ID code: '1EXI' 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' A M -11 beta 4 9 7 29 C1' C M -10 beta 25 30 28 48 C1' C M -9 beta 44 49 47 67 C1' C M -8 beta 63 68 66 86 C1' T M -7 beta 82 87 85 106 C1' C M -6 beta 102 107 105 125 C1' C M -5 beta 121 126 124 144 C1' C M -4 beta 140 145 143 163 C1' C M -3 beta 159 164 162 182 C1' T M -2 beta 178 183 181 202 C1' T M 1 beta 198 203 201 222 C1' A M 2 beta 218 223 221 243 C1' G M 3 beta 239 244 242 265 C1' G M 4 beta 261 266 264 287 C1' G M 5 beta 283 288 286 309 C1' G M 6 beta 305 310 308 331 C1' A M 7 beta 327 332 330 352 C1' G M 8 beta 348 353 351 374 C1' G M 9 beta 370 375 373 396 C1' G M 10 beta 392 397 395 418 C1' T M 11 beta 414 419 417 436 C1' A N -11 beta 432 437 435 457 C1' C N -10 beta 453 458 456 476 C1' C N -9 beta 472 477 475 495 C1' C N -8 beta 491 496 494 514 C1' T N -7 beta 510 515 513 534 C1' C N -6 beta 530 535 533 553 C1' C N -5 beta 549 554 552 572 C1' C N -4 beta 568 573 571 591 C1' C N -3 beta 587 592 590 610 C1' T N -2 beta 606 611 609 630 C1' T N 1 beta 626 631 629 650 C1' A N 2 beta 646 651 649 671 C1' G N 3 beta 667 672 670 693 C1' G N 4 beta 689 694 692 715 C1' G N 5 beta 711 716 714 737 C1' G N 6 beta 733 738 736 759 C1' A N 7 beta 755 760 758 780 C1' G N 8 beta 776 781 779 802 C1' G N 9 beta 798 803 801 824 C1' G N 10 beta 820 825 823 846 C1' T N 11 beta 842 847 845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A M -11 8 5 28 C2' C M -10 29 26 47 C2' C M -9 48 45 66 C2' C M -8 67 64 85 C2' T M -7 86 83 105 C2' C M -6 106 103 124 C2' C M -5 125 122 143 C2' C M -4 144 141 162 C2' C M -3 163 160 181 C2' T M -2 182 179 201 C2' T M 1 202 199 221 C2' A M 2 222 219 242 C2' G M 3 243 240 264 C2' G M 4 265 262 286 C2' G M 5 287 284 308 C2' G M 6 309 306 330 C2' A M 7 331 328 351 C2' G M 8 352 349 373 C2' G M 9 374 371 395 C2' G M 10 396 393 417 C2' T M 11 418 415 435 C2' A N -11 436 433 456 C2' C N -10 457 454 475 C2' C N -9 476 473 494 C2' C N -8 495 492 513 C2' T N -7 514 511 533 C2' C N -6 534 531 552 C2' C N -5 553 550 571 C2' C N -4 572 569 590 C2' C N -3 591 588 609 C2' T N -2 610 607 629 C2' T N 1 630 627 649 C2' A N 2 650 647 670 C2' G N 3 671 668 692 C2' G N 4 693 690 714 C2' G N 5 715 712 736 C2' G N 6 737 734 758 C2' A N 7 759 756 779 C2' G N 8 780 777 801 C2' G N 9 802 799 823 C2' G N 10 824 821 845 C2' T N 11 846 843 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A M -11 OK 3 6 7 26 C3' C M -10 OK 24 27 28 45 C3' C M -9 OK 43 46 47 64 C3' C M -8 OK 62 65 66 83 C3' T M -7 OK 81 84 85 103 C3' C M -6 OK 101 104 105 122 C3' C M -5 OK 120 123 124 141 C3' C M -4 OK 139 142 143 160 C3' C M -3 OK 158 161 162 179 C3' T M -2 OK 177 180 181 199 C3' T M 1 OK 197 200 201 219 C3' A M 2 OK 217 220 221 240 C3' G M 3 OK 238 241 242 262 C3' G M 4 OK 260 263 264 284 C3' G M 5 OK 282 285 286 306 C3' G M 6 OK 304 307 308 328 C3' A M 7 OK 326 329 330 349 C3' G M 8 OK 347 350 351 371 C3' G M 9 OK 369 372 373 393 C3' G M 10 OK 391 394 395 415 C3' T M 11 OK 413 416 417 433 C3' A N -11 OK 431 434 435 454 C3' C N -10 OK 452 455 456 473 C3' C N -9 OK 471 474 475 492 C3' C N -8 OK 490 493 494 511 C3' T N -7 OK 509 512 513 531 C3' C N -6 OK 529 532 533 550 C3' C N -5 OK 548 551 552 569 C3' C N -4 OK 567 570 571 588 C3' C N -3 OK 586 589 590 607 C3' T N -2 OK 605 608 609 627 C3' T N 1 OK 625 628 629 647 C3' A N 2 OK 645 648 649 668 C3' G N 3 OK 666 669 670 690 C3' G N 4 OK 688 691 692 712 C3' G N 5 OK 710 713 714 734 C3' G N 6 OK 732 735 736 756 C3' A N 7 OK 754 757 758 777 C3' G N 8 OK 775 778 779 799 C3' G N 9 OK 797 800 801 821 C3' G N 10 OK 819 822 823 843 C3' T N 11 OK 841 844 845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A M -11 OK 5 2 4 24 C4' C M -10 OK 26 23 25 43 C4' C M -9 OK 45 42 44 62 C4' C