ID code: '4PHY' 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' C A 1 beta 4 10 7 29 C1' G A 2 beta 24 30 27 52 C1' U A 3 beta 47 53 50 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' U A 6 beta 110 116 113 135 C1' C A 7 beta 130 136 133 155 C1' C A 8 beta 150 156 153 175 C1' C A 9 beta 170 176 173 195 C1' C A 10 beta 190 196 193 215 C1' A A 11 beta 210 216 213 237 C1' C A 12 beta 232 238 235 257 C1' C A 13 beta 252 258 255 277 C1' U A 14 beta 272 278 275 297 C1' C A 15 beta 292 298 295 317 C1' G A 16 beta 312 318 315 340 C1' G A 17 beta 335 341 338 363 C1' A A 18 beta 358 364 361 385 C1' U A 19 beta 380 386 383 405 C1' C A 20 beta 400 406 403 425 C1' A A 21 beta 420 426 423 447 C1' C A 22 beta 442 448 445 467 C1' U A 23 beta 462 468 465 487 C1' G A 24 beta 482 488 485 510 C1' C A 25 beta 505 511 508 530 C1' G A 26 beta 525 531 528 551 C1' G B 27 beta 546 552 549 574 C1' C B 28 beta 569 575 572 594 C1' A B 29 beta 589 595 592 616 C1' G B 30 beta 611 617 614 639 C1' G B 31 beta 634 640 637 662 C1' A B 32 beta 657 663 660 684 C1' A B 33 beta 679 685 682 706 C1' C B 34 beta 701 707 704 726 C1' C B 35 beta 721 727 724 746 C1' G B 36 beta 741 747 744 769 C1' A B 37 beta 764 770 767 791 C1' G B 38 beta 786 792 789 814 C1' A B 39 beta 809 815 812 836 C1' G B 40 beta 831 837 834 859 C1' G B 41 beta 854 860 857 882 C1' C B 42 beta 877 883 880 902 C1' A B 43 beta 897 903 900 924 C1' C B 44 beta 919 925 922 944 C1' G B 45 beta 939 945 942 967 C1' C B 46 beta 962 968 965 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' G A 2 OK 29 25 28 50 C2' U A 3 OK 52 48 51 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' U A 6 OK 115 111 114 133 C2' C A 7 OK 135 131 134 153 C2' C A 8 OK 155 151 154 173 C2' C A 9 OK 175 171 174 193 C2' C A 10 OK 195 191 194 213 C2' A A 11 OK 215 211 214 235 C2' C A 12 OK 237 233 236 255 C2' C A 13 OK 257 253 256 275 C2' U A 14 OK 277 273 276 295 C2' C A 15 OK 297 293 296 315 C2' G A 16 OK 317 313 316 338 C2' G A 17 OK 340 336 339 361 C2' A A 18 OK 363 359 362 383 C2' U A 19 OK 385 381 384 403 C2' C A 20 OK 405 401 404 423 C2' A A 21 OK 425 421 424 445 C2' C A 22 OK 447 443 446 465 C2' U A 23 OK 467 463 466 485 C2' G A 24 OK 487 483 486 508 C2' C A 25 OK 510 506 509 528 C2' G A 26 OK 530 526 529 549 C2' G B 27 OK 551 547 550 572 C2' C B 28 OK 574 570 573 592 C2' A B 29 OK 594 590 593 614 C2' G B 30 OK 616 612 615 637 C2' G B 31 OK 639 635 638 660 C2' A B 32 OK 662 658 661 682 C2' A B 33 OK 684 680 683 704 C2' C B 34 OK 706 702 705 724 C2' C B 35 OK 726 722 725 744 C2' G B 36 OK 746 742 745 767 C2' A B 37 OK 769 765 768 789 C2' G B 38 OK 791 787 790 812 C2' A B 39 OK 814 810 813 834 C2' G B 40 OK 836 832 835 857 C2' G B 41 OK 859 855 858 880 C2' C B 42 OK 882 878 881 900 C2' A B 43 OK 902 898 901 922 C2' C B 44 OK 924 920 923 942 C2' G B 45 OK 944 940 943 965 C2' C B 46 OK 967 963 966 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' G A 2 OK 23 26 27 48 C3' U A 3 OK 46 49 50 