ID code: '1K78' 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' G C 3 beta 7 12 10 33 C1' T C 4 beta 29 34 32 53 C1' G C 5 beta 49 54 52 75 C1' C C 6 beta 71 76 74 94 C1' C C 7 beta 90 95 93 113 C1' G C 8 beta 109 114 112 135 C1' G C 9 beta 131 136 134 157 C1' A C 10 beta 153 158 156 178 C1' G C 11 beta 174 179 177 200 C1' A C 12 beta 196 201 199 221 C1' T C 13 beta 217 222 220 241 C1' G C 14 beta 237 242 240 263 C1' G C 15 beta 259 264 262 285 C1' G C 16 beta 281 286 284 307 C1' C C 17 beta 303 308 306 326 C1' T C 18 beta 322 327 325 346 C1' C C 19 beta 342 347 345 365 C1' C C 20 beta 361 366 364 384 C1' A C 21 beta 380 385 383 405 C1' G C 22 beta 401 406 404 427 C1' T C 23 beta 423 428 426 447 C1' G C 24 beta 443 448 446 469 C1' G C 25 beta 465 470 468 491 C1' C C 26 beta 487 492 490 510 C1' C C 27 beta 506 511 509 530 C1' G D 3 beta 526 531 529 552 C1' G D 4 beta 548 553 551 574 C1' C D 5 beta 570 575 573 593 C1' C D 6 beta 589 594 592 612 C1' A D 7 beta 608 613 611 633 C1' C D 8 beta 629 634 632 652 C1' T D 9 beta 648 653 651 672 C1' G D 10 beta 668 673 671 694 C1' G D 11 beta 690 695 693 716 C1' A D 12 beta 712 717 715 737 C1' G D 13 beta 733 738 736 759 C1' C D 14 beta 755 760 758 778 C1' C D 15 beta 774 779 777 797 C1' C D 16 beta 793 798 796 816 C1' A D 17 beta 812 817 815 837 C1' T D 18 beta 833 838 836 857 C1' C D 19 beta 853 858 856 876 C1' T D 20 beta 872 877 875 896 C1' C D 21 beta 892 897 895 915 C1' C D 22 beta 911 916 914 934 C1' G D 23 beta 930 935 933 956 C1' G D 24 beta 952 957 955 978 C1' C D 25 beta 974 979 977 997 C1' A D 26 beta 993 998 996 1018 C1' C D 27 beta 1014 1019 1017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G C 3 11 8 32 C2' T C 4 33 30 52 C2' G C 5 53 50 74 C2' C C 6 75 72 93 C2' C C 7 94 91 112 C2' G C 8 113 110 134 C2' G C 9 135 132 156 C2' A C 10 157 154 177 C2' G C 11 178 175 199 C2' A C 12 200 197 220 C2' T C 13 221 218 240 C2' G C 14 241 238 262 C2' G C 15 263 260 284 C2' G C 16 285 282 306 C2' C C 17 307 304 325 C2' T C 18 326 323 345 C2' C C 19 346 343 364 C2' C C 20 365 362 383 C2' A C 21 384 381 404 C2' G C 22 405 402 426 C2' T C 23 427 424 446 C2' G C 24 447 444 468 C2' G C 25 469 466 490 C2' C C 26 491 488 509 C2' C C 27 510 507 529 C2' G D 3 530 527 551 C2' G D 4 552 549 573 C2' C D 5 574 571 592 C2' C D 6 593 590 611 C2' A D 7 612 609 632 C2' C D 8 633 630 651 C2' T D 9 652 649 671 C2' G D 10 672 669 693 C2' G D 11 694 691 715 C2' A D 12 716 713 736 C2' G D 13 737 734 758 C2' C D 14 759 756 777 C2' C D 15 778 775 796 C2' C D 16 797 794 815 C2' A D 17 816 813 836 C2' T D 18 837 834 856 C2' C D 19 857 854 875 C2' T D 20 876 873 895 C2' C D 21 896 893 914 C2' C D 22 915 912 933 C2' G D 23 934 931 955 C2' G D 24 956 953 977 C2' C D 25 978 975 996 C2' A D 26 997 994 1017 C2' C D 27 1018 1015 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G C 3 OK 6 9 10 30 C3' T C 4 OK 28 31 32 50 C3' G C 5 OK 48 51 52 72 C3' C C 6 OK 70 73 74 91 C3' C C 7 OK 89 92 93 110 C3' G C 8 OK 108 111 112 132 C3' G C 9 OK 130 133 134 154 C3' A C 10 OK 152 155 156 175 C3' G C 11 OK 173 176 177 197 C3' A C 12 OK 195 198 199 218 C3' T C 13 OK 216 219 220 238 C3' G C 14 OK 236 239 