ID code: '5HNJ' 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 beta 4 10 7 32 C1' U A 2 beta 27 33 30 52 C1' A A 3 beta 47 53 50 72 C1' RSQ A 4 beta 80 64 74 96 C1' G A 5 beta 91 97 94 119 C1' U A 6 beta 114 120 117 139 C1' A A 7 beta 134 140 137 161 C1' C A 8 beta 156 162 159 179 C1' G B 1 beta 174 180 177 202 C1' U B 2 beta 197 203 200 222 C1' A B 3 beta 217 223 220 242 C1' RSQ B 4 beta 250 234 244 266 C1' G B 5 beta 261 267 264 289 C1' U B 6 beta 284 290 287 309 C1' A B 7 beta 304 310 307 331 C1' C B 8 beta 326 332 329 349 C1' G C 1 beta 344 350 347 372 C1' U C 2 beta 367 373 370 392 C1' A C 3 beta 387 393 390 412 C1' RSQ C 4 beta 420 404 414 436 C1' G C 5 beta 431 437 434 459 C1' U C 6 beta 454 460 457 479 C1' A C 7 beta 474 480 477 501 C1' C C 8 beta 496 502 499 519 C1' G D 1 beta 514 520 517 542 C1' U D 2 beta 537 543 540 562 C1' A D 3 beta 557 563 560 582 C1' RSQ D 4 beta 590 574 584 606 C1' G D 5 beta 601 607 604 629 C1' U D 6 beta 624 630 627 649 C1' A D 7 beta 644 650 647 671 C1' C D 8 beta 666 672 669 689 C1' G E 1 beta 684 690 687 712 C1' U E 2 beta 707 713 710 732 C1' A E 3 beta 727 733 730 752 C1' RSQ E 4 beta 760 744 754 776 C1' G E 5 beta 771 777 774 799 C1' U E 6 beta 794 800 797 819 C1' A E 7 beta 814 820 817 841 C1' C E 8 beta 836 842 839 859 C1' G F 1 beta 854 860 857 882 C1' U F 2 beta 877 883 880 902 C1' A F 3 beta 897 903 900 922 C1' RSQ F 4 beta 930 914 924 946 C1' G F 5 beta 941 947 944 969 C1' U F 6 beta 964 970 967 989 C1' A F 7 beta 984 990 987 1011 C1' C F 8 beta 1006 1012 1009 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' U A 2 OK 32 28 31 50 C2' A A 3 OK 52 48 51 74 C2' RSQ A 4 OK 72 76 75 94 C2' G A 5 OK 96 92 95 117 C2' U A 6 OK 119 115 118 137 C2' A A 7 OK 139 135 138 159 C2' C A 8 OK 161 157 160 177 C2' G B 1 OK 179 175 178 200 C2' U B 2 OK 202 198 201 220 C2' A B 3 OK 222 218 221 244 C2' RSQ B 4 OK 242 246 245 264 C2' G B 5 OK 266 262 265 287 C2' U B 6 OK 289 285 288 307 C2' A B 7 OK 309 305 308 329 C2' C B 8 OK 331 327 330 347 C2' G C 1 OK 349 345 348 370 C2' U C 2 OK 372 368 371 390 C2' A C 3 OK 392 388 391 414 C2' RSQ C 4 OK 412 416 415 434 C2' G C 5 OK 436 432 435 457 C2' U C 6 OK 459 455 458 477 C2' A C 7 OK 479 475 478 499 C2' C C 8 OK 501 497 500 517 C2' G D 1 OK 519 515 518 540 C2' U D 2 OK 542 538 541 560 C2' A D 3 OK 562 558 561 584 C2' RSQ D 4 OK 582 586 585 604 C2' G D 5 OK 606 602 605 627 C2' U D 6 OK 629 625 628 647 C2' A D 7 OK 649 645 648 669 C2' C D 8 OK 671 667 670 687 C2' G E 1 OK 689 685 688 710 C2' U E 2 OK 712 708 711 730 C2' A E 3 OK 732 728 731 754 C2' RSQ E 4 OK 752 756 755 774 C2' G E 5 OK 776 772 775 797 C2' U E 6 OK 799 795 798 817 C2' A E 7 OK 819 815 818 839 C2' C E 8 OK 841 837 840 857 C2' G F 1 OK 859 855 858 880 C2' U F 2 OK 882 878 881 900 C2' A F 3 OK 902 898 901 924 C2' RSQ F 4 OK 922 926 925 944 C2' G F 5 OK 946 942 945 967 C2' U F 6 OK 969 965 968 987 C2' A F 7 OK 989 985 988 1009 C2' C F 8 OK 1011 1007 1010 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' U