ID code: '5CKK' 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' --------------------------------------------------------------------------------- 11 C1' DA Y 1 beta 7 12 10 32 C1' DT Y 2 beta 28 33 31 52 C1' DC Y 3 beta 48 53 51 71 C1' DC Y 4 beta 67 72 70 90 C1' DG Y 5 beta 86 91 89 112 C1' DA Y 6 beta 108 113 111 133 C1' DT Y 7 beta 129 134 132 153 C1' DG Y 8 beta 149 154 152 175 C1' DG Y 9 beta 171 176 174 197 C1' DA Y 10 beta 193 198 196 218 C1' DT Y 11 beta 214 219 217 238 C1' DC Y 12 beta 234 239 237 257 C1' DA Y 13 beta 253 258 256 278 C1' DT Y 14 beta 274 279 277 298 C1' DA Y 15 beta 294 299 297 319 C1' DC Y 16 beta 315 320 318 338 C1' DG Y 17 beta 334 339 337 360 C1' DG Y 18 beta 356 361 359 382 C1' DT Y 19 beta 378 383 381 402 C1' DC Y 20 beta 398 403 401 421 C1' DG Y 21 beta 417 422 420 443 C1' DG Y 22 beta 439 444 442 465 C1' DA Y 23 beta 461 466 464 486 C1' DG Y 24 beta 482 487 485 508 C1' DG Y 25 beta 504 509 507 530 C1' DG Y 26 beta 526 531 529 552 C1' DG Y 27 beta 548 553 551 574 C1' DT Y 28 beta 570 575 573 594 C1' DT Y 29 beta 590 595 593 614 C1' DT Y 30 beta 610 615 613 634 C1' DG Y 31 beta 630 635 633 656 C1' DC Y 32 beta 652 657 655 675 C1' DC Y 33 beta 671 676 674 694 C1' DG Y 34 beta 690 695 693 716 C1' DT Y 35 beta 712 717 715 736 C1' DT Y 36 beta 732 737 735 756 C1' DT Y 37 beta 752 757 755 776 C1' DA Y 38 beta 772 777 775 797 C1' DA Y 39 beta 793 798 796 818 C1' DG Y 40 beta 814 819 817 840 C1' DT Y 41 beta 836 841 839 860 C1' DG Y 42 beta 856 861 859 882 C1' DC Y 43 beta 878 883 881 901 C1' DC Y 44 beta 897 902 900 922 C1' G D -6 beta 917 923 920 945 C1' C D -5 beta 940 946 943 965 C1' A D -4 beta 960 966 963 987 C1' C D -3 beta 982 988 985 1007 C1' U D -2 beta 1002 1008 1005 1027 C1' A D -1 beta 1022 1028 1025 1049 C1' G D 1 beta 1044 1050 1047 1072 C1' A D 2 beta 1067 1073 1070 1094 C1' U D 3 beta 1089 1095 1092 1114 C1' C D 4 beta 1109 1115 1112 1134 C1' G D 5 beta 1129 1135 1132 1157 C1' G D 6 beta 1152 1158 1155 1180 C1' A D 7 beta 1175 1181 1178 1202 C1' U D 8 beta 1197 1203 1200 1222 C1' G D 9 beta 1217 1223 1220 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DA Y 1 11 8 31 C2' DT Y 2 32 29 51 C2' DC Y 3 52 49 70 C2' DC Y 4 71 68 89 C2' DG Y 5 90 87 111 C2' DA Y 6 112 109 132 C2' DT Y 7 133 130 152 C2' DG Y 8 153 150 174 C2' DG Y 9 175 172 196 C2' DA Y 10 197 194 217 C2' DT Y 11 218 215 237 C2' DC Y 12 238 235 256 C2' DA Y 13 257 254 277 C2' DT Y 14 278 275 297 C2' DA Y 15 298 295 318 C2' DC Y 16 319 316 337 C2' DG Y 17 338 335 359 C2' DG Y 18 360 357 381 C2' DT Y 19 382 379 401 C2' DC Y 20 402 399 420 C2' DG Y 21 421 418 442 C2' DG Y 22 443 440 464 C2' DA Y 23 465 462 485 C2' DG Y 24 486 483 507 C2' DG Y 25 508 505 529 C2' DG Y 26 530 527 551 C2' DG Y 27 552 549 573 C2' DT Y 28 574 571 593 C2' DT Y 29 594 591 613 C2' DT Y 30 614 611 633 C2' DG Y 31 634 631 655 C2' DC Y 32 656 653 674 C2' DC Y 33 675 672 693 C2' DG Y 34 694 691 715 C2' DT Y 35 716 713 735 C2' DT Y 36 736 