ID code: '2ASL' 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' --------------------------------------------------------------------------------- 8 C1' DG D 801 beta 4 9 7 30 C1' DG D 802 beta 26 31 29 52 C1' DT D 803 beta 48 53 51 72 C1' DT D 804 beta 68 73 71 92 C1' DG D 805 beta 88 93 91 114 C1' DG D 806 beta 110 115 113 136 C1' DA D 807 beta 132 137 135 157 C1' DT D 808 beta 153 158 156 177 C1' DG D 809 beta 173 178 176 199 C1' DG D 810 beta 195 200 198 221 C1' DT D 811 beta 217 222 220 241 C1' DA D 812 beta 237 242 240 262 C1' DG D 813 beta 258 263 261 282 C1' DOC D 814 beta 286 274 283 300 C1' DA E 903 beta 296 301 299 321 C1' DA E 904 beta 317 322 320 342 C1' DC E 905 beta 338 343 341 361 C1' 8OG E 906 beta 357 362 360 384 C1' DC E 907 beta 380 385 383 403 C1' DT E 908 beta 399 404 402 423 C1' DA E 909 beta 419 424 422 444 C1' DC E 910 beta 440 445 443 463 C1' DC E 911 beta 459 464 462 482 C1' DA E 912 beta 478 483 481 503 C1' DT E 913 beta 499 504 502 523 C1' DC E 914 beta 519 524 522 542 C1' DC E 915 beta 538 543 541 561 C1' DA E 916 beta 557 562 560 582 C1' DA E 917 beta 578 583 581 603 C1' DC E 918 beta 599 604 602 622 C1' DC E 919 beta 618 623 621 639 C1' DG H1801 beta 635 640 638 661 C1' DG H1802 beta 657 662 660 683 C1' DT H1803 beta 679 684 682 703 C1' DT H1804 beta 699 704 702 723 C1' DG H1805 beta 719 724 722 745 C1' DG H1806 beta 741 746 744 767 C1' DA H1807 beta 763 768 766 788 C1' DT H1808 beta 784 789 787 808 C1' DG H1809 beta 804 809 807 830 C1' DG H1810 beta 826 831 829 852 C1' DT H1811 beta 848 853 851 872 C1' DA H1812 beta 868 873 871 893 C1' DG H1813 beta 889 894 892 913 C1' DOC H1814 beta 917 905 914 931 C1' DA J1903 beta 927 932 930 952 C1' DA J1904 beta 948 953 951 973 C1' DC J1905 beta 969 974 972 992 C1' 8OG J1906 beta 988 993 991 1015 C1' DC J1907 beta 1011 1016 1014 1034 C1' DT J1908 beta 1030 1035 1033 1054 C1' DA J1909 beta 1050 1055 1053 1075 C1' DC J1910 beta 1071 1076 1074 1094 C1' DC J1911 beta 1090 1095 1093 1113 C1' DA J1912 beta 1109 1114 1112 1134 C1' DT J1913 beta 1130 1135 1133 1154 C1' DC J1914 beta 1150 1155 1153 1173 C1' DC J1915 beta 1169 1174 1172 1192 C1' DA J1916 beta 1188 1193 1191 1213 C1' DA J1917 beta 1209 1214 1212 1234 C1' DC J1918 beta 1230 1235 1233 1253 C1' DC J1919 beta 1249 1254 1252 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG D 801 8 5 29 C2' DG D 802 30 27 51 C2' DT D 803 52 49 71 C2' DT D 804 72 69 91 C2' DG D 805 92 89 113 C2' DG D 806 114 111 135 C2' DA D 807 136 133 156 C2' DT D 808 157 154 176 C2' DG D 809 177 174 198 C2' DG D 810 199 196 220 C2' DT D 811 221 218 240 C2' DA D 812 241 238 261 C2' DG D 813 262 259 283 C2' DOC D 814 282 284 299 C2' DA E 903 300 297 320 C2' DA E 904 321 318 341 C2' DC E 905 342 339 360 C2' 8OG E 906 361 358 383 C2' DC E 907 384 381 402 C2' DT E 908 403 400 422 C2' DA E 909 423 420 443 C2' DC E 910 444 441 462 C2' DC E 911 463 460 481 C2' DA E 912 482 479 502 C2' DT E 913 503 500 522 C2' DC E 914 523 520 541 C2' DC E 915 542 539 560 C2' DA E 916 561 558 581 C2' DA E 917 582 579 602 C2' DC E 918 603 600 621 C2' DC E 919 622 619 638 C2' DG H1801 639 636 660 C2' DG H1802 661 658 682 C2' DT H1803 683 680 702 C2' DT H1804 703 