ID code: '4IQS' 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' G A 3 beta 47 53 50 73 C1' US5 A 4 beta 80 65 74 95 C1' A A 5 beta 90 96 93 117 C1' C A 6 beta 112 118 115 137 C1' A A 7 beta 132 138 135 159 C1' C A 8 beta 154 160 157 177 C1' G B 1 beta 172 178 175 200 C1' U B 2 beta 195 201 198 220 C1' G B 3 beta 215 221 218 241 C1' US5 B 4 beta 248 233 242 263 C1' A B 5 beta 258 264 261 285 C1' C B 6 beta 280 286 283 305 C1' A B 7 beta 300 306 303 327 C1' C B 8 beta 322 328 325 345 C1' G C 1 beta 340 346 343 368 C1' U C 2 beta 363 369 366 388 C1' G C 3 beta 383 389 386 409 C1' US5 C 4 beta 416 401 410 431 C1' A C 5 beta 426 432 429 453 C1' C C 6 beta 448 454 451 473 C1' A C 7 beta 468 474 471 495 C1' C C 8 beta 490 496 493 513 C1' G D 1 beta 508 514 511 536 C1' U D 2 beta 531 537 534 556 C1' G D 3 beta 551 557 554 577 C1' US5 D 4 beta 584 569 578 599 C1' A D 5 beta 594 600 597 621 C1' C D 6 beta 616 622 619 641 C1' A D 7 beta 636 642 639 663 C1' C D 8 beta 658 664 661 681 C1' G E 1 beta 676 682 679 704 C1' U E 2 beta 699 705 702 724 C1' G E 3 beta 719 725 722 745 C1' US5 E 4 beta 752 737 746 767 C1' A E 5 beta 762 768 765 789 C1' C E 6 beta 784 790 787 809 C1' A E 7 beta 804 810 807 831 C1' C E 8 beta 826 832 829 849 C1' G F 1 beta 844 850 847 872 C1' U F 2 beta 867 873 870 892 C1' G F 3 beta 887 893 890 913 C1' US5 F 4 beta 920 905 914 935 C1' A F 5 beta 930 936 933 957 C1' C F 6 beta 952 958 955 977 C1' A F 7 beta 972 978 975 999 C1' C F 8 beta 994 1000 997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK 52 48 51 74 C2' US5 A 4 OK 73 77 75 93 C2' A A 5 OK 95 91 94 115 C2' C A 6 OK 117 113 116 135 C2' A A 7 OK 137 133 136 157 C2' C A 8 OK 159 155 158 175 C2' G B 1 OK 177 173 176 198 C2' U B 2 OK 200 196 199 218 C2' G B 3 OK 220 216 219 242 C2' US5 B 4 OK 241 245 243 261 C2' A B 5 OK 263 259 262 283 C2' C B 6 OK 285 281 284 303 C2' A B 7 OK 305 301 304 325 C2' C B 8 OK 327 323 326 343 C2' G C 1 OK 345 341 344 366 C2' U C 2 OK 368 364 367 386 C2' G C 3 OK 388 384 387 410 C2' US5 C 4 OK 409 413 411 429 C2' A C 5 OK 431 427 430 451 C2' C C 6 OK 453 449 452 471 C2' A C 7 OK 473 469 472 493 C2' C C 8 OK 495 491 494 511 C2' G D 1 OK 513 509 512 534 C2' U D 2 OK 536 532 535 554 C2' G D 3 OK 556 552 555 578 C2' US5 D 4 OK 577 581 579 597 C2' A D 5 OK 599 595 598 619 C2' C D 6 OK 621 617 620 639 C2' A D 7 OK 641 637 640 661 C2' C D 8 OK 663 659 662 679 C2' G E 1 OK 681 677 680 702 C2' U E 2 OK 704 700 703 722 C2' G E 3 OK 724 720 723 746 C2' US5 E 4 OK 745 749 747 765 C2' A E 5 OK 767 763 766 787 C2' C E 6 OK 789 785 788 807 C2' A E 7 OK 809 805 808 829 C2' C E 8 OK 831 827 830 847 C2' G F 1 OK 849 845 848 870 C2' U F 2 OK 872 868 871 890 C2' G F 3 OK 892 888 891 914 C2' US5 F 4 OK 913 917 915 933 C2' A F 5 OK 935 931 934 955 C2' C F 6 OK 957 953 956 975 C2' A F 7 OK 977 973 976 997 C2' C F 8 OK 999 995 998 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK 