ID code: '5HN2' 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 156 162 159 181 C1' G B 1 beta 176 182 179 204 C1' U B 2 beta 199 205 202 224 C1' A B 3 beta 219 225 222 244 C1' RSQ B 4 beta 252 236 246 268 C1' G B 5 beta 263 269 266 291 C1' U B 6 beta 286 292 289 311 C1' A B 7 beta 306 312 309 333 C1' C B 8 beta 328 334 331 351 C1' G C 1 beta 346 352 349 374 C1' U C 2 beta 369 375 372 394 C1' A C 3 beta 389 395 392 414 C1' RSQ C 4 beta 422 406 416 438 C1' G C 5 beta 433 439 436 461 C1' U C 6 beta 456 462 459 481 C1' A C 7 beta 476 482 479 503 C1' C C 8 beta 498 504 501 521 C1' G D 1 beta 516 522 519 544 C1' U D 2 beta 539 545 542 564 C1' A D 3 beta 559 565 562 584 C1' RSQ D 4 beta 592 576 586 608 C1' G D 5 beta 603 609 606 631 C1' U D 6 beta 626 632 629 651 C1' A D 7 beta 646 652 649 673 C1' C D 8 beta 668 674 671 691 C1' G E 1 beta 686 692 689 714 C1' U E 2 beta 709 715 712 734 C1' A E 3 beta 729 735 732 754 C1' RSQ E 4 beta 762 746 756 778 C1' G E 5 beta 773 779 776 801 C1' U E 6 beta 796 802 799 821 C1' A E 7 beta 816 822 819 843 C1' C E 8 beta 838 844 841 861 C1' G F 1 beta 856 862 859 884 C1' U F 2 beta 879 885 882 904 C1' A F 3 beta 899 905 902 924 C1' RSQ F 4 beta 932 916 926 948 C1' G F 5 beta 943 949 946 971 C1' U F 6 beta 966 972 969 991 C1' A F 7 beta 986 992 989 1013 C1' C F 8 beta 1008 1014 1011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 161 157 160 179 C2' G B 1 OK 181 177 180 202 C2' U B 2 OK 204 200 203 222 C2' A B 3 OK 224 220 223 246 C2' RSQ B 4 OK 244 248 247 266 C2' G B 5 OK 268 264 267 289 C2' U B 6 OK 291 287 290 309 C2' A B 7 OK 311 307 310 331 C2' C B 8 OK 333 329 332 349 C2' G C 1 OK 351 347 350 372 C2' U C 2 OK 374 370 373 392 C2' A C 3 OK 394 390 393 416 C2' RSQ C 4 OK 414 418 417 436 C2' G C 5 OK 438 434 437 459 C2' U C 6 OK 461 457 460 479 C2' A C 7 OK 481 477 480 501 C2' C C 8 OK 503 499 502 519 C2' G D 1 OK 521 517 520 542 C2' U D 2 OK 544 540 543 562 C2' A D 3 OK 564 560 563 586 C2' RSQ D 4 OK 584 588 587 606 C2' G D 5 OK 608 604 607 629 C2' U D 6 OK 631 627 630 649 C2' A D 7 OK 651 647 650 671 C2' C D 8 OK 673 669 672 689 C2' G E 1 OK 691 687 690 712 C2' U E 2 OK 714 710 713 732 C2' A E 3 OK 734 730 733 756 C2' RSQ E 4 OK 754 758 757 776 C2' G E 5 OK 778 774 777 799 C2' U E 6 OK 801 797 800 819 C2' A E 7 OK 821 817 820 841 C2' C E 8 OK 843 839 842 859 C2' G F 1 OK 861 857 860 882 C2' U F 2 OK 884 880 883 902 C2' A F 3 OK 904 900 903 926 C2' RSQ F 4 OK 924 928 927 946 C2' G F 5 OK 948 944 947 969 C2' U F 6 OK 971 967 970 989 C2' A F 7 OK 991 987 990 1011 C2' C F 8 OK 1013 1009 1012 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 155 158 159 177 C3' G B 1 OK 175 178 179 200 C3' U B 2 OK 198 201 202 220 C3' A B 3 OK 218 221 222 248 C3' RSQ B 4 OK 251 249 246 264 C3' G B 5 OK 262 265 266 287 C3' U B 6 OK 285 288 289 307 C3' A B 7 OK 305 308 309 329 C3' C B 8 OK 327 330 331 347 C3' G C 1 OK 345 348 349 370 C3' U C 2 OK 368 371 372 390 C3' A C 3 OK 388 391 392 418 C3' RSQ C 4 OK 421 419 416 434 C3' G C 5 OK 432 435 436 457 C3' U C 6 OK 455 458 459 477 C3' A C 7 OK 475 478 479 499 C3' C C 8 OK 497 500 501 517 C3' G D 1 OK 515 518 519 540 C3' U D 2 OK 538 541 542 560 C3' A D 3 OK 558 561 562 588 C3' RSQ D 4 OK 591 589 586 604 C3' G D 5 OK 602 605 606 627 C3' U D 6 OK 625 628 629 647 C3' A D 7 OK 645 648 649 669 C3' C D 8 OK 667 670 671 687 C3' G E 1 OK 685 688 689 710 C3' U E 2 OK 708 711 712 730 C3' A E 3 OK 728 731 732 758 C3' RSQ E 4 OK 761 759 756 774 C3' G E 5 OK 772 775 776 797 C3' U E 6 OK 795 798 799 817 C3' A E 7 OK 815 818 819 839 C3' C E 8 OK 837 840 841 857 C3' G F 1 OK 855 858 859 880 C3' U F 2 OK 878 881 882 900 C3' A F 3 OK 898 901 902 928 C3' RSQ F 4 OK 931 929 926 944 C3' G F 5 OK 942 945 946 967 C3' U F 6 OK 965 968 969 987 C3' A F 7 OK 985 988 989 1009 C3' C F 8 OK 1007 1010 1011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 157 154 156 175 C4' G B 1 177 176 198 C4' U B 