G C 7 beta 967 973 970 995 C1' A C 8 beta 990 996 993 1017 C1' A C 9 beta 1012 1018 1015 1039 C1' C C 10 beta 1034 1040 1037 1059 C1' C C 11 beta 1054 1060 1057 1079 C1' G C 12 beta 1074 1080 1077 1102 C1' G C 13 beta 1097 1103 1100 1125 C1' G C 14 beta 1120 1126 1123 1148 C1' G C 15 beta 1143 1149 1146 1171 C1' A C 16 beta 1166 1172 1169 1193 C1' G C 17 beta 1188 1194 1191 1216 C1' C C 18 beta 1211 1217 1214 1236 C1' C C 19 beta 1231 1237 1234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK 75 71 74 96 C2' A A 5 OK 98 94 97 118 C2' A A 6 OK 120 116 119 140 C2' G A 7 OK 142 138 141 163 C2' A A 8 OK 165 161 164 185 C2' A A 9 OK 187 183 186 207 C2' C A 10 OK 209 205 208 227 C2' C A 11 OK 229 225 228 247 C2' G A 12 OK 249 245 248 270 C2' G A 13 OK 272 268 271 293 C2' G A 14 OK 295 291 294 316 C2' G A 15 OK 318 314 317 339 C2' A A 16 OK 341 337 340 361 C2' G A 17 OK 363 359 362 384 C2' C A 18 OK 386 382 385 404 C2' C A 19 OK 406 402 405 422 C2' G B 1 OK 424 420 423 445 C2' G B 2 OK 447 443 446 468 C2' C B 3 OK 470 466 469 488 C2' G B 4 OK 490 486 489 511 C2' A B 5 OK 513 509 512 533 C2' A B 6 OK 535 531 534 555 C2' G B 7 OK 557 553 556 578 C2' A B 8 OK 580 576 579 600 C2' A B 9 OK 602 598 601 622 C2' C B 10 OK 624 620 623 642 C2' C B 11 OK 644 640 643 662 C2' G B 12 OK 664 660 663 685 C2' G B 13 OK 687 683 686 708 C2' G B 14 OK 710 706 709 731 C2' G B 15 OK 733 729 732 754 C2' A B 16 OK 756 752 755 776 C2' G B 17 OK 778 774 777 799 C2' C B 18 OK 801 797 800 819 C2' C B 19 OK 821 817 820 837 C2' G C 1 OK 839 835 838 860 C2' G C 2 OK 862 858 861 883 C2' C C 3 OK 885 881 884 903 C2' G C 4 OK 905 901 904 926 C2' A C 5 OK 928 924 927 948 C2' A C 6 OK 950 946 949 970 C2' G C 7 OK 972 968 971 993 C2' A C 8 OK 995 991 994 1015 C2' A C 9 OK 1017 1013 1016 1037 C2' C C 10 OK 1039 1035 1038 1057 C2' C C 11 OK 1059 1055 1058 1077 C2' G C 12 OK 1079 1075 1078 1100 C2' G C 13 OK 1102 1098 1101 1123 C2' G C 14 OK 1125 1121 1124 1146 C2' G C 15 OK 1148 1144 1147 1169 C2' A C 16 OK 1171 1167 1170 1191 C2' G C 17 OK 1193 1189 1192 1214 C2' C C 18 OK 1216 1212 1215 1234 C2' C C 19 OK 1236 1232 1235 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK 69 72 73 94 C3' A A 5 OK 92 95 96 116 C3' A A 6 OK 114 117 118 138 C3' G A 7 OK 136 139 140 161 C3' A A 8 OK 159 162 163 183 C3' A A 9 OK 181 184 185 205 C3' C A 10 OK 203 206 207 225 C3' C A 11 OK 223 226 227 245 C3' G A 12 OK 243 246 247 268 C3' G A 13 OK 266 269 270 291 C3' G A 14 OK 289 292 293 314 C3' G A 15 OK 312 315 316 337 C3' A A 16 OK 335 338 339 359 C3' G A 17 OK 357 360 361 382 C3' C A 18 OK 380 383 384 402 C3' C A 19 OK 400 403 404 420 C3' G B 1 OK 418 421 422 443 C3' G B 2 OK 441 444 445 466 C3' C B 3 OK 464 467 468 486 C3' G B 4 OK 484 487 488 509 C3' A B 5 OK 507 510 511 531 C3' A B 6 OK 529 532 533 553 C3' G B 7 OK 551 554 555 576 C3' A B 8 OK 574 577 578 598 C3' A B 9 OK 596 599 600 620 C3' C B 10 OK 618 621 622 640 C3' C B 11 OK 638 641 642 660 C3' G B 12 OK 658 661 662 683 C3' G B 13 OK 681 684 685 706 C3' G B 14 OK 704 707 708 729 C3' G B 15 OK 727 730 731 752 C3' A B 16 OK 750 753 754 774 C3' G B 17 OK 772 775 776 797 