700 722 C2' DG H1805 723 720 744 C2' DG H1806 745 742 766 C2' DA H1807 767 764 787 C2' DT H1808 788 785 807 C2' DG H1809 808 805 829 C2' DG H1810 830 827 851 C2' DT H1811 852 849 871 C2' DA H1812 872 869 892 C2' DG H1813 893 890 914 C2' DOC H1814 913 915 930 C2' DA J1903 931 928 951 C2' DA J1904 952 949 972 C2' DC J1905 973 970 991 C2' 8OG J1906 992 989 1014 C2' DC J1907 1015 1012 1033 C2' DT J1908 1034 1031 1053 C2' DA J1909 1054 1051 1074 C2' DC J1910 1075 1072 1093 C2' DC J1911 1094 1091 1112 C2' DA J1912 1113 1110 1133 C2' DT J1913 1134 1131 1153 C2' DC J1914 1154 1151 1172 C2' DC J1915 1173 1170 1191 C2' DA J1916 1192 1189 1212 C2' DA J1917 1213 1210 1233 C2' DC J1918 1234 1231 1252 C2' DC J1919 1253 1250 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG D 801 OK 3 6 7 27 C3' DG D 802 OK 25 28 29 49 C3' DT D 803 OK 47 50 51 69 C3' DT D 804 OK 67 70 71 89 C3' DG D 805 OK 87 90 91 111 C3' DG D 806 OK 109 112 113 133 C3' DA D 807 OK 131 134 135 154 C3' DT D 808 OK 152 155 156 174 C3' DG D 809 OK 172 175 176 196 C3' DG D 810 OK 194 197 198 218 C3' DT D 811 OK 216 219 220 238 C3' DA D 812 OK 236 239 240 259 C3' DG D 813 OK 257 260 261 284 C3' DOC D 814 285 283 297 C3' DA E 903 OK 295 298 299 318 C3' DA E 904 OK 316 319 320 339 C3' DC E 905 OK 337 340 341 358 C3' 8OG E 906 OK 356 359 360 381 C3' DC E 907 OK 379 382 383 400 C3' DT E 908 OK 398 401 402 420 C3' DA E 909 OK 418 421 422 441 C3' DC E 910 OK 439 442 443 460 C3' DC E 911 OK 458 461 462 479 C3' DA E 912 OK 477 480 481 500 C3' DT E 913 OK 498 501 502 520 C3' DC E 914 OK 518 521 522 539 C3' DC E 915 OK 537 540 541 558 C3' DA E 916 OK 556 559 560 579 C3' DA E 917 OK 577 580 581 600 C3' DC E 918 OK 598 601 602 619 C3' DC E 919 OK 617 620 621 636 C3' DG H1801 OK 634 637 638 658 C3' DG H1802 OK 656 659 660 680 C3' DT H1803 OK 678 681 682 700 C3' DT H1804 OK 698 701 702 720 C3' DG H1805 OK 718 721 722 742 C3' DG H1806 OK 740 743 744 764 C3' DA H1807 OK 762 765 766 785 C3' DT H1808 OK 783 786 787 805 C3' DG H1809 OK 803 806 807 827 C3' DG H1810 OK 825 828 829 849 C3' DT H1811 OK 847 850 851 869 C3' DA H1812 OK 867 870 871 890 C3' DG H1813 OK 888 891 892 915 C3' DOC H1814 916 914 928 C3' DA J1903 OK 926 929 930 949 C3' DA J1904 OK 947 950 951 970 C3' DC J1905 OK 968 971 972 989 C3' 8OG J1906 OK 987 990 991 1012 C3' DC J1907 OK 1010 1013 1014 1031 C3' DT J1908 OK 1029 1032 1033 1051 C3' DA J1909 OK 1049 1052 1053 1072 C3' DC J1910 OK 1070 1073 1074 1091 C3' DC J1911 OK 1089 1092 1093 1110 C3' DA J1912 OK 1108 1111 1112 1131 C3' DT J1913 OK 1129 1132 1133 1151 C3' DC J1914 OK 1149 1152 1153 1170 C3' DC J1915 OK 1168 1171 1172 1189 C3' DA J1916 OK 1187 1190 1191 1210 C3' DA J1917 OK 1208 1211 1212 1231 C3' DC J1918 OK 1229 1232 1233 1250 C3' DC J1919 OK 1248 1251 1252 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG D 801 OK 5 2 4 25 C4' DG D 802 OK 27 24 26 47 C4' DT D 803 OK 49 46 48 67 C4' DT D 804 OK 69 66 68 87 C4' DG D 805 OK 89 86 88 109 C4' DG D 806 OK 111 108 110 131 C4' DA D 807 OK 133 130 132 152 C4' DT D 808 OK 154 151 153 172 C4' DG D 809 OK 174 171 173 194 C4' DG D 810 OK 196 193 195 216 C4' DT D 811 OK 218 215 217 236 C4' DA D 812 OK 238 235 237 257 C4' DG D 813 OK 