A 2 OK 26 29 30 48 C3' A A 3 OK 46 49 50 76 C3' RSQ A 4 OK 79 77 74 92 C3' G A 5 OK 90 93 94 115 C3' U A 6 OK 113 116 117 135 C3' A A 7 OK 133 136 137 157 C3' C A 8 OK 155 158 159 175 C3' G B 1 OK 173 176 177 198 C3' U B 2 OK 196 199 200 218 C3' A B 3 OK 216 219 220 246 C3' RSQ B 4 OK 249 247 244 262 C3' G B 5 OK 260 263 264 285 C3' U B 6 OK 283 286 287 305 C3' A B 7 OK 303 306 307 327 C3' C B 8 OK 325 328 329 345 C3' G C 1 OK 343 346 347 368 C3' U C 2 OK 366 369 370 388 C3' A C 3 OK 386 389 390 416 C3' RSQ C 4 OK 419 417 414 432 C3' G C 5 OK 430 433 434 455 C3' U C 6 OK 453 456 457 475 C3' A C 7 OK 473 476 477 497 C3' C C 8 OK 495 498 499 515 C3' G D 1 OK 513 516 517 538 C3' U D 2 OK 536 539 540 558 C3' A D 3 OK 556 559 560 586 C3' RSQ D 4 OK 589 587 584 602 C3' G D 5 OK 600 603 604 625 C3' U D 6 OK 623 626 627 645 C3' A D 7 OK 643 646 647 667 C3' C D 8 OK 665 668 669 685 C3' G E 1 OK 683 686 687 708 C3' U E 2 OK 706 709 710 728 C3' A E 3 OK 726 729 730 756 C3' RSQ E 4 OK 759 757 754 772 C3' G E 5 OK 770 773 774 795 C3' U E 6 OK 793 796 797 815 C3' A E 7 OK 813 816 817 837 C3' C E 8 OK 835 838 839 855 C3' G F 1 OK 853 856 857 878 C3' U F 2 OK 876 879 880 898 C3' A F 3 OK 896 899 900 926 C3' RSQ F 4 OK 929 927 924 942 C3' G F 5 OK 940 943 944 965 C3' U F 6 OK 963 966 967 985 C3' A F 7 OK 983 986 987 1007 C3' C F 8 OK 1005 1008 1009 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' U A 2 OK 28 25 27 46 C4' A A 3 OK 48 45 47 79 C4' RSQ A 4 OK 76 81 80 90 C4' G A 5 OK 92 89 91 113 C4' U A 6 OK 115 112 114 133 C4' A A 7 OK 135 132 134 155 C4' C A 8 OK 157 154 156 173 C4' G B 1 OK 175 172 174 196 C4' U B 2 OK 198 195 197 216 C4' A B 3 OK 218 215 217 249 C4' RSQ B 4 OK 246 251 250 260 C4' G B 5 OK 262 259 261 283 C4' U B 6 OK 285 282 284 303 C4' A B 7 OK 305 302 304 325 C4' C B 8 OK 327 324 326 343 C4' G C 1 OK 345 342 344 366 C4' U C 2 OK 368 365 367 386 C4' A C 3 OK 388 385 387 419 C4' RSQ C 4 OK 416 421 420 430 C4' G C 5 OK 432 429 431 453 C4' U C 6 OK 455 452 454 473 C4' A C 7 OK 475 472 474 495 C4' C C 8 OK 497 494 496 513 C4' G D 1 OK 515 512 514 536 C4' U D 2 OK 538 535 537 556 C4' A D 3 OK 558 555 557 589 C4' RSQ D 4 OK 586 591 590 600 C4' G D 5 OK 602 599 601 623 C4' U D 6 OK 625 622 624 643 C4' A D 7 OK 645 642 644 665 C4' C D 8 OK 667 664 666 683 C4' G E 1 OK 685 682 684 706 C4' U E 2 OK 708 705 707 726 C4' A E 3 OK 728 725 727 759 C4' RSQ E 4 OK 756 761 760 770 C4' G E 5 OK 772 769 771 793 C4' U E 6 OK 795 792 794 813 C4' A E 7 OK 815 812 814 835 C4' C E 8 OK 837 834 836 853 C4' G F 1 OK 855 852 854 876 C4' U F 2 OK 878 875 877 896 C4' A F 3 OK 898 895 897 929 C4' RSQ F 4 OK 926 931 930 940 C4' G F 5 OK 942 939 941 963 C4' U F 6 OK 965 962 964 983 C4' A F 7 OK 985 982 984 1005 C4' C F 8 OK 1007 1004 1006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' U A 2 24 26 45 C5' A A 3 44 46 81 C5' RSQ A 4 82 79 89 C5' G A 5 88 90 112 C5' U A 6 111 113 132 C5' A A 7 131 133 154 C5' C A 8 153 155 172 C5' G B 1 171 173 195 C5' U