C3' C B 18 OK 795 798 799 817 C3' C B 19 OK 815 818 819 835 C3' G C 1 OK 833 836 837 858 C3' G C 2 OK 856 859 860 881 C3' C C 3 OK 879 882 883 901 C3' G C 4 OK 899 902 903 924 C3' A C 5 OK 922 925 926 946 C3' A C 6 OK 944 947 948 968 C3' G C 7 OK 966 969 970 991 C3' A C 8 OK 989 992 993 1013 C3' A C 9 OK 1011 1014 1015 1035 C3' C C 10 OK 1033 1036 1037 1055 C3' C C 11 OK 1053 1056 1057 1075 C3' G C 12 OK 1073 1076 1077 1098 C3' G C 13 OK 1096 1099 1100 1121 C3' G C 14 OK 1119 1122 1123 1144 C3' G C 15 OK 1142 1145 1146 1167 C3' A C 16 OK 1165 1168 1169 1189 C3' G C 17 OK 1187 1190 1191 1212 C3' C C 18 OK 1210 1213 1214 1232 C3' C C 19 OK 1230 1233 1234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK 71 68 70 92 C4' A A 5 OK 94 91 93 114 C4' A A 6 OK 116 113 115 136 C4' G A 7 OK 138 135 137 159 C4' A A 8 OK 161 158 160 181 C4' A A 9 OK 183 180 182 203 C4' C A 10 OK 205 202 204 223 C4' C A 11 OK 225 222 224 243 C4' G A 12 OK 245 242 244 266 C4' G A 13 OK 268 265 267 289 C4' G A 14 OK 291 288 290 312 C4' G A 15 OK 314 311 313 335 C4' A A 16 OK 337 334 336 357 C4' G A 17 OK 359 356 358 380 C4' C A 18 OK 382 379 381 400 C4' C A 19 OK 402 399 401 418 C4' G B 1 OK 420 417 419 441 C4' G B 2 OK 443 440 442 464 C4' C B 3 OK 466 463 465 484 C4' G B 4 OK 486 483 485 507 C4' A B 5 OK 509 506 508 529 C4' A B 6 OK 531 528 530 551 C4' G B 7 OK 553 550 552 574 C4' A B 8 OK 576 573 575 596 C4' A B 9 OK 598 595 597 618 C4' C B 10 OK 620 617 619 638 C4' C B 11 OK 640 637 639 658 C4' G B 12 OK 660 657 659 681 C4' G B 13 OK 683 680 682 704 C4' G B 14 OK 706 703 705 727 C4' G B 15 OK 729 726 728 750 C4' A B 16 OK 752 749 751 772 C4' G B 17 OK 774 771 773 795 C4' C B 18 OK 797 794 796 815 C4' C B 19 OK 817 814 816 833 C4' G C 1 OK 835 832 834 856 C4' G C 2 OK 858 855 857 879 C4' C C 3 OK 881 878 880 899 C4' G C 4 OK 901 898 900 922 C4' A C 5 OK 924 921 923 944 C4' A C 6 OK 946 943 945 966 C4' G C 7 OK 968 965 967 989 C4' A C 8 OK 991 988 990 1011 C4' A C 9 OK 1013 1010 1012 1033 C4' C C 10 OK 1035 1032 1034 1053 C4' C C 11 OK 1055 1052 1054 1073 C4' G C 12 OK 1075 1072 1074 1096 C4' G C 13 OK 1098 1095 1097 1119 C4' G C 14 OK 1121 1118 1120 1142 C4' G C 15 OK 1144 1141 1143 1165 C4' A C 16 OK 1167 1164 1166 1187 C4' G C 17 OK 1189 1186 1188 1210 C4' C C 18 OK 1212 1209 1211 1230 C4' C C 19 OK 1232 1229 1231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 67 69 91 C5' A A 5 90 92 113 C5' A A 6 112 114 135 C5' G A 7 134 136 158 C5' A A 8 157 159 180 C5' A A 9 179 181 202 C5' C A 10 201 203 222 C5' C A 11 221 223 242 C5' G A 12 241 243 265 C5' G A 13 264 266 288 C5' G A 14 287 289 311 C5' G A 15 310 312 334 C5' A A 16 333 335 356 C5' G A 17 355 357 379 C5' C A 18 378 380 399 C5' C A 19 398 400 417 C5' G B 1 416 418 440 C5' G B 2 439 441 463 C5' C B 3 462 464 483 C5' G B 4 482 484 506 C5' A B 5 505 507 528 C5' A B 6 527 529 550 C5' G B 7 549 551 573 C5' A B 8 572 574 595 C5' A B 9 594 596 617 C5' C B 10 616 618 637 C5' C B 11 636 638 657 C5' G B 12 656 658 680 C5' G B 13 679 681 703 C5' G B 14 702 704 726 C5' G B 15 725 727 749 C5' A B 16 748 750 771 C5' G B 17 770 772 794 C5' C B 18 793 795 