ID code: '1RLG' 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 C 1 beta 4 10 7 32 C1' C C 2 beta 27 33 30 52 C1' 5BU C 3 beta 47 53 50 73 C1' C C 4 beta 68 74 71 93 C1' 5BU C 5 beta 88 94 91 114 C1' G C 6 beta 109 115 112 137 C1' A C 7 beta 132 138 135 159 C1' C C 8 beta 154 160 157 179 C1' C C 9 beta 174 180 177 199 C1' G C 10 beta 194 200 197 222 C1' A C 11 beta 217 223 220 244 C1' A C 12 beta 239 245 242 266 C1' A C 13 beta 261 267 264 288 C1' G C 14 beta 283 289 286 311 C1' G C 15 beta 306 312 309 334 C1' C C 16 beta 329 335 332 354 C1' G C 17 beta 349 355 352 377 C1' U C 18 beta 372 378 375 397 C1' G C 19 beta 392 398 395 420 C1' A C 20 beta 415 421 418 442 C1' 5BU C 21 beta 437 443 440 463 C1' G C 22 beta 458 464 461 486 C1' A C 23 beta 481 487 484 508 C1' G C 24 beta 503 509 506 531 C1' C C 25 beta 526 532 529 549 C1' G D 1 beta 544 550 547 572 C1' C D 2 beta 567 573 570 592 C1' 5BU D 3 beta 587 593 590 613 C1' C D 4 beta 608 614 611 633 C1' 5BU D 5 beta 628 634 631 654 C1' G D 6 beta 649 655 652 677 C1' A D 7 beta 672 678 675 699 C1' C D 8 beta 694 700 697 719 C1' C D 9 beta 714 720 717 739 C1' G D 10 beta 734 740 737 762 C1' A D 11 beta 757 763 760 784 C1' A D 12 beta 779 785 782 806 C1' A D 13 beta 801 807 804 828 C1' G D 14 beta 823 829 826 851 C1' G D 15 beta 846 852 849 874 C1' C D 16 beta 869 875 872 894 C1' G D 17 beta 889 895 892 917 C1' U D 18 beta 912 918 915 937 C1' G D 19 beta 932 938 935 960 C1' A D 20 beta 955 961 958 982 C1' 5BU D 21 beta 977 983 980 1003 C1' G D 22 beta 998 1004 1001 1026 C1' A D 23 beta 1021 1027 1024 1048 C1' G D 24 beta 1043 1049 1046 1071 C1' C D 25 beta 1066 1072 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 OK 9 5 8 30 C2' C C 2 OK 32 28 31 50 C2' 5BU C 3 OK 52 48 51 71 C2' C C 4 OK 73 69 72 91 C2' 5BU C 5 OK 93 89 92 112 C2' G C 6 OK 114 110 113 135 C2' A C 7 OK 137 133 136 157 C2' C C 8 OK 159 155 158 177 C2' C C 9 OK 179 175 178 197 C2' G C 10 OK 199 195 198 220 C2' A C 11 OK 222 218 221 242 C2' A C 12 OK 244 240 243 264 C2' A C 13 OK 266 262 265 286 C2' G C 14 OK 288 284 287 309 C2' G C 15 OK 311 307 310 332 C2' C C 16 OK 334 330 333 352 C2' G C 17 OK 354 350 353 375 C2' U C 18 OK 377 373 376 395 C2' G C 19 OK 397 393 396 418 C2' A C 20 OK 420 416 419 440 C2' 5BU C 21 OK 442 438 441 461 C2' G C 22 OK 463 459 462 484 C2' A C 23 OK 486 482 485 506 C2' G C 24 OK 508 504 507 529 C2' C C 25 OK 531 527 530 547 C2' G D 1 OK 549 545 548 570 C2' C D 2 OK 572 568 571 590 C2' 5BU D 3 OK 592 588 591 611 C2' C D 4 OK 613 609 612 631 C2' 5BU D 5 OK 633 629 632 652 C2' G D 6 OK 654 650 653 675 C2' A D 7 OK 677 673 676 697 C2' C D 8 OK 699 695 698 717 C2' C D 9 OK 719 715 718 737 C2' G D 10 OK 739 735 738 760 C2' A D 11 OK 762 758 761 782 C2' A D 12 OK 784 780 783 804 C2' A D 13 OK 806 802 805 826 C2' G D 14 OK 828 824 827 849 C2' G D 15 OK 851 847 850 872 C2' C D 16 OK 874 870 873 892 C2' G D 17 OK 894 890 893 915 C2' U D 18 OK 917 913 916 935 C2' G D 19 OK 937 933 936 958 C2' A D 20 OK 960 956 959 980 C2' 5BU D 21 OK 982 978 981 1001 C2' G D 22 OK 1003 999 1002 1024 C2' A D 23 OK 1026 1022 1025 1046 C2' G D 24 OK 1048 1044 1047 1069 C2' C D 25 OK 1071 1067 1070 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 28 C3' C C 2 OK 26 29 30 48 C3' 5BU C 3 OK 46 49 50 69 C3' C