ID code: '3SYW' 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' U A 1 alpha beta 4 24 10 7 40 C1' U A 2 alpha beta 35 55 41 38 70 C1' G A 3 alpha beta 65 88 71 68 104 C1' G A 4 alpha beta 99 122 105 102 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' C A 6 alpha beta 167 187 173 170 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' U A 8 alpha beta 229 249 235 232 264 C1' G A 9 beta 259 265 262 287 C1' C A 10 beta 282 288 285 307 C1' U A 11 beta 302 308 305 327 C1' G A 12 alpha beta 322 345 328 325 361 C1' C A 13 alpha beta 356 376 362 359 392 C1' U A 14 alpha beta 387 407 393 390 558 C1' U A 17 alpha beta 553 573 559 556 588 C1' C A 18 alpha beta 583 603 589 586 619 C1' C A 19 alpha beta 614 635 620 617 649 C1' U B 1 alpha beta 644 664 650 647 680 C1' U B 2 alpha beta 675 695 681 678 710 C1' G B 3 alpha beta 705 728 711 708 744 C1' G B 4 alpha beta 739 762 745 742 778 C1' G B 5 alpha beta 773 796 779 776 812 C1' C B 6 alpha beta 807 827 813 810 843 C1' C B 7 alpha beta 838 858 844 841 874 C1' U B 8 alpha beta 869 889 875 872 904 C1' G B 9 alpha beta 899 922 905 902 938 C1' C B 10 beta 933 939 936 958 C1' U B 11 beta 953 959 956 978 C1' G B 12 beta 973 979 976 1001 C1' C B 13 beta 996 1002 999 1021 C1' U B 14 alpha beta 1016 1036 1022 1019 1187 C1' U B 17 alpha beta 1182 1202 1188 1185 1217 C1' C B 18 alpha beta 1212 1232 1218 1215 1248 C1' C B 19 alpha beta 1243 1264 1249 1246 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' U A 2 OK OK 40 36 53 39 68 C2' G A 3 OK OK 70 66 86 69 102 C2' G A 4 OK OK 104 100 120 103 136 C2' G A 5 OK OK 138 134 154 137 170 C2' C A 6 OK OK 172 168 185 171 201 C2' C A 7 OK OK 203 199 216 202 232 C2' U A 8 OK OK 234 230 247 233 262 C2' G A 9 OK 264 260 263 285 C2' C A 10 OK 287 283 286 305 C2' U A 11 OK 307 303 306 325 C2' G A 12 OK OK 327 323 343 326 359 C2' C A 13 OK OK 361 357 374 360 390 C2' U A 14 OK OK 392 388 405 391 556 C2' U A 17 OK OK 558 554 571 557 586 C2' C A 18 OK OK 588 584 601 587 617 C2' C A 19 OK OK 619 615 633 618 647 C2' U B 1 OK OK 649 645 662 648 678 C2' U B 2 OK OK 680 676 693 679 708 C2' G B 3 OK OK 710 706 726 709 742 C2' G B 4 OK OK 744 740 760 743 776 C2' G B 5 OK OK 778 774 794 777 810 C2' C B 6 OK OK 812 808 825 811 841 C2' C B 7 OK OK 843 839 856 842 872 C2' U B 8 OK OK 874 870 887 873 902 C2' G B 9 OK OK 904 900 920 903 936 C2' C B 10 OK 938 934 937 956 C2' U B 11 OK 958 954 957 976 C2' G B 12 OK 978 974 977 999 C2' C B 13 OK 1001 997 1000 1019 C2' U B 14 OK OK 1021 1017 1034 1020 1185 C2' U B 17 OK OK 1187 1183 1200 1186 1215 C2' C B 18 OK OK 1217 1213 1230 1216 1246 C2' C B 19 OK OK 1248 1244 1262 1247 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' U A 2 OK OK 34 52 37 38 66 C3' G A 3 OK OK 64 85 67 68 100 C3' G A 4 OK OK 98 119 101 102 134 C3' G A 5 OK OK 132 153 135 136 168 C3' C A 6 OK OK 166 184 169 170 199 C3' C A 7 OK OK 197 215 200 201 230 C3' U A 8 OK OK 228 246 231 232 260 C3' G A 9 OK 258 261 262 283 C3' C A 10 OK 281 284 285 303 C3' U A 11 OK 301 304 305 323 C3' G A 12 OK OK 321 342 324 325 357 C3' C A 13 OK OK 355 373 358 359 388 C3' U A 14 OK OK 386 404 389 390 554 C3' U A 17 OK OK 552 570 555 556 584 C3' C A 18 OK OK 582 600 585 586 615 C3' C A 19 OK OK 613 631 616 617 645 C3' U B 1 OK OK 643 661 646 647 676 C3' U B 2 OK OK 674 692 677 678 706 C3' G B 3 OK OK 704 725 707 708 740 C3' G B 4 OK OK 738 759 741 742 774 C3' G B 5 OK OK 772 793 775 776 808 C3' C B 6 OK OK 806 824 809 810 839 C3' C B 7 OK OK 837 855 840 841 870 C3' U B 8 OK OK 868 886 871 872 900 C3' G B 9 OK OK 898 919 901 902 934 C3' C B 10 OK 932 935 936 954 C3' U B 11 OK 952 955 956 974 C3' G B 12 OK 972 975 976 997 C3' C B 13 OK 995 998 999 1017 C3' U B 14 OK OK 1015 1033 1018 1019 1183 C3' U B 17 OK OK 1181 1199 1184 1185 1213 C3' C B 18 OK OK 1211 1229 1214 1215 1244 C3' C B 19 OK OK 1242 1260 1245 1246 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' U A 2 OK OK 36 51 33 35 64 C4' G A 3 OK OK 66 84 63 65 98 C4' G A 4 OK OK 100 118 97 99 132 C4' G A 5 OK OK 134 152 131 133 