ID code: '2KPV' 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' U A 6 alpha beta 174 194 180 177 209 C1' A A 7 alpha beta 204 226 210 207 242 C1' G A 8 alpha beta 237 260 243 240 276 C1' U A 9 alpha beta 271 291 277 274 306 C1' A A 10 alpha beta 301 323 307 304 339 C1' G A 11 alpha beta 334 357 340 337 373 C1' G A 12 alpha beta 368 391 374 371 407 C1' U A 13 alpha beta 402 422 408 405 437 C1' C A 14 alpha beta 432 452 438 435 468 C1' G A 15 alpha beta 463 486 469 466 502 C1' A A 16 alpha beta 497 519 503 500 535 C1' A A 17 alpha beta 530 552 536 533 568 C1' A A 18 alpha beta 563 585 569 566 601 C1' G A 19 alpha beta 596 619 602 599 635 C1' A A 20 alpha beta 630 652 636 633 668 C1' C A 21 alpha beta 663 683 669 666 699 C1' C A 22 alpha beta 694 714 700 697 730 C1' G A 23 alpha beta 725 748 731 728 764 C1' U A 24 alpha beta 759 779 765 762 794 C1' U A 25 alpha beta 789 809 795 792 824 C1' C A 26 alpha beta 819 839 825 822 855 C1' U A 27 alpha beta 850 870 856 853 885 C1' A A 28 alpha beta 880 902 886 883 918 C1' C A 29 alpha beta 913 933 919 916 949 C1' A A 30 alpha beta 944 966 950 947 982 C1' C A 31 alpha beta 977 997 983 980 1013 C1' U A 32 alpha beta 1008 1028 1014 1011 1043 C1' C A 33 alpha beta 1038 1058 1044 1041 1074 C1' C A 34 alpha beta 1069 1090 1075 1072 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 6 OK OK 179 175 192 178 207 C2' A A 7 OK OK 209 205 224 208 240 C2' G A 8 OK OK 242 238 258 241 274 C2' U A 9 OK OK 276 272 289 275 304 C2' A A 10 OK OK 306 302 321 305 337 C2' G A 11 OK OK 339 335 355 338 371 C2' G A 12 OK OK 373 369 389 372 405 C2' U A 13 OK OK 407 403 420 406 435 C2' C A 14 OK OK 437 433 450 436 466 C2' G A 15 OK OK 468 464 484 467 500 C2' A A 16 OK OK 502 498 517 501 533 C2' A A 17 OK OK 535 531 550 534 566 C2' A A 18 OK OK 568 564 583 567 599 C2' G A 19 OK OK 601 597 617 600 633 C2' A A 20 OK OK 635 631 650 634 666 C2' C A 21 OK OK 668 664 681 667 697 C2' C A 22 OK OK 699 695 712 698 728 C2' G A 23 OK OK 730 726 746 729 762 C2' U A 24 OK OK 764 760 777 763 792 C2' U A 25 OK OK 794 790 807 793 822 C2' C A 26 OK OK 824 820 837 823 853 C2' U A 27 OK OK 855 851 868 854 883 C2' A A 28 OK OK 885 881 900 884 916 C2' C A 29 OK OK 918 914 931 917 947 C2' A A 30 OK OK 949 945 964 948 980 C2' C A 31 OK OK 982 978 995 981 1011 C2' U A 32 OK OK 1013 1009 1026 1012 1041 C2' C A 33 OK OK 1043 1039 1056 1042 1072 C2' C A 34 OK OK 1074 1070 1088 1073 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 6 OK OK 173 191 176 177 205 C3' A A 7 OK OK 203 223 206 207 238 C3' G A 8 OK OK 236 257 239 240 272 C3' U A 9 OK OK 270 288 273 274 302 C3' A A 10 OK OK 300 320 303 304 335 C3' G A 11 OK OK 333 354 336 337 369 C3' G A 12 OK OK 367 388 370 371 403 C3' U A 13 OK OK 401 419 404 405 433 C3' C A 14 OK OK 431 449 434 435 464 C3' G A 15 OK OK 462 483 465 466 498 C3' A A 16 OK OK 496 516 499 500 531 C3' A A 17 OK OK 529 549 532 533 564 C3' A A 18 OK OK 562 582 565 566 597 C3' G A 19 OK OK 595 616 598 599 631 C3' A A 20 OK OK 629 649 632 633 664 C3' C A 21 OK OK 662 680 665 666 695 C3' C A 22 OK OK 693 711 696 697 726 C3' G A 23 OK OK 724 745 727 728 760 C3' U A 24 OK OK 758 776 761 762 790 C3' U A 25 OK OK 788 806 791 792 820 C3' C A 26 OK OK 818 836 821 822 851 C3' U A 27 OK OK 849 867 852 853 881 C3' A A 28 OK OK 879 899 882 883 914 C3' C A 29 OK OK 912 930 915 916 945 C3' A A 30 OK OK 943 963 946 947 978 C3' C A 31 OK OK 976 994 979 980 1009 C3' U A 32 OK OK 1007 1025 1010 1011 1039 C3' C A 33 OK OK 1037 1055 1040 1041 1070 C3' C A 34 OK OK 1068 1086 1071 1072 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 6 OK OK 175 190 172 174 203 C4' A A 7 OK OK 205 222 202 204 236 C4' G A 8 