ID code: '2KU0' 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' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' A A 6 alpha beta 174 196 180 177 212 C1' A A 7 alpha beta 207 229 213 210 245 C1' C A 8 alpha beta 240 260 246 243 276 C1' U A 9 alpha beta 271 291 277 274 306 C1' A A 10 alpha beta 301 323 307 304 339 C1' C A 11 alpha beta 334 354 340 337 370 C1' U A 12 alpha beta 365 385 371 368 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' U A 14 alpha beta 429 449 435 432 464 C1' C A 15 alpha beta 459 479 465 462 495 C1' U A 16 alpha beta 490 510 496 493 525 C1' U A 17 alpha beta 520 540 526 523 555 C1' C A 18 alpha beta 550 570 556 553 586 C1' C A 19 alpha beta 581 601 587 584 617 C1' U A 20 alpha beta 612 632 618 615 647 C1' U A 21 alpha beta 642 662 648 645 677 C1' C A 22 alpha beta 672 692 678 675 708 C1' G A 23 alpha beta 703 726 709 706 742 C1' G A 24 alpha beta 737 760 743 740 776 C1' G A 25 alpha beta 771 794 777 774 810 C1' U A 26 alpha beta 805 825 811 808 840 C1' C A 27 alpha beta 835 855 841 838 871 C1' G A 28 alpha beta 866 889 872 869 905 C1' U A 29 alpha beta 900 920 906 903 935 C1' G A 30 alpha beta 930 953 936 933 969 C1' C A 31 alpha beta 964 984 970 967 1000 C1' A A 32 alpha beta 995 1017 1001 998 1033 C1' G A 33 alpha beta 1028 1051 1034 1031 1067 C1' C A 34 alpha beta 1062 1082 1068 1065 1098 C1' C A 35 alpha beta 1093 1113 1099 1096 1129 C1' U A 36 alpha beta 1124 1144 1130 1127 1159 C1' C A 37 alpha beta 1154 1174 1160 1157 1190 C1' C A 38 alpha beta 1185 1206 1191 1188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' G A 5 OK OK 145 141 161 144 177 C2' A A 6 OK OK 179 175 194 178 210 C2' A A 7 OK OK 212 208 227 211 243 C2' C A 8 OK OK 245 241 258 244 274 C2' U A 9 OK OK 276 272 289 275 304 C2' A A 10 OK OK 306 302 321 305 337 C2' C A 11 OK OK 339 335 352 338 368 C2' U A 12 OK OK 370 366 383 369 398 C2' G A 13 OK OK 400 396 416 399 432 C2' U A 14 OK OK 434 430 447 433 462 C2' C A 15 OK OK 464 460 477 463 493 C2' U A 16 OK OK 495 491 508 494 523 C2' U A 17 OK OK 525 521 538 524 553 C2' C A 18 OK OK 555 551 568 554 584 C2' C A 19 OK OK 586 582 599 585 615 C2' U A 20 OK OK 617 613 630 616 645 C2' U A 21 OK OK 647 643 660 646 675 C2' C A 22 OK OK 677 673 690 676 706 C2' G A 23 OK OK 708 704 724 707 740 C2' G A 24 OK OK 742 738 758 741 774 C2' G A 25 OK OK 776 772 792 775 808 C2' U A 26 OK OK 810 806 823 809 838 C2' C A 27 OK OK 840 836 853 839 869 C2' G A 28 OK OK 871 867 887 870 903 C2' U A 29 OK OK 905 901 918 904 933 C2' G A 30 OK OK 935 931 951 934 967 C2' C A 31 OK OK 969 965 982 968 998 C2' A A 32 OK OK 1000 996 1015 999 1031 C2' G A 33 OK OK 1033 1029 1049 1032 1065 C2' C A 34 OK OK 1067 1063 1080 1066 1096 C2' C A 35 OK OK 1098 1094 1111 1097 1127 C2' U A 36 OK OK 1129 1125 1142 1128 1157 C2' C A 37 OK OK 1159 1155 1172 1158 1188 C2' C A 38 OK OK 1190 1186 1204 1189 