733 755 C2' DT Y 37 756 753 775 C2' DA Y 38 776 773 796 C2' DA Y 39 797 794 817 C2' DG Y 40 818 815 839 C2' DT Y 41 840 837 859 C2' DG Y 42 860 857 881 C2' DC Y 43 882 879 900 C2' DC Y 44 901 898 920 C2' G D -6 OK 922 918 921 943 C2' C D -5 OK 945 941 944 963 C2' A D -4 OK 965 961 964 985 C2' C D -3 OK 987 983 986 1005 C2' U D -2 OK 1007 1003 1006 1025 C2' A D -1 OK 1027 1023 1026 1047 C2' G D 1 OK 1049 1045 1048 1070 C2' A D 2 OK 1072 1068 1071 1092 C2' U D 3 OK 1094 1090 1093 1112 C2' C D 4 OK 1114 1110 1113 1132 C2' G D 5 OK 1134 1130 1133 1155 C2' G D 6 OK 1157 1153 1156 1178 C2' A D 7 OK 1180 1176 1179 1200 C2' U D 8 OK 1202 1198 1201 1220 C2' G D 9 OK 1222 1218 1221 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DA Y 1 OK 6 9 10 29 C3' DT Y 2 OK 27 30 31 49 C3' DC Y 3 OK 47 50 51 68 C3' DC Y 4 OK 66 69 70 87 C3' DG Y 5 OK 85 88 89 109 C3' DA Y 6 OK 107 110 111 130 C3' DT Y 7 OK 128 131 132 150 C3' DG Y 8 OK 148 151 152 172 C3' DG Y 9 OK 170 173 174 194 C3' DA Y 10 OK 192 195 196 215 C3' DT Y 11 OK 213 216 217 235 C3' DC Y 12 OK 233 236 237 254 C3' DA Y 13 OK 252 255 256 275 C3' DT Y 14 OK 273 276 277 295 C3' DA Y 15 OK 293 296 297 316 C3' DC Y 16 OK 314 317 318 335 C3' DG Y 17 OK 333 336 337 357 C3' DG Y 18 OK 355 358 359 379 C3' DT Y 19 OK 377 380 381 399 C3' DC Y 20 OK 397 400 401 418 C3' DG Y 21 OK 416 419 420 440 C3' DG Y 22 OK 438 441 442 462 C3' DA Y 23 OK 460 463 464 483 C3' DG Y 24 OK 481 484 485 505 C3' DG Y 25 OK 503 506 507 527 C3' DG Y 26 OK 525 528 529 549 C3' DG Y 27 OK 547 550 551 571 C3' DT Y 28 OK 569 572 573 591 C3' DT Y 29 OK 589 592 593 611 C3' DT Y 30 OK 609 612 613 631 C3' DG Y 31 OK 629 632 633 653 C3' DC Y 32 OK 651 654 655 672 C3' DC Y 33 OK 670 673 674 691 C3' DG Y 34 OK 689 692 693 713 C3' DT Y 35 OK 711 714 715 733 C3' DT Y 36 OK 731 734 735 753 C3' DT Y 37 OK 751 754 755 773 C3' DA Y 38 OK 771 774 775 794 C3' DA Y 39 OK 792 795 796 815 C3' DG Y 40 OK 813 816 817 837 C3' DT Y 41 OK 835 838 839 857 C3' DG Y 42 OK 855 858 859 879 C3' DC Y 43 OK 877 880 881 898 C3' DC Y 44 OK 896 899 900 918 C3' G D -6 OK 916 919 920 941 C3' C D -5 OK 939 942 943 961 C3' A D -4 OK 959 962 963 983 C3' C D -3 OK 981 984 985 1003 C3' U D -2 OK 1001 1004 1005 1023 C3' A D -1 OK 1021 1024 1025 1045 C3' G D 1 OK 1043 1046 1047 1068 C3' A D 2 OK 1066 1069 1070 1090 C3' U D 3 OK 1088 1091 1092 1110 C3' C D 4 OK 1108 1111 1112 1130 C3' G D 5 OK 1128 1131 1132 1153 C3' G D 6 OK 1151 1154 1155 1176 C3' A D 7 OK 1174 1177 1178 1198 C3' U D 8 OK 1196 1199 1200 1218 C3' G D 9 OK 1216 1219 1220 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DA Y 1 OK 8 5 7 27 C4' DT Y 2 OK 29 26 28 47 C4' DC Y 3 OK 49 46 48 66 C4' DC Y 4 OK 68 65 67 85 C4' DG Y 5 OK 87 84 86 107 C4' DA Y 6 OK 109 106 108 128 C4' DT Y 7 OK 130 127 129 148 C4' DG Y 8 OK 150 147 149 170 C4' DG Y 9 OK 172 169 171 192 C4' DA Y 10 OK 194 191 193 213 C4' DT Y 11 OK 215 212 214 233 C4' DC Y 12 OK 235 232 234 252 C4' DA Y 13 OK 254 251 253 273 C4' DT