240 260 C3' G C 15 OK 258 261 262 282 C3' G C 16 OK 280 283 284 304 C3' C C 17 OK 302 305 306 323 C3' T C 18 OK 321 324 325 343 C3' C C 19 OK 341 344 345 362 C3' C C 20 OK 360 363 364 381 C3' A C 21 OK 379 382 383 402 C3' G C 22 OK 400 403 404 424 C3' T C 23 OK 422 425 426 444 C3' G C 24 OK 442 445 446 466 C3' G C 25 OK 464 467 468 488 C3' C C 26 OK 486 489 490 507 C3' C C 27 OK 505 508 509 527 C3' G D 3 OK 525 528 529 549 C3' G D 4 OK 547 550 551 571 C3' C D 5 OK 569 572 573 590 C3' C D 6 OK 588 591 592 609 C3' A D 7 OK 607 610 611 630 C3' C D 8 OK 628 631 632 649 C3' T D 9 OK 647 650 651 669 C3' G D 10 OK 667 670 671 691 C3' G D 11 OK 689 692 693 713 C3' A D 12 OK 711 714 715 734 C3' G D 13 OK 732 735 736 756 C3' C D 14 OK 754 757 758 775 C3' C D 15 OK 773 776 777 794 C3' C D 16 OK 792 795 796 813 C3' A D 17 OK 811 814 815 834 C3' T D 18 OK 832 835 836 854 C3' C D 19 OK 852 855 856 873 C3' T D 20 OK 871 874 875 893 C3' C D 21 OK 891 894 895 912 C3' C D 22 OK 910 913 914 931 C3' G D 23 OK 929 932 933 953 C3' G D 24 OK 951 954 955 975 C3' C D 25 OK 973 976 977 994 C3' A D 26 OK 992 995 996 1015 C3' C D 27 OK 1013 1016 1017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G C 3 OK 8 5 7 28 C4' T C 4 OK 30 27 29 48 C4' G C 5 OK 50 47 49 70 C4' C C 6 OK 72 69 71 89 C4' C C 7 OK 91 88 90 108 C4' G C 8 OK 110 107 109 130 C4' G C 9 OK 132 129 131 152 C4' A C 10 OK 154 151 153 173 C4' G C 11 OK 175 172 174 195 C4' A C 12 OK 197 194 196 216 C4' T C 13 OK 218 215 217 236 C4' G C 14 OK 238 235 237 258 C4' G C 15 OK 260 257 259 280 C4' G C 16 OK 282 279 281 302 C4' C C 17 OK 304 301 303 321 C4' T C 18 OK 323 320 322 341 C4' C C 19 OK 343 340 342 360 C4' C C 20 OK 362 359 361 379 C4' A C 21 OK 381 378 380 400 C4' G C 22 OK 402 399 401 422 C4' T C 23 OK 424 421 423 442 C4' G C 24 OK 444 441 443 464 C4' G C 25 OK 466 463 465 486 C4' C C 26 OK 488 485 487 505 C4' C C 27 OK 507 504 506 525 C4' G D 3 OK 527 524 526 547 C4' G D 4 OK 549 546 548 569 C4' C D 5 OK 571 568 570 588 C4' C D 6 OK 590 587 589 607 C4' A D 7 OK 609 606 608 628 C4' C D 8 OK 630 627 629 647 C4' T D 9 OK 649 646 648 667 C4' G D 10 OK 669 666 668 689 C4' G D 11 OK 691 688 690 711 C4' A D 12 OK 713 710 712 732 C4' G D 13 OK 734 731 733 754 C4' C D 14 OK 756 753 755 773 C4' C D 15 OK 775 772 774 792 C4' C D 16 OK 794 791 793 811 C4' A D 17 OK 813 810 812 832 C4' T D 18 OK 834 831 833 852 C4' C D 19 OK 854 851 853 871 C4' T D 20 OK 873 870 872 891 C4' C D 21 OK 893 890 892 910 C4' C D 22 OK 912 909 911 929 C4' G D 23 OK 931 928 930 951 C4' G D 24 OK 953 950 952 973 C4' C D 25 OK 975 972 974 992 C4' A D 26 OK 994 991 993 1013 C4' C D 27 OK 1015 1012 1014 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G C 3 4 6 27 C5' T C 4 26 28 47 C5' G C 5 46 48 69 C5' C C 6 68 70 88 C5' C C 7 87 89 107 C5' G C 8 106 108 129 C5' G C 9 128 130 151 C5' A C 10 150 152 172 C5' G C 11 171 173 194 C5' A C 12 193 195 215 C5' T C 13 214 216 235 C5' G C 14 234 236 257 C5' G C 15 256 258 279 C5' G C 16 278 280 301 C5' C C 17 300 302 320 C5' T C 18 319 321 340 C5' C C 19 339 341 359 C5' C C 20 358 360 378 C5' A C 21 377 379 399 C5' G C 22 398 400 421 C5' T C 23 420 422 441 C5' G C 24 440 