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' U A 6 OK 109 112 113 131 C3' C A 7 OK 129 132 133 151 C3' C A 8 OK 149 152 153 171 C3' C A 9 OK 169 172 173 191 C3' C A 10 OK 189 192 193 211 C3' A A 11 OK 209 212 213 233 C3' C A 12 OK 231 234 235 253 C3' C A 13 OK 251 254 255 273 C3' U A 14 OK 271 274 275 293 C3' C A 15 OK 291 294 295 313 C3' G A 16 OK 311 314 315 336 C3' G A 17 OK 334 337 338 359 C3' A A 18 OK 357 360 361 381 C3' U A 19 OK 379 382 383 401 C3' C A 20 OK 399 402 403 421 C3' A A 21 OK 419 422 423 443 C3' C A 22 OK 441 444 445 463 C3' U A 23 OK 461 464 465 483 C3' G A 24 OK 481 484 485 506 C3' C A 25 OK 504 507 508 526 C3' G A 26 OK 524 527 528 547 C3' G B 27 OK 545 548 549 570 C3' C B 28 OK 568 571 572 590 C3' A B 29 OK 588 591 592 612 C3' G B 30 OK 610 613 614 635 C3' G B 31 OK 633 636 637 658 C3' A B 32 OK 656 659 660 680 C3' A B 33 OK 678 681 682 702 C3' C B 34 OK 700 703 704 722 C3' C B 35 OK 720 723 724 742 C3' G B 36 OK 740 743 744 765 C3' A B 37 OK 763 766 767 787 C3' G B 38 OK 785 788 789 810 C3' A B 39 OK 808 811 812 832 C3' G B 40 OK 830 833 834 855 C3' G B 41 OK 853 856 857 878 C3' C B 42 OK 876 879 880 898 C3' A B 43 OK 896 899 900 920 C3' C B 44 OK 918 921 922 940 C3' G B 45 OK 938 941 942 963 C3' C B 46 OK 961 964 965 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' G A 2 OK 25 22 24 46 C4' U A 3 OK 48 45 47 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' U A 6 OK 111 108 110 129 C4' C A 7 OK 131 128 130 149 C4' C A 8 OK 151 148 150 169 C4' C A 9 OK 171 168 170 189 C4' C A 10 OK 191 188 190 209 C4' A A 11 OK 211 208 210 231 C4' C A 12 OK 233 230 232 251 C4' C A 13 OK 253 250 252 271 C4' U A 14 OK 273 270 272 291 C4' C A 15 OK 293 290 292 311 C4' G A 16 OK 313 310 312 334 C4' G A 17 OK 336 333 335 357 C4' A A 18 OK 359 356 358 379 C4' U A 19 OK 381 378 380 399 C4' C A 20 OK 401 398 400 419 C4' A A 21 OK 421 418 420 441 C4' C A 22 OK 443 440 442 461 C4' U A 23 OK 463 460 462 481 C4' G A 24 OK 483 480 482 504 C4' C A 25 OK 506 503 505 524 C4' G A 26 OK 526 523 525 545 C4' G B 27 OK 547 544 546 568 C4' C B 28 OK 570 567 569 588 C4' A B 29 OK 590 587 589 610 C4' G B 30 OK 612 609 611 633 C4' G B 31 OK 635 632 634 656 C4' A B 32 OK 658 655 657 678 C4' A B 33 OK 680 677 679 700 C4' C B 34 OK 702 699 701 720 C4' C B 35 OK 722 719 721 740 C4' G B 36 OK 742 739 741 763 C4' A B 37 OK 765 762 764 785 C4' G B 38 OK 787 784 786 808 C4' A B 39 OK 810 807 809 830 C4' G B 40 OK 832 829 831 853 C4' G B 41 OK 855 852 854 876 C4' C B 42 OK 878 875 877 896 C4' A B 43 OK 898 895 897 918 C4' C B 44 OK 920 917 919 938 C4' G B 45 OK 940 937 939 961 C4' C B 46 OK 963 960 962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' G A 2 21 23 45 C5' U A 3 44 46 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' U A 6 107 109 128 C5' C A 7 127 129 148 C5' C A 8 147 149 168 C5' C A 9 167 169 188 C5' C A 10 187 189 208 C5' A A 11 207 209 230 C5' C A 12 229 231 250 C5' C A 13 249 251 270 C5' U A 14 269 271 290 C5' C