259 256 258 285 C4' DOC D 814 OK 284 287 286 295 C4' DA E 903 OK 297 294 296 316 C4' DA E 904 OK 318 315 317 337 C4' DC E 905 OK 339 336 338 356 C4' 8OG E 906 OK 358 355 357 379 C4' DC E 907 OK 381 378 380 398 C4' DT E 908 OK 400 397 399 418 C4' DA E 909 OK 420 417 419 439 C4' DC E 910 OK 441 438 440 458 C4' DC E 911 OK 460 457 459 477 C4' DA E 912 OK 479 476 478 498 C4' DT E 913 OK 500 497 499 518 C4' DC E 914 OK 520 517 519 537 C4' DC E 915 OK 539 536 538 556 C4' DA E 916 OK 558 555 557 577 C4' DA E 917 OK 579 576 578 598 C4' DC E 918 OK 600 597 599 617 C4' DC E 919 OK 619 616 618 634 C4' DG H1801 OK 636 633 635 656 C4' DG H1802 OK 658 655 657 678 C4' DT H1803 OK 680 677 679 698 C4' DT H1804 OK 700 697 699 718 C4' DG H1805 OK 720 717 719 740 C4' DG H1806 OK 742 739 741 762 C4' DA H1807 OK 764 761 763 783 C4' DT H1808 OK 785 782 784 803 C4' DG H1809 OK 805 802 804 825 C4' DG H1810 OK 827 824 826 847 C4' DT H1811 OK 849 846 848 867 C4' DA H1812 OK 869 866 868 888 C4' DG H1813 OK 890 887 889 916 C4' DOC H1814 OK 915 918 917 926 C4' DA J1903 OK 928 925 927 947 C4' DA J1904 OK 949 946 948 968 C4' DC J1905 OK 970 967 969 987 C4' 8OG J1906 OK 989 986 988 1010 C4' DC J1907 OK 1012 1009 1011 1029 C4' DT J1908 OK 1031 1028 1030 1049 C4' DA J1909 OK 1051 1048 1050 1070 C4' DC J1910 OK 1072 1069 1071 1089 C4' DC J1911 OK 1091 1088 1090 1108 C4' DA J1912 OK 1110 1107 1109 1129 C4' DT J1913 OK 1131 1128 1130 1149 C4' DC J1914 OK 1151 1148 1150 1168 C4' DC J1915 OK 1170 1167 1169 1187 C4' DA J1916 OK 1189 1186 1188 1208 C4' DA J1917 OK 1210 1207 1209 1229 C4' DC J1918 OK 1231 1228 1230 1248 C4' DC J1919 OK 1250 1247 1249 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG D 801 1 3 24 C5' DG D 802 23 25 46 C5' DT D 803 45 47 66 C5' DT D 804 65 67 86 C5' DG D 805 85 87 108 C5' DG D 806 107 109 130 C5' DA D 807 129 131 151 C5' DT D 808 150 152 171 C5' DG D 809 170 172 193 C5' DG D 810 192 194 215 C5' DT D 811 214 216 235 C5' DA D 812 234 236 256 C5' DG D 813 255 257 287 C5' DOC D 814 288 285 294 C5' DA E 903 293 295 315 C5' DA E 904 314 316 336 C5' DC E 905 335 337 355 C5' 8OG E 906 354 356 378 C5' DC E 907 377 379 397 C5' DT E 908 396 398 417 C5' DA E 909 416 418 438 C5' DC E 910 437 439 457 C5' DC E 911 456 458 476 C5' DA E 912 475 477 497 C5' DT E 913 496 498 517 C5' DC E 914 516 518 536 C5' DC E 915 535 537 555 C5' DA E 916 554 556 576 C5' DA E 917 575 577 597 C5' DC E 918 596 598 616 C5' DC E 919 615 617 633 C5' DG H1801 632 634 655 C5' DG H1802 654 656 677 C5' DT H1803 676 678 697 C5' DT H1804 696 698 717 C5' DG H1805 716 718 739 C5' DG H1806 738 740 761 C5' DA H1807 760 762 782 C5' DT H1808 781 783 802 C5' DG H1809 801 803 824 C5' DG H1810 823 825 846 C5' DT H1811 845 847 866 C5' DA H1812 865 867 887 C5' DG H1813 886 888 918 C5' DOC H1814 919 916 925 C5' DA J1903 924 926 946 C5' DA J1904 945 947 967 C5' DC J1905 966 968 986 C5' 8OG J1906 985 987 1009 C5' DC J1907 1008 1010 1028 C5' DT J1908 1027 1029 1048 C5' DA J1909 1047 1049 1069 C5' DC J1910 1068 1070 1088 C5' DC J1911 1087 1089 1107 C5' DA J1912 1106 1108 1128 C5' DT J1913 1127 1129 1148 C5' DC J1914 1147 1149 1167 C5' DC J1915 1166 1168 1186 C5' DA J1916 1185 1187 1207 C5' DA J1917 1206 