ID code: '4ENC' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 beta 7 13 10 35 C1' G A 2 beta 30 36 33 58 C1' G A 3 beta 53 59 56 81 C1' C A 4 beta 76 82 79 101 C1' G A 5 beta 96 102 99 124 C1' A A 6 beta 119 125 122 146 C1' U A 7 beta 141 147 144 166 C1' G A 8 beta 161 167 164 189 C1' A A 9 beta 184 190 187 211 C1' G A 10 beta 206 212 209 234 C1' G A 11 beta 229 235 232 257 C1' C A 12 beta 252 258 255 277 C1' C A 13 beta 272 278 275 297 C1' C A 14 beta 292 298 295 317 C1' G A 15 beta 312 318 315 340 C1' C A 16 beta 335 341 338 360 C1' C A 17 beta 355 361 358 380 C1' C A 18 beta 375 381 378 400 C1' A A 19 beta 395 401 398 422 C1' A A 20 beta 417 423 420 444 C1' A A 21 beta 439 445 442 466 C1' C A 22 beta 461 467 464 486 C1' U A 23 beta 481 487 484 506 C1' G A 24 beta 501 507 504 529 C1' C A 25 beta 524 530 527 549 C1' C A 26 beta 544 550 547 569 C1' C A 27 beta 564 570 567 589 C1' U A 28 beta 584 590 587 609 C1' G A 29 beta 604 610 607 632 C1' A A 30 beta 627 633 630 654 C1' A A 31 beta 649 655 652 676 C1' A A 32 beta 671 677 674 698 C1' A A 33 beta 693 699 696 720 C1' G A 34 beta 715 721 718 743 C1' G A 35 beta 738 744 741 766 C1' G A 36 beta 761 767 764 789 C1' C A 37 beta 784 790 787 809 C1' U A 38 beta 804 810 807 829 C1' G A 39 beta 824 830 827 852 C1' A A 40 beta 847 853 850 874 C1' U A 41 beta 869 875 872 894 C1' G A 42 beta 889 895 892 917 C1' G A 43 beta 912 918 915 940 C1' C A 44 beta 935 941 938 960 C1' C A 45 beta 955 961 958 980 C1' U A 46 beta 975 981 978 1000 C1' C A 47 beta 995 1001 998 1020 C1' U A 48 beta 1015 1021 1018 1040 C1' A A 49 beta 1035 1041 1038 1062 C1' C A 50 beta 1057 1063 1060 1082 C1' U A 51 beta 1077 1083 1080 1102 C1' G A 52 beta 1097 1103 1100 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK 12 8 11 33 C2' G A 2 OK 35 31 34 56 C2' G A 3 OK 58 54 57 79 C2' C A 4 OK 81 77 80 99 C2' G A 5 OK 101 97 100 122 C2' A A 6 OK 124 120 123 144 C2' U A 7 OK 146 142 145 164 C2' G A 8 OK 166 162 165 187 C2' A A 9 OK 189 185 188 209 C2' G A 10 OK 211 207 210 232 C2' G A 11 OK 234 230 233 255 C2' C A 12 OK 257 253 256 275 C2' C A 13 OK 277 273 276 295 C2' C A 14 OK 297 293 296 315 C2' G A 15 OK 317 313 316 338 C2' C A 16 OK 340 336 339 358 C2' C A 17 OK 360 356 359 378 C2' C A 18 OK 380 376 379 398 C2' A A 19 OK 400 396 399 420 C2' A A 20 OK 422 418 421 442 C2' A A 21 OK 444 440 443 464 C2' C A 22 OK 466 462 465 484 C2' U A 23 OK 486 482 485 504 C2' G A 24 OK 506 502 505 527 C2' C A 25 OK 529 525 528 547 C2' C A 26 OK 549 545 548 567 C2' C A 27 OK 569 565 568 587 C2' U A 28 OK 589 585 588 607 C2' G A 29 OK 609 605 608 630 C2' A A 30 OK 632 628 631 652 C2' A A 31 OK 654 650 653 674 C2' A A 32 OK 676 672 675 696 C2' A A 33 OK 698 694 697 718 C2' G A 34 OK 720 716 719 741 C2' G A 35 OK 743 739 742 764 C2' G A 36 OK 766 762 765 787 C2' C A 37 OK 789 785 788 807 C2' U A 38 OK 809 805 808 827 C2' G A 39 OK 829 825 828 850 C2' A A 40 OK 852 848 851 872 C2' U A 41 OK 874 870 873 892 C2' G A 42 OK 894 890 893 915 C2' G A 43 OK 917 913 916 938 C2' C A 44 OK 940 936 939 958 C2' C A 45 OK 960 956 959 978 C2' U A 46 OK 980 976 979 998 C2' C A 47 OK 1000 996 999 1018 C2' U A 48 OK 1020 1016 1019 1038 C2' A A 49 OK 1040 1036 1039 1060 C2' C A 50 OK 1062 1058 1061 1080 C2' U A 51 OK 1082 1078 1081 1100 C2' G A 52 OK 1102 1098 1101 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 31 C3' G A 2 OK 29 32 33 54 C3' G A 3 OK 52 55 56 77 C3' C A 4 OK 75 78 79 97 