C 4 OK 67 70 71 89 C3' 5BU C 5 OK 87 90 91 110 C3' G C 6 OK 108 111 112 133 C3' A C 7 OK 131 134 135 155 C3' C C 8 OK 153 156 157 175 C3' C C 9 OK 173 176 177 195 C3' G C 10 OK 193 196 197 218 C3' A C 11 OK 216 219 220 240 C3' A C 12 OK 238 241 242 262 C3' A C 13 OK 260 263 264 284 C3' G C 14 OK 282 285 286 307 C3' G C 15 OK 305 308 309 330 C3' C C 16 distorted 328 331 332 350 C3' G C 17 OK 348 351 352 373 C3' U C 18 OK 371 374 375 393 C3' G C 19 OK 391 394 395 416 C3' A C 20 OK 414 417 418 438 C3' 5BU C 21 OK 436 439 440 459 C3' G C 22 OK 457 460 461 482 C3' A C 23 OK 480 483 484 504 C3' G C 24 OK 502 505 506 527 C3' C C 25 OK 525 528 529 545 C3' G D 1 OK 543 546 547 568 C3' C D 2 OK 566 569 570 588 C3' 5BU D 3 OK 586 589 590 609 C3' C D 4 OK 607 610 611 629 C3' 5BU D 5 OK 627 630 631 650 C3' G D 6 OK 648 651 652 673 C3' A D 7 OK 671 674 675 695 C3' C D 8 OK 693 696 697 715 C3' C D 9 OK 713 716 717 735 C3' G D 10 OK 733 736 737 758 C3' A D 11 OK 756 759 760 780 C3' A D 12 OK 778 781 782 802 C3' A D 13 OK 800 803 804 824 C3' G D 14 OK 822 825 826 847 C3' G D 15 OK 845 848 849 870 C3' C D 16 distorted 868 871 872 890 C3' G D 17 OK 888 891 892 913 C3' U D 18 OK 911 914 915 933 C3' G D 19 OK 931 934 935 956 C3' A D 20 OK 954 957 958 978 C3' 5BU D 21 OK 976 979 980 999 C3' G D 22 OK 997 1000 1001 1022 C3' A D 23 OK 1020 1023 1024 1044 C3' G D 24 OK 1042 1045 1046 1067 C3' C D 25 OK 1065 1068 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 26 C4' C C 2 OK 28 25 27 46 C4' 5BU C 3 OK 48 45 47 67 C4' C C 4 OK 69 66 68 87 C4' 5BU C 5 OK 89 86 88 108 C4' G C 6 OK 110 107 109 131 C4' A C 7 OK 133 130 132 153 C4' C C 8 OK 155 152 154 173 C4' C C 9 OK 175 172 174 193 C4' G C 10 OK 195 192 194 216 C4' A C 11 OK 218 215 217 238 C4' A C 12 OK 240 237 239 260 C4' A C 13 OK 262 259 261 282 C4' G C 14 OK 284 281 283 305 C4' G C 15 OK 307 304 306 328 C4' C C 16 OK 330 327 329 348 C4' G C 17 OK 350 347 349 371 C4' U C 18 OK 373 370 372 391 C4' G C 19 OK 393 390 392 414 C4' A C 20 OK 416 413 415 436 C4' 5BU C 21 OK 438 435 437 457 C4' G C 22 OK 459 456 458 480 C4' A C 23 OK 482 479 481 502 C4' G C 24 OK 504 501 503 525 C4' C C 25 OK 527 524 526 543 C4' G D 1 OK 545 542 544 566 C4' C D 2 OK 568 565 567 586 C4' 5BU D 3 OK 588 585 587 607 C4' C D 4 OK 609 606 608 627 C4' 5BU D 5 OK 629 626 628 648 C4' G D 6 OK 650 647 649 671 C4' A D 7 OK 673 670 672 693 C4' C D 8 OK 695 692 694 713 C4' C D 9 OK 715 712 714 733 C4' G D 10 OK 735 732 734 756 C4' A D 11 OK 758 755 757 778 C4' A D 12 OK 780 777 779 800 C4' A D 13 OK 802 799 801 822 C4' G D 14 OK 824 821 823 845 C4' G D 15 OK 847 844 846 868 C4' C D 16 OK 870 867 869 888 C4' G D 17 OK 890 887 889 911 C4' U D 18 OK 913 910 912 931 C4' G D 19 OK 933 930 932 954 C4' A D 20 OK 956 953 955 976 C4' 5BU D 21 OK 978 975 977 997 C4' G D 22 OK 999 996 998 1020 C4' A D 23 OK 1022 1019 1021 1042 C4' G D 24 OK 1044 1041 1043 1065 C4' C D 25 OK 1067 1064 1066 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 25 C5' C C 2 24 26 45 C5' 5BU C 3 44 46 66 C5' C C 4 65 67 86 C5' 5BU C 5 85 87 107 C5' G C 6 106 108 130 C5' A C 7 129 131 152 C5' C C 8 151 153 172 C5' C C 9 171 173 192 C5' G C 10 191 193 215 C5' A C 11 214 216 237 C5' A C 12 236 238 259 C5' A C 13 258 260 281 C5' G C 14 280 282 304 C5' G C 15 303 305 