442 463 C5' G C 25 462 464 485 C5' C C 26 484 486 504 C5' C C 27 503 505 524 C5' G D 3 523 525 546 C5' G D 4 545 547 568 C5' C D 5 567 569 587 C5' C D 6 586 588 606 C5' A D 7 605 607 627 C5' C D 8 626 628 646 C5' T D 9 645 647 666 C5' G D 10 665 667 688 C5' G D 11 687 689 710 C5' A D 12 709 711 731 C5' G D 13 730 732 753 C5' C D 14 752 754 772 C5' C D 15 771 773 791 C5' C D 16 790 792 810 C5' A D 17 809 811 831 C5' T D 18 830 832 851 C5' C D 19 850 852 870 C5' T D 20 869 871 890 C5' C D 21 889 891 909 C5' C D 22 908 910 928 C5' G D 23 927 929 950 C5' G D 24 949 951 972 C5' C D 25 971 973 991 C5' A D 26 990 992 1012 C5' C D 27 1011 1013 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G C 3 distorted distorted 2 3 4 23 P T C 4 distorted distorted 9 24 25 26 43 P G C 5 distorted distorted 31 44 45 46 65 P C C 6 distorted distorted 51 66 67 68 84 P C C 7 distorted distorted 73 85 86 87 103 P G C 8 distorted distorted 92 104 105 106 125 P G C 9 distorted distorted 111 126 127 128 147 P A C 10 distorted distorted 133 148 149 150 168 P G C 11 distorted distorted 155 169 170 171 190 P A C 12 distorted distorted 176 191 192 193 211 P T C 13 distorted distorted 198 212 213 214 231 P G C 14 distorted distorted 219 232 233 234 253 P G C 15 distorted distorted 239 254 255 256 275 P G C 16 distorted distorted 261 276 277 278 297 P C C 17 distorted distorted 283 298 299 300 316 P T C 18 distorted distorted 305 317 318 319 336 P C C 19 distorted distorted 324 337 338 339 355 P C C 20 distorted distorted 344 356 357 358 374 P A C 21 distorted distorted 363 375 376 377 395 P G C 22 distorted distorted 382 396 397 398 417 P T C 23 distorted distorted 403 418 419 420 437 P G C 24 distorted distorted 425 438 439 440 459 P G C 25 distorted distorted 445 460 461 462 481 P C C 26 distorted distorted 467 482 483 484 500 P C C 27 distorted distorted 489 501 502 503 520 P G D 3 distorted distorted 521 522 523 542 P G D 4 distorted distorted 528 543 544 545 564 P C D 5 distorted distorted 550 565 566 567 583 P C D 6 distorted distorted 572 584 585 586 602 P A D 7 distorted distorted 591 603 604 605 623 P C D 8 distorted distorted 610 624 625 626 642 P T D 9 distorted distorted 631 643 644 645 662 P G D 10 distorted distorted 650 663 664 665 684 P G D 11 distorted distorted 670 685 686 687 706 P A D 12 distorted distorted 692 707 708 709 727 P G D 13 distorted distorted 714 728 729 730 749 P C D 14 distorted distorted 735 750 751 752 768 P C D 15 distorted distorted 757 769 770 771 787 P C D 16 distorted distorted 776 788 789 790 806 P A D 17 distorted distorted 795 807 808 809 827 P T D 18 distorted distorted 814 828 829 830 847 P C D 19 distorted distorted 835 848 849 850 866 P T D 20 distorted distorted 855 867 868 869 886 P C D 21 distorted distorted 874 887 888 889 905 P C D 22 distorted distorted 894 906 907 908 924 P G D 23 distorted distorted 913 925 926 927 946 P G D 24 distorted distorted 932 947 948 949 968 P C D 25 distorted distorted 954 969 970 971 987 P A D 26 distorted distorted 976 988 989 990 1008 P C D 27 distorted distorted 995 1009 1010 1011 ---------------------------------------------------------------------------------