C3' G A 5 OK 95 98 99 120 C3' A A 6 OK 118 121 122 142 C3' U A 7 OK 140 143 144 162 C3' G A 8 OK 160 163 164 185 C3' A A 9 OK 183 186 187 207 C3' G A 10 OK 205 208 209 230 C3' G A 11 OK 228 231 232 253 C3' C A 12 OK 251 254 255 273 C3' C A 13 OK 271 274 275 293 C3' C A 14 OK 291 294 295 313 C3' G A 15 OK 311 314 315 336 C3' C A 16 OK 334 337 338 356 C3' C A 17 OK 354 357 358 376 C3' C A 18 OK 374 377 378 396 C3' A A 19 OK 394 397 398 418 C3' A A 20 OK 416 419 420 440 C3' A A 21 OK 438 441 442 462 C3' C A 22 OK 460 463 464 482 C3' U A 23 OK 480 483 484 502 C3' G A 24 OK 500 503 504 525 C3' C A 25 OK 523 526 527 545 C3' C A 26 OK 543 546 547 565 C3' C A 27 OK 563 566 567 585 C3' U A 28 OK 583 586 587 605 C3' G A 29 OK 603 606 607 628 C3' A A 30 OK 626 629 630 650 C3' A A 31 OK 648 651 652 672 C3' A A 32 OK 670 673 674 694 C3' A A 33 OK 692 695 696 716 C3' G A 34 OK 714 717 718 739 C3' G A 35 OK 737 740 741 762 C3' G A 36 OK 760 763 764 785 C3' C A 37 OK 783 786 787 805 C3' U A 38 OK 803 806 807 825 C3' G A 39 OK 823 826 827 848 C3' A A 40 OK 846 849 850 870 C3' U A 41 OK 868 871 872 890 C3' G A 42 OK 888 891 892 913 C3' G A 43 OK 911 914 915 936 C3' C A 44 OK 934 937 938 956 C3' C A 45 OK 954 957 958 976 C3' U A 46 OK 974 977 978 996 C3' C A 47 OK 994 997 998 1016 C3' U A 48 OK 1014 1017 1018 1036 C3' A A 49 OK 1034 1037 1038 1058 C3' C A 50 OK 1056 1059 1060 1078 C3' U A 51 OK 1076 1079 1080 1098 C3' G A 52 OK 1096 1099 1100 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 29 C4' G A 2 OK 31 28 30 52 C4' G A 3 OK 54 51 53 75 C4' C A 4 OK 77 74 76 95 C4' G A 5 OK 97 94 96 118 C4' A A 6 OK 120 117 119 140 C4' U A 7 OK 142 139 141 160 C4' G A 8 OK 162 159 161 183 C4' A A 9 OK 185 182 184 205 C4' G A 10 OK 207 204 206 228 C4' G A 11 OK 230 227 229 251 C4' C A 12 OK 253 250 252 271 C4' C A 13 OK 273 270 272 291 C4' C A 14 OK 293 290 292 311 C4' G A 15 OK 313 310 312 334 C4' C A 16 OK 336 333 335 354 C4' C A 17 OK 356 353 355 374 C4' C A 18 OK 376 373 375 394 C4' A A 19 OK 396 393 395 416 C4' A A 20 OK 418 415 417 438 C4' A A 21 OK 440 437 439 460 C4' C A 22 OK 462 459 461 480 C4' U A 23 OK 482 479 481 500 C4' G A 24 OK 502 499 501 523 C4' C A 25 OK 525 522 524 543 C4' C A 26 OK 545 542 544 563 C4' C A 27 OK 565 562 564 583 C4' U A 28 OK 585 582 584 603 C4' G A 29 OK 605 602 604 626 C4' A A 30 OK 628 625 627 648 C4' A A 31 OK 650 647 649 670 C4' A A 32 OK 672 669 671 692 C4' A A 33 OK 694 691 693 714 C4' G A 34 OK 716 713 715 737 C4' G A 35 OK 739 736 738 760 C4' G A 36 OK 762 759 761 783 C4' C A 37 OK 785 782 784 803 C4' U A 38 OK 805 802 804 823 C4' G A 39 OK 825 822 824 846 C4' A A 40 OK 848 845 847 868 C4' U A 41 OK 870 867 869 888 C4' G A 42 OK 890 887 889 911 C4' G A 43 OK 913 910 912 934 C4' C A 44 OK 936 933 935 954 C4' C A 45 OK 956 953 955 974 C4' U A 46 OK 976 973 975 994 C4' C A 47 OK 996 993 995 1014 C4' U A 48 OK 1016 1013 1015 1034 C4' A A 49 OK 1036 1033 1035 1056 C4' C A 50 OK 1058 1055 1057 1076 C4' U A 51 OK 1078 1075 1077 1096 C4' G A 52 OK 1098 1095 1097 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 28 C5' G A 2 27 29 51 C5' G A 3 50 52 74 C5' C A 4 73 75 94 C5' G A 5 93 95 117 C5' A A 6 116 118 139 C5' U A 7 138 140 159 C5' G A 8 158 160 182 C5' A A 9 181 183 204 C5' G A 10 203 205 227 C5' G A 11 226 228 250 C5' C A 12 249 251 270 C5' C A 13 269 271 290 C5' C A 14 289 291 310 C5' G A 15 309 311 333 C5' C A 16 332 334 353 C5' C A 17 352 354 373 C5' C