46 49 50 77 C3' US5 A 4 OK 79 78 74 91 C3' A A 5 OK 89 92 93 113 C3' C A 6 OK 111 114 115 133 C3' A A 7 OK 131 134 135 155 C3' C A 8 OK 153 156 157 173 C3' G B 1 OK 171 174 175 196 C3' U B 2 OK 194 197 198 216 C3' G B 3 OK 214 217 218 245 C3' US5 B 4 OK 247 246 242 259 C3' A B 5 OK 257 260 261 281 C3' C B 6 OK 279 282 283 301 C3' A B 7 OK 299 302 303 323 C3' C B 8 OK 321 324 325 341 C3' G C 1 OK 339 342 343 364 C3' U C 2 OK 362 365 366 384 C3' G C 3 OK 382 385 386 413 C3' US5 C 4 OK 415 414 410 427 C3' A C 5 OK 425 428 429 449 C3' C C 6 OK 447 450 451 469 C3' A C 7 OK 467 470 471 491 C3' C C 8 OK 489 492 493 509 C3' G D 1 OK 507 510 511 532 C3' U D 2 OK 530 533 534 552 C3' G D 3 OK 550 553 554 581 C3' US5 D 4 OK 583 582 578 595 C3' A D 5 OK 593 596 597 617 C3' C D 6 OK 615 618 619 637 C3' A D 7 OK 635 638 639 659 C3' C D 8 OK 657 660 661 677 C3' G E 1 OK 675 678 679 700 C3' U E 2 OK 698 701 702 720 C3' G E 3 OK 718 721 722 749 C3' US5 E 4 OK 751 750 746 763 C3' A E 5 OK 761 764 765 785 C3' C E 6 OK 783 786 787 805 C3' A E 7 OK 803 806 807 827 C3' C E 8 OK 825 828 829 845 C3' G F 1 OK 843 846 847 868 C3' U F 2 OK 866 869 870 888 C3' G F 3 OK 886 889 890 917 C3' US5 F 4 OK 919 918 914 931 C3' A F 5 OK 929 932 933 953 C3' C F 6 OK 951 954 955 973 C3' A F 7 OK 971 974 975 995 C3' C F 8 OK 993 996 997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK 48 45 47 79 C4' US5 A 4 OK 77 81 80 89 C4' A A 5 OK 91 88 90 111 C4' C A 6 OK 113 110 112 131 C4' A A 7 OK 133 130 132 153 C4' C A 8 OK 155 152 154 171 C4' G B 1 OK 173 170 172 194 C4' U B 2 OK 196 193 195 214 C4' G B 3 OK 216 213 215 247 C4' US5 B 4 OK 245 249 248 257 C4' A B 5 OK 259 256 258 279 C4' C B 6 OK 281 278 280 299 C4' A B 7 OK 301 298 300 321 C4' C B 8 OK 323 320 322 339 C4' G C 1 OK 341 338 340 362 C4' U C 2 OK 364 361 363 382 C4' G C 3 OK 384 381 383 415 C4' US5 C 4 OK 413 417 416 425 C4' A C 5 OK 427 424 426 447 C4' C C 6 OK 449 446 448 467 C4' A C 7 OK 469 466 468 489 C4' C C 8 OK 491 488 490 507 C4' G D 1 OK 509 506 508 530 C4' U D 2 OK 532 529 531 550 C4' G D 3 OK 552 549 551 583 C4' US5 D 4 OK 581 585 584 593 C4' A D 5 OK 595 592 594 615 C4' C D 6 OK 617 614 616 635 C4' A D 7 OK 637 634 636 657 C4' C D 8 OK 659 656 658 675 C4' G E 1 OK 677 674 676 698 C4' U E 2 OK 700 697 699 718 C4' G E 3 OK 720 717 719 751 C4' US5 E 4 OK 749 753 752 761 C4' A E 5 OK 763 760 762 783 C4' C E 6 OK 785 782 784 803 C4' A E 7 OK 805 802 804 825 C4' C E 8 OK 827 824 826 843 C4' G F 1 OK 845 842 844 866 C4' U F 2 OK 868 865 867 886 C4' G F 3 OK 888 885 887 919 C4' US5 F 4 OK 917 921 920 929 C4' A F 5 OK 931 928 930 951 C4' C F 6 OK 953 950 952 971 C4' A F 7 OK 973 970 972 993 C4' C F 8 OK 995 992 994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 44 46 81 C5' US5 A 4 82 79 88 C5' A A 5 87 89 110 C5' C A 6 109 111 130 C5' A A 7 129 131 152 C5' C A 8 151 153 170 C5' G