Y 14 OK 275 272 274 293 C4' DA Y 15 OK 295 292 294 314 C4' DC Y 16 OK 316 313 315 333 C4' DG Y 17 OK 335 332 334 355 C4' DG Y 18 OK 357 354 356 377 C4' DT Y 19 OK 379 376 378 397 C4' DC Y 20 OK 399 396 398 416 C4' DG Y 21 OK 418 415 417 438 C4' DG Y 22 OK 440 437 439 460 C4' DA Y 23 OK 462 459 461 481 C4' DG Y 24 OK 483 480 482 503 C4' DG Y 25 OK 505 502 504 525 C4' DG Y 26 OK 527 524 526 547 C4' DG Y 27 OK 549 546 548 569 C4' DT Y 28 OK 571 568 570 589 C4' DT Y 29 OK 591 588 590 609 C4' DT Y 30 OK 611 608 610 629 C4' DG Y 31 OK 631 628 630 651 C4' DC Y 32 OK 653 650 652 670 C4' DC Y 33 OK 672 669 671 689 C4' DG Y 34 OK 691 688 690 711 C4' DT Y 35 OK 713 710 712 731 C4' DT Y 36 OK 733 730 732 751 C4' DT Y 37 OK 753 750 752 771 C4' DA Y 38 OK 773 770 772 792 C4' DA Y 39 OK 794 791 793 813 C4' DG Y 40 OK 815 812 814 835 C4' DT Y 41 OK 837 834 836 855 C4' DG Y 42 OK 857 854 856 877 C4' DC Y 43 OK 879 876 878 896 C4' DC Y 44 OK 898 895 897 916 C4' G D -6 OK 918 915 917 939 C4' C D -5 OK 941 938 940 959 C4' A D -4 OK 961 958 960 981 C4' C D -3 OK 983 980 982 1001 C4' U D -2 OK 1003 1000 1002 1021 C4' A D -1 OK 1023 1020 1022 1043 C4' G D 1 OK 1045 1042 1044 1066 C4' A D 2 OK 1068 1065 1067 1088 C4' U D 3 OK 1090 1087 1089 1108 C4' C D 4 OK 1110 1107 1109 1128 C4' G D 5 OK 1130 1127 1129 1151 C4' G D 6 OK 1153 1150 1152 1174 C4' A D 7 OK 1176 1173 1175 1196 C4' U D 8 OK 1198 1195 1197 1216 C4' G D 9 OK 1218 1215 1217 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DA Y 1 4 6 26 C5' DT Y 2 25 27 46 C5' DC Y 3 45 47 65 C5' DC Y 4 64 66 84 C5' DG Y 5 83 85 106 C5' DA Y 6 105 107 127 C5' DT Y 7 126 128 147 C5' DG Y 8 146 148 169 C5' DG Y 9 168 170 191 C5' DA Y 10 190 192 212 C5' DT Y 11 211 213 232 C5' DC Y 12 231 233 251 C5' DA Y 13 250 252 272 C5' DT Y 14 271 273 292 C5' DA Y 15 291 293 313 C5' DC Y 16 312 314 332 C5' DG Y 17 331 333 354 C5' DG Y 18 353 355 376 C5' DT Y 19 375 377 396 C5' DC Y 20 395 397 415 C5' DG Y 21 414 416 437 C5' DG Y 22 436 438 459 C5' DA Y 23 458 460 480 C5' DG Y 24 479 481 502 C5' DG Y 25 501 503 524 C5' DG Y 26 523 525 546 C5' DG Y 27 545 547 568 C5' DT Y 28 567 569 588 C5' DT Y 29 587 589 608 C5' DT Y 30 607 609 628 C5' DG Y 31 627 629 650 C5' DC Y 32 649 651 669 C5' DC Y 33 668 670 688 C5' DG Y 34 687 689 710 C5' DT Y 35 709 711 730 C5' DT Y 36 729 731 750 C5' DT Y 37 749 751 770 C5' DA Y 38 769 771 791 C5' DA Y 39 790 792 812 C5' DG Y 40 811 813 834 C5' DT Y 41 833 835 854 C5' DG Y 42 853 855 876 C5' DC Y 43 875 877 895 C5' DC Y 44 894 896 915 C5' G D -6 914 916 938 C5' C D -5 937 939 958 C5' A D -4 957 959 980 C5' C D -3 979 981 1000 C5' U D -2 999 1001 1020 C5' A D -1 1019 1021 1042 C5' G D 1 1041 1043 1065 C5' A D 2 1064 1066 1087 C5' U D 3 1086 1088 1107 C5' C D 4 1106 1108 1127 C5' G D 5 1126 1128 1150 C5' G D 6 1149 1151 1173 C5' A D 7 1172 1174 1195 C5' U D 8 1194 1196 1215 C5' G D 9 1214 1216 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DA Y 1 distorted distorted 2 3 4 22 