2 OK 200 197 199 218 C4' A B 3 OK 220 217 219 251 C4' RSQ B 4 OK 248 253 252 262 C4' G B 5 OK 264 261 263 285 C4' U B 6 OK 287 284 286 305 C4' A B 7 OK 307 304 306 327 C4' C B 8 OK 329 326 328 345 C4' G C 1 OK 347 344 346 368 C4' U C 2 OK 370 367 369 388 C4' A C 3 OK 390 387 389 421 C4' RSQ C 4 OK 418 423 422 432 C4' G C 5 OK 434 431 433 455 C4' U C 6 OK 457 454 456 475 C4' A C 7 OK 477 474 476 497 C4' C C 8 OK 499 496 498 515 C4' G D 1 OK 517 514 516 538 C4' U D 2 OK 540 537 539 558 C4' A D 3 OK 560 557 559 591 C4' RSQ D 4 OK 588 593 592 602 C4' G D 5 OK 604 601 603 625 C4' U D 6 OK 627 624 626 645 C4' A D 7 OK 647 644 646 667 C4' C D 8 OK 669 666 668 685 C4' G E 1 OK 687 684 686 708 C4' U E 2 OK 710 707 709 728 C4' A E 3 OK 730 727 729 761 C4' RSQ E 4 OK 758 763 762 772 C4' G E 5 OK 774 771 773 795 C4' U E 6 OK 797 794 796 815 C4' A E 7 OK 817 814 816 837 C4' C E 8 OK 839 836 838 855 C4' G F 1 OK 857 854 856 878 C4' U F 2 OK 880 877 879 898 C4' A F 3 OK 900 897 899 931 C4' RSQ F 4 OK 928 933 932 942 C4' G F 5 OK 944 941 943 965 C4' U F 6 OK 967 964 966 985 C4' A F 7 OK 987 984 986 1007 C4' C F 8 OK 1009 1006 1008 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 8 153 155 197 C5' U B 2 196 198 217 C5' A B 3 216 218 253 C5' RSQ B 4 254 251 261 C5' G B 5 260 262 284 C5' U B 6 283 285 304 C5' A B 7 303 305 326 C5' C B 8 325 327 344 C5' G C 1 343 345 367 C5' U C 2 366 368 387 C5' A C 3 386 388 423 C5' RSQ C 4 424 421 431 C5' G C 5 430 432 454 C5' U C 6 453 455 474 C5' A C 7 473 475 496 C5' C C 8 495 497 514 C5' G D 1 513 515 537 C5' U D 2 536 538 557 C5' A D 3 556 558 593 C5' RSQ D 4 594 591 601 C5' G D 5 600 602 624 C5' U D 6 623 625 644 C5' A D 7 643 645 666 C5' C D 8 665 667 684 C5' G E 1 683 685 707 C5' U E 2 706 708 727 C5' A E 3 726 728 763 C5' RSQ E 4 764 761 771 C5' G E 5 770 772 794 C5' U E 6 793 795 814 C5' A E 7 813 815 836 C5' C E 8 835 837 854 C5' G F 1 853 855 877 C5' U F 2 876 878 897 C5' A F 3 896 898 933 C5' RSQ F 4 934 931 941 C5' G F 5 940 942 964 C5' U F 6 963 965 984 C5' A F 7 983 985 1006 C5' C F 8 1005 1007 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 136 151 152 153 193 P U B 2 distorted distorted 178 194 195 196 213 P A B 3 distorted distorted 201 214 215 216 235 P RSQ B 4 distorted distorted 221 255 256 254 257 P G B 5 distorted distorted 249 258 259 260 280 P U B 6 distorted distorted 265 281 282 283 300 P A B 7 distorted distorted 288 301 302 303 322 P C B 8 distorted distorted 308 323 324 325 363 P U C 2 distorted distorted 348 364 365 366 383 P A C 3 distorted distorted 371 384 385 386 405 P RSQ C 4 distorted distorted 391 425 426 424 427 P G C 5 distorted distorted 419 428 429 430 450 P U C 6 distorted distorted 435 451 452 453 470 P A C 7 distorted distorted 458 471 472 473 492 P C C 8 distorted distorted 478 493 494 495 533 P U D 2 distorted distorted 518 534 535 536 553 P A D 3 distorted distorted 541 554 555 556 575 P RSQ D 4 distorted distorted 561 595 596 594 597 P G D 5 distorted distorted 589 598 599 600 620 P U D 6 distorted distorted 605 621 622 623 640 P A D 7 distorted distorted 628 641 642 643 662 P C D 8 distorted distorted 648 663 664 665 703 P U E 2 distorted distorted 688 704 705 706 723 P A E 3 distorted distorted 711 724 725 726 745 P RSQ E 4 distorted distorted 731 765 766 764 767 P G E 5 distorted distorted 759 768 769 770 790 P U E 6 distorted distorted 775 791 792 793 810 P A E 7 distorted distorted 798 811 812 813 832 P C E 8 distorted distorted 818 833 834 835 873 P U F 2 distorted distorted 858 874 875 876 893 P A F 3 distorted distorted 881 894 895 896 915 P RSQ F 4 distorted distorted 901 935 936 934 937 P G F 5 distorted distorted 929 938 939 940 960 P U F 6 distorted distorted 945 961 962 963 980 P A F 7 distorted distorted 968 981 982 983 1002 P C F 8 distorted distorted 988 1003 1004 1005 ---------------------------------------------------------------------------------