327 C5' C C 16 326 328 347 C5' G C 17 346 348 370 C5' U C 18 369 371 390 C5' G C 19 389 391 413 C5' A C 20 412 414 435 C5' 5BU C 21 434 436 456 C5' G C 22 455 457 479 C5' A C 23 478 480 501 C5' G C 24 500 502 524 C5' C C 25 523 525 542 C5' G D 1 541 543 565 C5' C D 2 564 566 585 C5' 5BU D 3 584 586 606 C5' C D 4 605 607 626 C5' 5BU D 5 625 627 647 C5' G D 6 646 648 670 C5' A D 7 669 671 692 C5' C D 8 691 693 712 C5' C D 9 711 713 732 C5' G D 10 731 733 755 C5' A D 11 754 756 777 C5' A D 12 776 778 799 C5' A D 13 798 800 821 C5' G D 14 820 822 844 C5' G D 15 843 845 867 C5' C D 16 866 868 887 C5' G D 17 886 888 910 C5' U D 18 909 911 930 C5' G D 19 929 931 953 C5' A D 20 952 954 975 C5' 5BU D 21 974 976 996 C5' G D 22 995 997 1019 C5' A D 23 1018 1020 1041 C5' G D 24 1040 1042 1064 C5' C D 25 1063 1065 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C C 2 distorted distorted 6 22 23 24 41 P 5BU C 3 distorted distorted 29 42 43 44 62 P C C 4 distorted distorted 49 63 64 65 82 P 5BU C 5 distorted distorted 70 83 84 85 103 P G C 6 distorted distorted 90 104 105 106 126 P A C 7 distorted distorted 111 127 128 129 148 P C C 8 distorted distorted 134 149 150 151 168 P C C 9 distorted distorted 156 169 170 171 188 P G C 10 distorted distorted 176 189 190 191 211 P A C 11 distorted distorted 196 212 213 214 233 P A C 12 distorted distorted 219 234 235 236 255 P A C 13 distorted distorted 241 256 257 258 277 P G C 14 distorted distorted 263 278 279 280 300 P G C 15 distorted distorted 285 301 302 303 323 P C C 16 distorted distorted 308 324 325 326 343 P G C 17 distorted distorted 331 344 345 346 366 P U C 18 distorted distorted 351 367 368 369 386 P G C 19 distorted distorted 374 387 388 389 409 P A C 20 distorted distorted 394 410 411 412 431 P 5BU C 21 distorted distorted 417 432 433 434 452 P G C 22 distorted distorted 439 453 454 455 475 P A C 23 distorted distorted 460 476 477 478 497 P G C 24 distorted distorted 483 498 499 500 520 P C C 25 distorted distorted 505 521 522 523 561 P C D 2 distorted distorted 546 562 563 564 581 P 5BU D 3 distorted distorted 569 582 583 584 602 P C D 4 distorted distorted 589 603 604 605 622 P 5BU D 5 distorted distorted 610 623 624 625 643 P G D 6 distorted distorted 630 644 645 646 666 P A D 7 distorted distorted 651 667 668 669 688 P C D 8 distorted distorted 674 689 690 691 708 P C D 9 distorted distorted 696 709 710 711 728 P G D 10 distorted distorted 716 729 730 731 751 P A D 11 distorted distorted 736 752 753 754 773 P A D 12 distorted distorted 759 774 775 776 795 P A D 13 distorted distorted 781 796 797 798 817 P G D 14 distorted distorted 803 818 819 820 840 P G D 15 distorted distorted 825 841 842 843 863 P C D 16 distorted distorted 848 864 865 866 883 P G D 17 distorted distorted 871 884 885 886 906 P U D 18 distorted distorted 891 907 908 909 926 P G D 19 distorted distorted 914 927 928 929 949 P A D 20 distorted distorted 934 950 951 952 971 P 5BU D 21 distorted distorted 957 972 973 974 992 P G D 22 distorted distorted 979 993 994 995 1015 P A D 23 distorted distorted 1000 1016 1017 1018 1037 P G D 24 distorted distorted 1023 1038 1039 1040 1060 P C D 25 distorted distorted 1045 1061 1062 1063 ---------------------------------------------------------------------------------