OK OK 238 256 235 237 270 C4' U A 9 OK OK 272 287 269 271 300 C4' A A 10 OK OK 302 319 299 301 333 C4' G A 11 OK OK 335 353 332 334 367 C4' G A 12 OK OK 369 387 366 368 401 C4' U A 13 OK OK 403 418 400 402 431 C4' C A 14 OK OK 433 448 430 432 462 C4' G A 15 OK OK 464 482 461 463 496 C4' A A 16 OK OK 498 515 495 497 529 C4' A A 17 OK OK 531 548 528 530 562 C4' A A 18 OK OK 564 581 561 563 595 C4' G A 19 OK OK 597 615 594 596 629 C4' A A 20 OK OK 631 648 628 630 662 C4' C A 21 OK OK 664 679 661 663 693 C4' C A 22 OK OK 695 710 692 694 724 C4' G A 23 OK OK 726 744 723 725 758 C4' U A 24 OK OK 760 775 757 759 788 C4' U A 25 OK OK 790 805 787 789 818 C4' C A 26 OK OK 820 835 817 819 849 C4' U A 27 OK OK 851 866 848 850 879 C4' A A 28 OK OK 881 898 878 880 912 C4' C A 29 OK OK 914 929 911 913 943 C4' A A 30 OK OK 945 962 942 944 976 C4' C A 31 OK OK 978 993 975 977 1007 C4' U A 32 OK OK 1009 1024 1006 1008 1037 C4' C A 33 OK OK 1039 1054 1036 1038 1068 C4' C A 34 OK OK 1070 1085 1067 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 6 OK OK 171 188 189 173 202 C5' A A 7 OK OK 201 220 221 203 235 C5' G A 8 OK OK 234 254 255 236 269 C5' U A 9 OK OK 268 285 286 270 299 C5' A A 10 OK OK 298 317 318 300 332 C5' G A 11 OK OK 331 351 352 333 366 C5' G A 12 OK OK 365 385 386 367 400 C5' U A 13 OK OK 399 416 417 401 430 C5' C A 14 OK OK 429 446 447 431 461 C5' G A 15 OK OK 460 480 481 462 495 C5' A A 16 OK OK 494 513 514 496 528 C5' A A 17 OK OK 527 546 547 529 561 C5' A A 18 OK OK 560 579 580 562 594 C5' G A 19 OK OK 593 613 614 595 628 C5' A A 20 OK OK 627 646 647 629 661 C5' C A 21 OK OK 660 677 678 662 692 C5' C A 22 OK OK 691 708 709 693 723 C5' G A 23 OK OK 722 742 743 724 757 C5' U A 24 OK OK 756 773 774 758 787 C5' U A 25 OK OK 786 803 804 788 817 C5' C A 26 OK OK 816 833 834 818 848 C5' U A 27 OK OK 847 864 865 849 878 C5' A A 28 OK OK 877 896 897 879 911 C5' C A 29 OK OK 910 927 928 912 942 C5' A A 30 OK OK 941 960 961 943 975 C5' C A 31 OK OK 974 991 992 976 1006 C5' U A 32 OK OK 1005 1022 1023 1007 1036 C5' C A 33 OK OK 1035 1052 1053 1037 1067 C5' C A 34 OK OK 1066 1083 1084 1068 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 6 distorted distorted 142 169 170 171 198 P A A 7 distorted distorted 176 199 200 201 231 P G A 8 distorted distorted 206 232 233 234 265 P U A 9 distorted distorted 239 266 267 268 295 P A A 10 distorted distorted 273 296 297 298 328 P G A 11 distorted distorted 303 329 330 331 362 P G A 12 distorted distorted 336 363 364 365 396 P U A 13 distorted distorted 370 397 398 399 426 P C A 14 distorted distorted 404 427 428 429 457 P G A 15 distorted distorted 434 458 459 460 491 P A A 16 distorted distorted 465 492 493 494 524 P A A 17 distorted distorted 499 525 526 527 557 P A A 18 distorted distorted 532 558 559 560 590 P G A 19 distorted distorted 565 591 592 593 624 P A A 20 distorted distorted 598 625 626 627 657 P C A 21 distorted distorted 632 658 659 660 688 P C A 22 distorted distorted 665 689 690 691 719 P G A 23 distorted distorted 696 720 721 722 753 P U A 24 distorted distorted 727 754 755 756 783 P U A 25 distorted distorted 761 784 785 786 813 P C A 26 distorted distorted 791 814 815 816 844 P U A 27 distorted distorted 821 845 846 847 874 P A A 28 distorted distorted 852 875 876 877 907 P C A 29 distorted distorted 882 908 909 910 938 P A A 30 distorted distorted 915 939 940 941 971 P C A 31 distorted distorted 946 972 973 974 1002 P U A 32 distorted distorted 979 1003 1004 1005 1032 P C A 33 distorted distorted 1010 1033 1034 1035 1063 P C A 34 distorted distorted 1040 1064 1065 1066 ---------------------------------------------------------------------------------