ID code: '1LFU' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 beta 4 9 7 42 C1' C A 2 beta 38 43 41 72 C1' G A 3 beta 68 73 71 105 C1' C A 4 beta 101 106 104 135 C1' A A 5 beta 131 136 134 167 C1' T A 6 beta 163 168 166 199 C1' G A 7 beta 195 200 198 232 C1' A A 8 beta 228 233 231 264 C1' T A 9 beta 260 265 263 296 C1' T A 10 beta 292 297 295 328 C1' G A 11 beta 324 329 327 361 C1' C A 12 beta 357 362 360 391 C1' C A 13 beta 387 392 390 421 C1' C A 14 beta 417 422 420 450 C1' G B 15 beta 446 451 449 484 C1' G B 16 beta 480 485 483 517 C1' G B 17 beta 513 518 516 550 C1' C B 18 beta 546 551 549 580 C1' A B 19 beta 576 581 579 612 C1' A B 20 beta 608 613 611 644 C1' T B 21 beta 640 645 643 676 C1' C B 22 beta 672 677 675 706 C1' A B 23 beta 702 707 705 738 C1' T B 24 beta 734 739 737 770 C1' G B 25 beta 766 771 769 803 C1' C B 26 beta 799 804 802 833 C1' G B 27 beta 829 834 832 866 C1' C B 28 beta 862 867 865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 41 C2' C A 2 42 39 71 C2' G A 3 72 69 104 C2' C A 4 105 102 134 C2' A A 5 135 132 166 C2' T A 6 167 164 198 C2' G A 7 199 196 231 C2' A A 8 232 229 263 C2' T A 9 264 261 295 C2' T A 10 296 293 327 C2' G A 11 328 325 360 C2' C A 12 361 358 390 C2' C A 13 391 388 420 C2' C A 14 421 418 449 C2' G B 15 450 447 483 C2' G B 16 484 481 516 C2' G B 17 517 514 549 C2' C B 18 550 547 579 C2' A B 19 580 577 611 C2' A B 20 612 609 643 C2' T B 21 644 641 675 C2' C B 22 676 673 705 C2' A B 23 706 703 737 C2' T B 24 738 735 769 C2' G B 25 770 767 802 C2' C B 26 803 800 832 C2' G B 27 833 830 865 C2' C B 28 866 863 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 39 C3' C A 2 OK 37 40 41 69 C3' G A 3 OK 67 70 71 102 C3' C A 4 OK 100 103 104 132 C3' A A 5 OK 130 133 134 164 C3' T A 6 OK 162 165 166 196 C3' G A 7 OK 194 197 198 229 C3' A A 8 OK 227 230 231 261 C3' T A 9 OK 259 262 263 293 C3' T A 10 OK 291 294 295 325 C3' G A 11 OK 323 326 327 358 C3' C A 12 OK 356 359 360 388 C3' C A 13 OK 386 389 390 418 C3' C A 14 OK 416 419 420 447 C3' G B 15 OK 445 448 449 481 C3' G B 16 OK 479 482 483 514 C3' G B 17 OK 512 515 516 547 C3' C B 18 OK 545 548 549 577 C3' A B 19 OK 575 578 579 609 C3' A B 20 OK 607 610 611 641 C3' T B 21 OK 639 642 643 673 C3' C B 22 OK 671 674 675 703 C3' A B 23 OK 701 704 705 735 C3' T B 24 OK 733 736 737 767 C3' G B 25 OK 765 768 769 800 C3' C B 26 OK 798 801 802 830 C3' G B 27 OK 828 831 832 863 C3' C B 28 OK 861 864 865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 37 C4' C A 2 OK 39 36 38 67 C4' G A 3 OK 69 66 68 100 C4' C A 4 OK 102 99 101 130 C4' A A 5 OK 132 129 131 162 C4' T A 6 OK 164 161 163 194 C4' G A 7 OK 196 193 195 227 C4' A A 8 OK 229 226 228 259 C4' T A 9 OK 261 258 260 291 C4' T A 10 OK 293 290 292 323 C4' G A 11 OK 325 322 324 356 C4' C A 12 OK 358 355 357 386 C4' C A 13 OK 388 385 387 416 C4' C A 14 OK 418 415 417 445 C4' G B 15 OK 447 444 446 479 C4' G B 16 OK 481 478 480 512 C4' G B 17 OK 514 511 513 545 C4' C B 18 OK 547 544 546 575 C4' A B 19 OK 577 574 576 607 C4' A B 20 OK 609 606 608 639 C4' T B 21 OK 641 638 640 671 C4' C B 22 OK 673 670 672 701 C4' A B 23 OK 703 700 702 733 C4' T B 24 OK 735 732 734 765 C4' G B 25 OK 767 764 766 798 C4' C B 26 OK 800 797 799 828 C4' G B 27 OK 830 827 829 861 C4' C B 28 OK 863 860 862 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 36 C5' C A 2 35 37 66 C5' G A 3 65 67 99 C5' C A 4 98 100 129 C5' A A 5 128 130 161 C5' T A 6 160 162 193 C5' G A 7 192 194 226 C5' A A 8 225 227 258 C5' T A 9 257 259 290 C5' T A 10 289 291 322 C5' G A 11 321 323 355 C5' C A 12 354 356 385 C5' C A 13 384 386 415 C5' C A 14 414 416 444 C5' G B 15 443 445 478 C5' G B 16 477 479 511 C5' G B 17 510 512 544 C5' C B 18 543 545 574 C5' A B 19 573 575 606 C5' A B 20 605 607 638 C5' T B 21 637 639 670 C5' C B 22 669 671 700 C5' A B 23 699 701 732 C5' T B 24 731 733 764 C5' G B 25 763 765 797 C5' C B 26 796 798 827 C5' G B 27 826 828 860 C5' C B 28 859 861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P C A 2 distorted distorted 6 33 34 35 62 P G A 3 distorted distorted 40 63 64 65 95 P C A 4 distorted distorted 70 96 97 98 125 P A A 5 distorted distorted 103 126 127 128 157 P T A 6 distorted distorted 133 158 159 160 189 P G A 7 distorted distorted 165 190 191 192 222 P A A 8 distorted distorted 197 223 224 225 254 P T A 9 distorted distorted 230 255 256 257 286 P T A 10 distorted distorted 262 287 288 289 318 P G A 11 distorted distorted 294 319 320 321 351 P C A 12 distorted distorted 326 352 353 354 381 P C A 13 distorted distorted 359 382 383 384 411 P C A 14 distorted distorted 389 412 413 414 474 P G B 16 distorted distorted 448 475 476 477 507 P G B 17 distorted distorted 482 508 509 510 540 P C B 18 distorted distorted 515 541 542 543 570 P A B 19 distorted distorted 548 571 572 573 602 P A B 20 distorted distorted 578 603 604 605 634 P T B 21 distorted distorted 610 635 636 637 666 P C B 22 distorted distorted 642 667 668 669 696 P A B 23 distorted distorted 674 697 698 699 728 P T B 24 distorted distorted 704 729 730 731 760 P G B 25 distorted distorted 736 761 762 763 793 P C B 26 distorted distorted 768 794 795 796 823 P G B 27 distorted distorted 801 824 825 826 856 P C B 28 distorted distorted 831 857 858 859 ---------------------------------------------------------------------------------