A 15 289 291 310 C5' G A 16 309 311 333 C5' G A 17 332 334 356 C5' A A 18 355 357 378 C5' U A 19 377 379 398 C5' C A 20 397 399 418 C5' A A 21 417 419 440 C5' C A 22 439 441 460 C5' U A 23 459 461 480 C5' G A 24 479 481 503 C5' C A 25 502 504 523 C5' G A 26 522 524 544 C5' G B 27 543 545 567 C5' C B 28 566 568 587 C5' A B 29 586 588 609 C5' G B 30 608 610 632 C5' G B 31 631 633 655 C5' A B 32 654 656 677 C5' A B 33 676 678 699 C5' C B 34 698 700 719 C5' C B 35 718 720 739 C5' G B 36 738 740 762 C5' A B 37 761 763 784 C5' G B 38 783 785 807 C5' A B 39 806 808 829 C5' G B 40 828 830 852 C5' G B 41 851 853 875 C5' C B 42 874 876 895 C5' A B 43 894 896 917 C5' C B 44 916 918 937 C5' G B 45 936 938 960 C5' C B 46 959 961 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 2 distorted distorted 6 19 20 21 41 P U A 3 distorted distorted 26 42 43 44 61 P G A 4 distorted distorted 49 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P U A 6 distorted distorted 92 105 106 107 124 P C A 7 distorted distorted 112 125 126 127 144 P C A 8 distorted distorted 132 145 146 147 164 P C A 9 distorted distorted 152 165 166 167 184 P C A 10 distorted distorted 172 185 186 187 204 P A A 11 distorted distorted 192 205 206 207 226 P C A 12 distorted distorted 212 227 228 229 246 P C A 13 distorted distorted 234 247 248 249 266 P U A 14 distorted distorted 254 267 268 269 286 P C A 15 distorted distorted 274 287 288 289 306 P G A 16 distorted distorted 294 307 308 309 329 P G A 17 distorted distorted 314 330 331 332 352 P A A 18 distorted distorted 337 353 354 355 374 P U A 19 distorted distorted 360 375 376 377 394 P C A 20 distorted distorted 382 395 396 397 414 P A A 21 distorted distorted 402 415 416 417 436 P C A 22 distorted distorted 422 437 438 439 456 P U A 23 distorted distorted 444 457 458 459 476 P G A 24 distorted distorted 464 477 478 479 499 P C A 25 distorted distorted 484 500 501 502 519 P G A 26 distorted distorted 507 520 521 522 563 P C B 28 distorted distorted 548 564 565 566 583 P A B 29 distorted distorted 571 584 585 586 605 P G B 30 distorted distorted 591 606 607 608 628 P G B 31 distorted distorted 613 629 630 631 651 P A B 32 distorted distorted 636 652 653 654 673 P A B 33 distorted distorted 659 674 675 676 695 P C B 34 distorted distorted 681 696 697 698 715 P C B 35 distorted distorted 703 716 717 718 735 P G B 36 distorted distorted 723 736 737 738 758 P A B 37 distorted distorted 743 759 760 761 780 P G B 38 distorted distorted 766 781 782 783 803 P A B 39 distorted distorted 788 804 805 806 825 P G B 40 distorted distorted 811 826 827 828 848 P G B 41 distorted distorted 833 849 850 851 871 P C B 42 distorted distorted 856 872 873 874 891 P A B 43 distorted distorted 879 892 893 894 913 P C B 44 distorted distorted 899 914 915 916 933 P G B 45 distorted distorted 921 934 935 936 956 P C B 46 distorted distorted 941 957 958 959 ---------------------------------------------------------------------------------