814 C5' C B 19 813 815 832 C5' G C 1 831 833 855 C5' G C 2 854 856 878 C5' C C 3 877 879 898 C5' G C 4 897 899 921 C5' A C 5 920 922 943 C5' A C 6 942 944 965 C5' G C 7 964 966 988 C5' A C 8 987 989 1010 C5' A C 9 1009 1011 1032 C5' C C 10 1031 1033 1052 C5' C C 11 1051 1053 1072 C5' G C 12 1071 1073 1095 C5' G C 13 1094 1096 1118 C5' G C 14 1117 1119 1141 C5' G C 15 1140 1142 1164 C5' A C 16 1163 1165 1186 C5' G C 17 1185 1187 1209 C5' C C 18 1208 1210 1229 C5' C C 19 1228 1230 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 52 65 66 67 87 P A A 5 distorted distorted 72 88 89 90 109 P A A 6 distorted distorted 95 110 111 112 131 P G A 7 distorted distorted 117 132 133 134 154 P A A 8 distorted distorted 139 155 156 157 176 P A A 9 distorted distorted 162 177 178 179 198 P C A 10 distorted distorted 184 199 200 201 218 P C A 11 distorted distorted 206 219 220 221 238 P G A 12 distorted distorted 226 239 240 241 261 P G A 13 distorted distorted 246 262 263 264 284 P G A 14 distorted distorted 269 285 286 287 307 P G A 15 distorted distorted 292 308 309 310 330 P A A 16 distorted distorted 315 331 332 333 352 P G A 17 distorted distorted 338 353 354 355 375 P C A 18 distorted distorted 360 376 377 378 395 P C A 19 distorted distorted 383 396 397 398 436 P G B 2 distorted distorted 421 437 438 439 459 P C B 3 distorted distorted 444 460 461 462 479 P G B 4 distorted distorted 467 480 481 482 502 P A B 5 distorted distorted 487 503 504 505 524 P A B 6 distorted distorted 510 525 526 527 546 P G B 7 distorted distorted 532 547 548 549 569 P A B 8 distorted distorted 554 570 571 572 591 P A B 9 distorted distorted 577 592 593 594 613 P C B 10 distorted distorted 599 614 615 616 633 P C B 11 distorted distorted 621 634 635 636 653 P G B 12 distorted distorted 641 654 655 656 676 P G B 13 distorted distorted 661 677 678 679 699 P G B 14 distorted distorted 684 700 701 702 722 P G B 15 distorted distorted 707 723 724 725 745 P A B 16 distorted distorted 730 746 747 748 767 P G B 17 distorted distorted 753 768 769 770 790 P C B 18 distorted distorted 775 791 792 793 810 P C B 19 distorted distorted 798 811 812 813 851 P G C 2 distorted distorted 836 852 853 854 874 P C C 3 distorted distorted 859 875 876 877 894 P G C 4 distorted distorted 882 895 896 897 917 P A C 5 distorted distorted 902 918 919 920 939 P A C 6 distorted distorted 925 940 941 942 961 P G C 7 distorted distorted 947 962 963 964 984 P A C 8 distorted distorted 969 985 986 987 1006 P A C 9 distorted distorted 992 1007 1008 1009 1028 P C C 10 distorted distorted 1014 1029 1030 1031 1048 P C C 11 distorted distorted 1036 1049 1050 1051 1068 P G C 12 distorted distorted 1056 1069 1070 1071 1091 P G C 13 distorted distorted 1076 1092 1093 1094 1114 P G C 14 distorted distorted 1099 1115 1116 1117 1137 P G C 15 distorted distorted 1122 1138 1139 1140 1160 P A C 16 distorted distorted 1145 1161 1162 1163 1182 P G C 17 distorted distorted 1168 1183 1184 1185 1205 P C C 18 distorted distorted 1190 1206 1207 1208 1225 P C C 19 distorted distorted 1213 1226 1227 1228 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