B 2 194 196 215 C5' A B 3 214 216 251 C5' RSQ B 4 252 249 259 C5' G B 5 258 260 282 C5' U B 6 281 283 302 C5' A B 7 301 303 324 C5' C B 8 323 325 342 C5' G C 1 341 343 365 C5' U C 2 364 366 385 C5' A C 3 384 386 421 C5' RSQ C 4 422 419 429 C5' G C 5 428 430 452 C5' U C 6 451 453 472 C5' A C 7 471 473 494 C5' C C 8 493 495 512 C5' G D 1 511 513 535 C5' U D 2 534 536 555 C5' A D 3 554 556 591 C5' RSQ D 4 592 589 599 C5' G D 5 598 600 622 C5' U D 6 621 623 642 C5' A D 7 641 643 664 C5' C D 8 663 665 682 C5' G E 1 681 683 705 C5' U E 2 704 706 725 C5' A E 3 724 726 761 C5' RSQ E 4 762 759 769 C5' G E 5 768 770 792 C5' U E 6 791 793 812 C5' A E 7 811 813 834 C5' C E 8 833 835 852 C5' G F 1 851 853 875 C5' U F 2 874 876 895 C5' A F 3 894 896 931 C5' RSQ F 4 932 929 939 C5' G F 5 938 940 962 C5' U F 6 961 963 982 C5' A F 7 981 983 1004 C5' C F 8 1003 1005 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 2 distorted distorted 6 22 23 24 41 P A A 3 distorted distorted 29 42 43 44 63 P RSQ A 4 distorted distorted 49 83 84 82 85 P G A 5 distorted distorted 77 86 87 88 108 P U A 6 distorted distorted 93 109 110 111 128 P A A 7 distorted distorted 116 129 130 131 150 P C A 8 distorted distorted 136 151 152 153 191 P U B 2 distorted distorted 176 192 193 194 211 P A B 3 distorted distorted 199 212 213 214 233 P RSQ B 4 distorted distorted 219 253 254 252 255 P G B 5 distorted distorted 247 256 257 258 278 P U B 6 distorted distorted 263 279 280 281 298 P A B 7 distorted distorted 286 299 300 301 320 P C B 8 distorted distorted 306 321 322 323 361 P U C 2 distorted distorted 346 362 363 364 381 P A C 3 distorted distorted 369 382 383 384 403 P RSQ C 4 distorted distorted 389 423 424 422 425 P G C 5 distorted distorted 417 426 427 428 448 P U C 6 distorted distorted 433 449 450 451 468 P A C 7 distorted distorted 456 469 470 471 490 P C C 8 distorted distorted 476 491 492 493 531 P U D 2 distorted distorted 516 532 533 534 551 P A D 3 distorted distorted 539 552 553 554 573 P RSQ D 4 distorted distorted 559 593 594 592 595 P G D 5 distorted distorted 587 596 597 598 618 P U D 6 distorted distorted 603 619 620 621 638 P A D 7 distorted distorted 626 639 640 641 660 P C D 8 distorted distorted 646 661 662 663 701 P U E 2 distorted distorted 686 702 703 704 721 P A E 3 distorted distorted 709 722 723 724 743 P RSQ E 4 distorted distorted 729 763 764 762 765 P G E 5 distorted distorted 757 766 767 768 788 P U E 6 distorted distorted 773 789 790 791 808 P A E 7 distorted distorted 796 809 810 811 830 P C E 8 distorted distorted 816 831 832 833 871 P U F 2 distorted distorted 856 872 873 874 891 P A F 3 distorted distorted 879 892 893 894 913 P RSQ F 4 distorted distorted 899 933 934 932 935 P G F 5 distorted distorted 927 936 937 938 958 P U F 6 distorted distorted 943 959 960 961 978 P A F 7 distorted distorted 966 979 980 981 1000 P C F 8 distorted distorted 986 1001 1002 1003 ---------------------------------------------------------------------------------