166 C4' C A 6 OK OK 168 183 165 167 197 C4' C A 7 OK OK 199 214 196 198 228 C4' U A 8 OK OK 230 245 227 229 258 C4' G A 9 OK 260 257 259 281 C4' C A 10 OK 283 280 282 301 C4' U A 11 OK 303 300 302 321 C4' G A 12 OK OK 323 341 320 322 355 C4' C A 13 OK OK 357 372 354 356 386 C4' U A 14 OK OK 388 403 385 387 552 C4' U A 17 OK OK 554 569 551 553 582 C4' C A 18 OK OK 584 599 581 583 613 C4' C A 19 OK OK 615 630 612 614 643 C4' U B 1 OK OK 645 660 642 644 674 C4' U B 2 OK OK 676 691 673 675 704 C4' G B 3 OK OK 706 724 703 705 738 C4' G B 4 OK OK 740 758 737 739 772 C4' G B 5 OK OK 774 792 771 773 806 C4' C B 6 OK OK 808 823 805 807 837 C4' C B 7 OK OK 839 854 836 838 868 C4' U B 8 OK OK 870 885 867 869 898 C4' G B 9 OK OK 900 918 897 899 932 C4' C B 10 OK 934 931 933 952 C4' U B 11 OK 954 951 953 972 C4' G B 12 OK 974 971 973 995 C4' C B 13 OK 997 994 996 1015 C4' U B 14 OK OK 1017 1032 1014 1016 1181 C4' U B 17 OK OK 1183 1198 1180 1182 1211 C4' C B 18 OK OK 1213 1228 1210 1212 1242 C4' C B 19 OK OK 1244 1259 1241 1243 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' U A 2 OK OK 32 49 50 34 63 C5' G A 3 OK OK 62 82 83 64 97 C5' G A 4 OK OK 96 116 117 98 131 C5' G A 5 OK OK 130 150 151 132 165 C5' C A 6 OK OK 164 181 182 166 196 C5' C A 7 OK OK 195 212 213 197 227 C5' U A 8 OK OK 226 243 244 228 257 C5' G A 9 256 258 280 C5' C A 10 279 281 300 C5' U A 11 299 301 320 C5' G A 12 OK OK 319 339 340 321 354 C5' C A 13 OK OK 353 370 371 355 385 C5' U A 14 OK OK 384 401 402 386 551 C5' U A 17 OK OK 550 567 568 552 581 C5' C A 18 OK OK 580 597 598 582 612 C5' C A 19 OK OK 611 628 629 613 642 C5' U B 1 OK OK 641 658 659 643 673 C5' U B 2 OK OK 672 689 690 674 703 C5' G B 3 OK OK 702 722 723 704 737 C5' G B 4 OK OK 736 756 757 738 771 C5' G B 5 OK OK 770 790 791 772 805 C5' C B 6 OK OK 804 821 822 806 836 C5' C B 7 OK OK 835 852 853 837 867 C5' U B 8 OK OK 866 883 884 868 897 C5' G B 9 OK OK 896 916 917 898 931 C5' C B 10 930 932 951 C5' U B 11 950 952 971 C5' G B 12 970 972 994 C5' C B 13 993 995 1014 C5' U B 14 OK OK 1013 1030 1031 1015 1180 C5' U B 17 OK OK 1179 1196 1197 1181 1210 C5' C B 18 OK OK 1209 1226 1227 1211 1241 C5' C B 19 OK OK 1240 1257 1258 1242 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P U A 2 distorted distorted 6 30 31 32 59 P G A 3 distorted distorted 37 60 61 62 93 P G A 4 distorted distorted 67 94 95 96 127 P G A 5 distorted distorted 101 128 129 130 161 P C A 6 distorted distorted 135 162 163 164 192 P C A 7 distorted distorted 169 193 194 195 223 P U A 8 distorted distorted 200 224 225 226 253 P G A 9 distorted distorted 231 254 255 256 276 P C A 10 distorted distorted 261 277 278 279 296 P U A 11 distorted distorted 284 297 298 299 316 P G A 12 distorted distorted 304 317 318 319 350 P C A 13 distorted distorted 324 351 352 353 381 P U A 14 distorted distorted 358 382 383 384 411 P G A 15 389 412 P G A 15 389 479 P G A 16 480 P G A 16 547 P U A 17 distorted distorted 548 549 550 577 P C A 18 distorted distorted 555 578 579 580 608 P C A 19 distorted distorted 585 609 610 611 669 P U B 2 distorted distorted 646 670 671 672 699 P G B 3 distorted distorted 677 700 701 702 733 P G B 4 distorted distorted 707 734 735 736 767 P G B 5 distorted distorted 741 768 769 770 801 P C B 6 distorted distorted 775 802 803 804 832 P C B 7 distorted distorted 809 833 834 835 863 P U B 8 distorted distorted 840 864 865 866 893 P G B 9 distorted distorted 871 894 895 896 927 P C B 10 distorted distorted 901 928 929 930 947 P U B 11 distorted distorted 935 948 949 950 967 P G B 12 distorted distorted 955 968 969 970 990 P C B 13 distorted distorted 975 991 992 993 1010 P U B 14 distorted distorted 998 1011 1012 1013 1040 P G B 15 1018 1041 P G B 15 1018 1108 P G B 16 1109 P G B 16 1176 P U B 17 distorted distorted 1177 1178 1179 1206 P C B 18 distorted distorted 1184 1207 1208 1209 1237 P C B 19 distorted distorted 1214 1238 1239 1240 1270 P PO4 A 20 1275 P PO4 B 20 ---------------------------------------------------------------------------------