1208 1228 C5' DC J1918 1227 1229 1247 C5' DC J1919 1246 1248 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DG D 802 distorted distorted 6 21 22 23 42 P DT D 803 distorted distorted 28 43 44 45 62 P DT D 804 distorted distorted 50 63 64 65 82 P DG D 805 distorted distorted 70 83 84 85 104 P DG D 806 distorted distorted 90 105 106 107 126 P DA D 807 distorted distorted 112 127 128 129 147 P DT D 808 distorted distorted 134 148 149 150 167 P DG D 809 distorted distorted 155 168 169 170 189 P DG D 810 distorted distorted 175 190 191 192 211 P DT D 811 distorted distorted 197 212 213 214 231 P DA D 812 distorted distorted 219 232 233 234 252 P DG D 813 distorted distorted 239 253 254 255 289 P DOC D 814 distorted distorted 260 290 291 288 311 P DA E 904 distorted distorted 298 312 313 314 332 P DC E 905 distorted distorted 319 333 334 335 351 P 8OG E 906 distorted distorted 340 352 353 354 374 P DC E 907 distorted distorted 359 375 376 377 393 P DT E 908 distorted distorted 382 394 395 396 413 P DA E 909 distorted distorted 401 414 415 416 434 P DC E 910 distorted distorted 421 435 436 437 453 P DC E 911 distorted distorted 442 454 455 456 472 P DA E 912 distorted distorted 461 473 474 475 493 P DT E 913 distorted distorted 480 494 495 496 513 P DC E 914 distorted distorted 501 514 515 516 532 P DC E 915 distorted distorted 521 533 534 535 551 P DA E 916 distorted distorted 540 552 553 554 572 P DA E 917 distorted distorted 559 573 574 575 593 P DC E 918 distorted distorted 580 594 595 596 612 P DC E 919 distorted distorted 601 613 614 615 651 P DG H1802 distorted distorted 637 652 653 654 673 P DT H1803 distorted distorted 659 674 675 676 693 P DT H1804 distorted distorted 681 694 695 696 713 P DG H1805 distorted distorted 701 714 715 716 735 P DG H1806 distorted distorted 721 736 737 738 757 P DA H1807 distorted distorted 743 758 759 760 778 P DT H1808 distorted distorted 765 779 780 781 798 P DG H1809 distorted distorted 786 799 800 801 820 P DG H1810 distorted distorted 806 821 822 823 842 P DT H1811 distorted distorted 828 843 844 845 862 P DA H1812 distorted distorted 850 863 864 865 883 P DG H1813 distorted distorted 870 884 885 886 920 P DOC H1814 distorted distorted 891 921 922 919 942 P DA J1904 distorted distorted 929 943 944 945 963 P DC J1905 distorted distorted 950 964 965 966 982 P 8OG J1906 distorted distorted 971 983 984 985 1005 P DC J1907 distorted distorted 990 1006 1007 1008 1024 P DT J1908 distorted distorted 1013 1025 1026 1027 1044 P DA J1909 distorted distorted 1032 1045 1046 1047 1065 P DC J1910 distorted distorted 1052 1066 1067 1068 1084 P DC J1911 distorted distorted 1073 1085 1086 1087 1103 P DA J1912 distorted distorted 1092 1104 1105 1106 1124 P DT J1913 distorted distorted 1111 1125 1126 1127 1144 P DC J1914 distorted distorted 1132 1145 1146 1147 1163 P DC J1915 distorted distorted 1152 1164 1165 1166 1182 P DA J1916 distorted distorted 1171 1183 1184 1185 1203 P DA J1917 distorted distorted 1190 1204 1205 1206 1224 P DC J1918 distorted distorted 1211 1225 1226 1227 1243 P DC J1919 distorted distorted 1232 1244 1245 1246 ---------------------------------------------------------------------------------