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' G A 5 OK OK 139 160 142 143 175 C3' A A 6 OK OK 173 193 176 177 208 C3' A A 7 OK OK 206 226 209 210 241 C3' C A 8 OK OK 239 257 242 243 272 C3' U A 9 OK OK 270 288 273 274 302 C3' A A 10 OK OK 300 320 303 304 335 C3' C A 11 OK OK 333 351 336 337 366 C3' U A 12 OK OK 364 382 367 368 396 C3' G A 13 OK OK 394 415 397 398 430 C3' U A 14 OK OK 428 446 431 432 460 C3' C A 15 OK OK 458 476 461 462 491 C3' U A 16 OK OK 489 507 492 493 521 C3' U A 17 OK OK 519 537 522 523 551 C3' C A 18 OK OK 549 567 552 553 582 C3' C A 19 OK OK 580 598 583 584 613 C3' U A 20 OK OK 611 629 614 615 643 C3' U A 21 OK OK 641 659 644 645 673 C3' C A 22 OK OK 671 689 674 675 704 C3' G A 23 OK OK 702 723 705 706 738 C3' G A 24 OK OK 736 757 739 740 772 C3' G A 25 OK OK 770 791 773 774 806 C3' U A 26 OK OK 804 822 807 808 836 C3' C A 27 OK OK 834 852 837 838 867 C3' G A 28 OK OK 865 886 868 869 901 C3' U A 29 OK OK 899 917 902 903 931 C3' G A 30 OK OK 929 950 932 933 965 C3' C A 31 OK OK 963 981 966 967 996 C3' A A 32 OK OK 994 1014 997 998 1029 C3' G A 33 OK OK 1027 1048 1030 1031 1063 C3' C A 34 OK OK 1061 1079 1064 1065 1094 C3' C A 35 OK OK 1092 1110 1095 1096 1125 C3' U A 36 OK OK 1123 1141 1126 1127 1155 C3' C A 37 OK OK 1153 1171 1156 1157 1186 C3' C A 38 OK OK 1184 1202 1187 1188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' G A 5 OK OK 141 159 138 140 173 C4' A A 6 OK OK 175 192 172 174 206 C4' A A 7 OK OK 208 225 205 207 239 C4' C A 8 OK OK 241 256 238 240 270 C4' U A 9 OK OK 272 287 269 271 300 C4' A A 10 OK OK 302 319 299 301 333 C4' C A 11 OK OK 335 350 332 334 364 C4' U A 12 OK OK 366 381 363 365 394 C4' G A 13 OK OK 396 414 393 395 428 C4' U A 14 OK OK 430 445 427 429 458 C4' C A 15 OK OK 460 475 457 459 489 C4' U A 16 OK OK 491 506 488 490 519 C4' U A 17 OK OK 521 536 518 520 549 C4' C A 18 OK OK 551 566 548 550 580 C4' C A 19 OK OK 582 597 579 581 611 C4' U A 20 OK OK 613 628 610 612 641 C4' U A 21 OK OK 643 658 640 642 671 C4' C A 22 OK OK 673 688 670 672 702 C4' G A 23 OK OK 704 722 701 703 736 C4' G A 24 OK OK 738 756 735 737 770 C4' G A 25 OK OK 772 790 769 771 804 C4' U A 26 OK OK 806 821 803 805 834 C4' C A 27 OK OK 836 851 833 835 865 C4' G A 28 OK OK 867 885 864 866 899 C4' U A 29 OK OK 901 916 898 900 929 C4' G A 30 OK OK 931 949 928 930 963 C4' C A 31 OK OK 965 980 962 964 994 C4' A A 32 OK OK 996 1013 993 995 1027 C4' G A 33 OK OK 1029 1047 1026 1028 1061 C4' C A 34 OK OK 1063 1078 1060 1062 1092 C4' C A 35 OK OK 1094 1109 1091 1093 1123 C4' U A 36 OK OK 1125 1140 1122 1124 1153 C4' C A 37 OK OK 1155 1170 1152 1154 1184 C4' C A 38 OK OK 1186 1201 1183 1185 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' G A 5 OK OK 137 157 158 139 172 C5' A A 6 OK OK 171 190 191 173 205 C5' A A 7 OK OK 204 223 224 206 238 C5' C A 8 OK OK 237 254 255 239 269 C5' U A 9 OK OK 268 285 286 270 299 C5' A A 10 OK OK 298 317 318 