P DT Y 2 distorted distorted 9 23 24 25 42 P DC Y 3 distorted distorted 30 43 44 45 61 P DC Y 4 distorted distorted 50 62 63 64 80 P DG Y 5 distorted distorted 69 81 82 83 102 P DA Y 6 distorted distorted 88 103 104 105 123 P DT Y 7 distorted distorted 110 124 125 126 143 P DG Y 8 distorted distorted 131 144 145 146 165 P DG Y 9 distorted distorted 151 166 167 168 187 P DA Y 10 distorted distorted 173 188 189 190 208 P DT Y 11 distorted distorted 195 209 210 211 228 P DC Y 12 distorted distorted 216 229 230 231 247 P DA Y 13 distorted distorted 236 248 249 250 268 P DT Y 14 distorted distorted 255 269 270 271 288 P DA Y 15 distorted distorted 276 289 290 291 309 P DC Y 16 distorted distorted 296 310 311 312 328 P DG Y 17 distorted distorted 317 329 330 331 350 P DG Y 18 distorted distorted 336 351 352 353 372 P DT Y 19 distorted distorted 358 373 374 375 392 P DC Y 20 distorted distorted 380 393 394 395 411 P DG Y 21 distorted distorted 400 412 413 414 433 P DG Y 22 distorted distorted 419 434 435 436 455 P DA Y 23 distorted distorted 441 456 457 458 476 P DG Y 24 distorted distorted 463 477 478 479 498 P DG Y 25 distorted distorted 484 499 500 501 520 P DG Y 26 distorted distorted 506 521 522 523 542 P DG Y 27 distorted distorted 528 543 544 545 564 P DT Y 28 distorted distorted 550 565 566 567 584 P DT Y 29 distorted distorted 572 585 586 587 604 P DT Y 30 distorted distorted 592 605 606 607 624 P DG Y 31 distorted distorted 612 625 626 627 646 P DC Y 32 distorted distorted 632 647 648 649 665 P DC Y 33 distorted distorted 654 666 667 668 684 P DG Y 34 distorted distorted 673 685 686 687 706 P DT Y 35 distorted distorted 692 707 708 709 726 P DT Y 36 distorted distorted 714 727 728 729 746 P DT Y 37 distorted distorted 734 747 748 749 766 P DA Y 38 distorted distorted 754 767 768 769 787 P DA Y 39 distorted distorted 774 788 789 790 808 P DG Y 40 distorted distorted 795 809 810 811 830 P DT Y 41 distorted distorted 816 831 832 833 850 P DG Y 42 distorted distorted 838 851 852 853 872 P DC Y 43 distorted distorted 858 873 874 875 891 P DC Y 44 distorted distorted 880 892 893 894 911 P G D -6 distorted distorted 912 913 914 934 P C D -5 distorted distorted 919 935 936 937 954 P A D -4 distorted distorted 942 955 956 957 976 P C D -3 distorted distorted 962 977 978 979 996 P U D -2 distorted distorted 984 997 998 999 1016 P A D -1 distorted distorted 1004 1017 1018 1019 1038 P G D 1 distorted distorted 1024 1039 1040 1041 1061 P A D 2 distorted distorted 1046 1062 1063 1064 1083 P U D 3 distorted distorted 1069 1084 1085 1086 1103 P C D 4 distorted distorted 1091 1104 1105 1106 1123 P G D 5 distorted distorted 1111 1124 1125 1126 1146 P G D 6 distorted distorted 1131 1147 1148 1149 1169 P A D 7 distorted distorted 1154 1170 1171 1172 1191 P U D 8 distorted distorted 1177 1192 1193 1194 1211 P G D 9 distorted distorted 1199 1212 1213 1214 ---------------------------------------------------------------------------------