A 18 372 374 393 C5' A A 19 392 394 415 C5' A A 20 414 416 437 C5' A A 21 436 438 459 C5' C A 22 458 460 479 C5' U A 23 478 480 499 C5' G A 24 498 500 522 C5' C A 25 521 523 542 C5' C A 26 541 543 562 C5' C A 27 561 563 582 C5' U A 28 581 583 602 C5' G A 29 601 603 625 C5' A A 30 624 626 647 C5' A A 31 646 648 669 C5' A A 32 668 670 691 C5' A A 33 690 692 713 C5' G A 34 712 714 736 C5' G A 35 735 737 759 C5' G A 36 758 760 782 C5' C A 37 781 783 802 C5' U A 38 801 803 822 C5' G A 39 821 823 845 C5' A A 40 844 846 867 C5' U A 41 866 868 887 C5' G A 42 886 888 910 C5' G A 43 909 911 933 C5' C A 44 932 934 953 C5' C A 45 952 954 973 C5' U A 46 972 974 993 C5' C A 47 992 994 1013 C5' U A 48 1012 1014 1033 C5' A A 49 1032 1034 1055 C5' C A 50 1054 1056 1075 C5' U A 51 1074 1076 1095 C5' G A 52 1094 1096 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 24 P G A 2 distorted distorted 9 25 26 27 47 P G A 3 distorted distorted 32 48 49 50 70 P C A 4 distorted distorted 55 71 72 73 90 P G A 5 distorted distorted 78 91 92 93 113 P A A 6 distorted distorted 98 114 115 116 135 P U A 7 distorted distorted 121 136 137 138 155 P G A 8 distorted distorted 143 156 157 158 178 P A A 9 distorted distorted 163 179 180 181 200 P G A 10 distorted distorted 186 201 202 203 223 P G A 11 distorted distorted 208 224 225 226 246 P C A 12 distorted distorted 231 247 248 249 266 P C A 13 distorted distorted 254 267 268 269 286 P C A 14 distorted distorted 274 287 288 289 306 P G A 15 distorted distorted 294 307 308 309 329 P C A 16 distorted distorted 314 330 331 332 349 P C A 17 distorted distorted 337 350 351 352 369 P C A 18 distorted distorted 357 370 371 372 389 P A A 19 distorted distorted 377 390 391 392 411 P A A 20 distorted distorted 397 412 413 414 433 P A A 21 distorted distorted 419 434 435 436 455 P C A 22 distorted distorted 441 456 457 458 475 P U A 23 distorted distorted 463 476 477 478 495 P G A 24 distorted distorted 483 496 497 498 518 P C A 25 distorted distorted 503 519 520 521 538 P C A 26 distorted distorted 526 539 540 541 558 P C A 27 distorted distorted 546 559 560 561 578 P U A 28 distorted distorted 566 579 580 581 598 P G A 29 distorted distorted 586 599 600 601 621 P A A 30 distorted distorted 606 622 623 624 643 P A A 31 distorted distorted 629 644 645 646 665 P A A 32 distorted distorted 651 666 667 668 687 P A A 33 distorted distorted 673 688 689 690 709 P G A 34 distorted distorted 695 710 711 712 732 P G A 35 distorted distorted 717 733 734 735 755 P G A 36 distorted distorted 740 756 757 758 778 P C A 37 distorted distorted 763 779 780 781 798 P U A 38 distorted distorted 786 799 800 801 818 P G A 39 distorted distorted 806 819 820 821 841 P A A 40 distorted distorted 826 842 843 844 863 P U A 41 distorted distorted 849 864 865 866 883 P G A 42 distorted distorted 871 884 885 886 906 P G A 43 distorted distorted 891 907 908 909 929 P C A 44 distorted distorted 914 930 931 932 949 P C A 45 distorted distorted 937 950 951 952 969 P U A 46 distorted distorted 957 970 971 972 989 P C A 47 distorted distorted 977 990 991 992 1009 P U A 48 distorted distorted 997 1010 1011 1012 1029 P A A 49 distorted distorted 1017 1030 1031 1032 1051 P C A 50 distorted distorted 1037 1052 1053 1054 1071 P U A 51 distorted distorted 1059 1072 1073 1074 1091 P G A 52 distorted distorted 1079 1092 1093 1094 ---------------------------------------------------------------------------------