300 332 C5' C A 11 OK OK 331 348 349 333 363 C5' U A 12 OK OK 362 379 380 364 393 C5' G A 13 OK OK 392 412 413 394 427 C5' U A 14 OK OK 426 443 444 428 457 C5' C A 15 OK OK 456 473 474 458 488 C5' U A 16 OK OK 487 504 505 489 518 C5' U A 17 OK OK 517 534 535 519 548 C5' C A 18 OK OK 547 564 565 549 579 C5' C A 19 OK OK 578 595 596 580 610 C5' U A 20 OK OK 609 626 627 611 640 C5' U A 21 OK OK 639 656 657 641 670 C5' C A 22 OK OK 669 686 687 671 701 C5' G A 23 OK OK 700 720 721 702 735 C5' G A 24 OK OK 734 754 755 736 769 C5' G A 25 OK OK 768 788 789 770 803 C5' U A 26 OK OK 802 819 820 804 833 C5' C A 27 OK OK 832 849 850 834 864 C5' G A 28 OK OK 863 883 884 865 898 C5' U A 29 OK OK 897 914 915 899 928 C5' G A 30 OK OK 927 947 948 929 962 C5' C A 31 OK OK 961 978 979 963 993 C5' A A 32 OK OK 992 1011 1012 994 1026 C5' G A 33 OK OK 1025 1045 1046 1027 1060 C5' C A 34 OK OK 1059 1076 1077 1061 1091 C5' C A 35 OK OK 1090 1107 1108 1092 1122 C5' U A 36 OK OK 1121 1138 1139 1123 1152 C5' C A 37 OK OK 1151 1168 1169 1153 1183 C5' C A 38 OK OK 1182 1199 1200 1184 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P G A 5 distorted distorted 108 135 136 137 168 P A A 6 distorted distorted 142 169 170 171 201 P A A 7 distorted distorted 176 202 203 204 234 P C A 8 distorted distorted 209 235 236 237 265 P U A 9 distorted distorted 242 266 267 268 295 P A A 10 distorted distorted 273 296 297 298 328 P C A 11 distorted distorted 303 329 330 331 359 P U A 12 distorted distorted 336 360 361 362 389 P G A 13 distorted distorted 367 390 391 392 423 P U A 14 distorted distorted 397 424 425 426 453 P C A 15 distorted distorted 431 454 455 456 484 P U A 16 distorted distorted 461 485 486 487 514 P U A 17 distorted distorted 492 515 516 517 544 P C A 18 distorted distorted 522 545 546 547 575 P C A 19 distorted distorted 552 576 577 578 606 P U A 20 distorted distorted 583 607 608 609 636 P U A 21 distorted distorted 614 637 638 639 666 P C A 22 distorted distorted 644 667 668 669 697 P G A 23 distorted distorted 674 698 699 700 731 P G A 24 distorted distorted 705 732 733 734 765 P G A 25 distorted distorted 739 766 767 768 799 P U A 26 distorted distorted 773 800 801 802 829 P C A 27 distorted distorted 807 830 831 832 860 P G A 28 distorted distorted 837 861 862 863 894 P U A 29 distorted distorted 868 895 896 897 924 P G A 30 distorted distorted 902 925 926 927 958 P C A 31 distorted distorted 932 959 960 961 989 P A A 32 distorted distorted 966 990 991 992 1022 P G A 33 distorted distorted 997 1023 1024 1025 1056 P C A 34 distorted distorted 1030 1057 1058 1059 1087 P C A 35 distorted distorted 1064 1088 1089 1090 1118 P U A 36 distorted distorted 1095 1119 1120 1121 1148 P C A 37 distorted distorted 1126 1149 1150 1151 1179 P C A 38 distorted distorted 1156 1180 1181 1182 ---------------------------------------------------------------------------------