B 1 169 171 193 C5' U B 2 192 194 213 C5' G B 3 212 214 249 C5' US5 B 4 250 247 256 C5' A B 5 255 257 278 C5' C B 6 277 279 298 C5' A B 7 297 299 320 C5' C B 8 319 321 338 C5' G C 1 337 339 361 C5' U C 2 360 362 381 C5' G C 3 380 382 417 C5' US5 C 4 418 415 424 C5' A C 5 423 425 446 C5' C C 6 445 447 466 C5' A C 7 465 467 488 C5' C C 8 487 489 506 C5' G D 1 505 507 529 C5' U D 2 528 530 549 C5' G D 3 548 550 585 C5' US5 D 4 586 583 592 C5' A D 5 591 593 614 C5' C D 6 613 615 634 C5' A D 7 633 635 656 C5' C D 8 655 657 674 C5' G E 1 673 675 697 C5' U E 2 696 698 717 C5' G E 3 716 718 753 C5' US5 E 4 754 751 760 C5' A E 5 759 761 782 C5' C E 6 781 783 802 C5' A E 7 801 803 824 C5' C E 8 823 825 842 C5' G F 1 841 843 865 C5' U F 2 864 866 885 C5' G F 3 884 886 921 C5' US5 F 4 922 919 928 C5' A F 5 927 929 950 C5' C F 6 949 951 970 C5' A F 7 969 971 992 C5' C F 8 991 993 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P US5 A 4 OK OK 49 83 76 82 84 P A A 5 distorted distorted 78 85 86 87 106 P C A 6 distorted distorted 92 107 108 109 126 P A A 7 distorted distorted 114 127 128 129 148 P C A 8 distorted distorted 134 149 150 151 189 P U B 2 distorted distorted 174 190 191 192 209 P G B 3 distorted distorted 197 210 211 212 232 P US5 B 4 distorted distorted 217 251 244 250 252 P A B 5 distorted distorted 246 253 254 255 274 P C B 6 distorted distorted 260 275 276 277 294 P A B 7 distorted distorted 282 295 296 297 316 P C B 8 distorted distorted 302 317 318 319 357 P U C 2 distorted distorted 342 358 359 360 377 P G C 3 distorted distorted 365 378 379 380 400 P US5 C 4 distorted distorted 385 419 412 418 420 P A C 5 distorted distorted 414 421 422 423 442 P C C 6 distorted distorted 428 443 444 445 462 P A C 7 distorted distorted 450 463 464 465 484 P C C 8 distorted distorted 470 485 486 487 525 P U D 2 distorted distorted 510 526 527 528 545 P G D 3 distorted distorted 533 546 547 548 568 P US5 D 4 OK OK 553 587 580 586 588 P A D 5 distorted distorted 582 589 590 591 610 P C D 6 distorted distorted 596 611 612 613 630 P A D 7 distorted distorted 618 631 632 633 652 P C D 8 distorted distorted 638 653 654 655 693 P U E 2 distorted distorted 678 694 695 696 713 P G E 3 distorted distorted 701 714 715 716 736 P US5 E 4 OK OK 721 755 748 754 756 P A E 5 distorted distorted 750 757 758 759 778 P C E 6 distorted distorted 764 779 780 781 798 P A E 7 distorted distorted 786 799 800 801 820 P C E 8 distorted distorted 806 821 822 823 861 P U F 2 distorted distorted 846 862 863 864 881 P G F 3 distorted distorted 869 882 883 884 904 P US5 F 4 distorted distorted 889 923 916 922 924 P A F 5 distorted distorted 918 925 926 927 946 P C F 6 distorted distorted 932 947 948 949 966 P A F 7 distorted distorted 954 967 968 969 988 P C F 8 distorted distorted 974 989 990 991 ---------------------------------------------------------------------------------