M -8 OK 64 61 63 81 C4' T M -7 OK 83 80 82 101 C4' C M -6 OK 103 100 102 120 C4' C M -5 OK 122 119 121 139 C4' C M -4 OK 141 138 140 158 C4' C M -3 OK 160 157 159 177 C4' T M -2 OK 179 176 178 197 C4' T M 1 OK 199 196 198 217 C4' A M 2 OK 219 216 218 238 C4' G M 3 OK 240 237 239 260 C4' G M 4 OK 262 259 261 282 C4' G M 5 OK 284 281 283 304 C4' G M 6 OK 306 303 305 326 C4' A M 7 OK 328 325 327 347 C4' G M 8 OK 349 346 348 369 C4' G M 9 OK 371 368 370 391 C4' G M 10 OK 393 390 392 413 C4' T M 11 OK 415 412 414 431 C4' A N -11 OK 433 430 432 452 C4' C N -10 OK 454 451 453 471 C4' C N -9 OK 473 470 472 490 C4' C N -8 OK 492 489 491 509 C4' T N -7 OK 511 508 510 529 C4' C N -6 OK 531 528 530 548 C4' C N -5 OK 550 547 549 567 C4' C N -4 OK 569 566 568 586 C4' C N -3 OK 588 585 587 605 C4' T N -2 OK 607 604 606 625 C4' T N 1 OK 627 624 626 645 C4' A N 2 OK 647 644 646 666 C4' G N 3 OK 668 665 667 688 C4' G N 4 OK 690 687 689 710 C4' G N 5 OK 712 709 711 732 C4' G N 6 OK 734 731 733 754 C4' A N 7 OK 756 753 755 775 C4' G N 8 OK 777 774 776 797 C4' G N 9 OK 799 796 798 819 C4' G N 10 OK 821 818 820 841 C4' T N 11 OK 843 840 842 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A M -11 1 3 23 C5' C M -10 22 24 42 C5' C M -9 41 43 61 C5' C M -8 60 62 80 C5' T M -7 79 81 100 C5' C M -6 99 101 119 C5' C M -5 118 120 138 C5' C M -4 137 139 157 C5' C M -3 156 158 176 C5' T M -2 175 177 196 C5' T M 1 195 197 216 C5' A M 2 215 217 237 C5' G M 3 236 238 259 C5' G M 4 258 260 281 C5' G M 5 280 282 303 C5' G M 6 302 304 325 C5' A M 7 324 326 346 C5' G M 8 345 347 368 C5' G M 9 367 369 390 C5' G M 10 389 391 412 C5' T M 11 411 413 430 C5' A N -11 429 431 451 C5' C N -10 450 452 470 C5' C N -9 469 471 489 C5' C N -8 488 490 508 C5' T N -7 507 509 528 C5' C N -6 527 529 547 C5' C N -5 546 548 566 C5' C N -4 565 567 585 C5' C N -3 584 586 604 C5' T N -2 603 605 624 C5' T N 1 623 625 644 C5' A N 2 643 645 665 C5' G N 3 664 666 687 C5' G N 4 686 688 709 C5' G N 5 708 710 731 C5' G N 6 730 732 753 C5' A N 7 752 754 774 C5' G N 8 773 775 796 C5' G N 9 795 797 818 C5' G N 10 817 819 840 C5' T N 11 839 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P C M -10 distorted distorted 6 20 21 22 38 P C M -9 distorted distorted 27 39 40 41 57 P C M -8 distorted distorted 46 58 59 60 76 P T M -7 distorted distorted 65 77 78 79 96 P C M -6 distorted distorted 84 97 98 99 115 P C M -5 distorted distorted 104 116 117 118 134 P C M -4 distorted distorted 123 135 136 137 153 P C M -3 distorted distorted 142 154 155 156 172 P T M -2 distorted distorted 161 173 174 175 192 P T M 1 distorted distorted 180 193 194 195 212 P A M 2 distorted distorted 200 213 214 215 233 P G M 3 distorted distorted 220 234 235 236 255 P G M 4 distorted distorted 241 256 257 258 277 P G M 5 distorted distorted 263 278 279 280 299 P G M 6 distorted distorted 285 300 301 302 321 P A M 7 distorted distorted 307 322 323 324 342 P G M 8 distorted distorted 329 343 344 345 364 P G M 9 distorted distorted 350 365 366 367 386 P G M 10 distorted distorted 372 387 388 389 408 P T M 11 distorted distorted 394 409 410 411 447 P C N -10 distorted distorted 434 448 449 450 466 P C N -9 distorted distorted 455 467 468 469 485 P C N -8 distorted distorted 474 486 487 488 504 P T N -7 distorted distorted 493 505 506 507 524 P C N -6 distorted distorted 512 525 526 527 543 P C N -5 distorted distorted 532 544 545 546 562 P C N -4 distorted distorted 551 563 564 565 581 P C N -3 distorted distorted 570 582 583 584 600 P T N -2 distorted distorted 589 601 602 603 620 P T N 1 distorted distorted 608 621 622 623 640 P A N 2 distorted distorted 628 641 642 643 661 P G N 3 distorted distorted 648 662 663 664 683 P G N 4 distorted distorted 669 684 685 686 705 P G N 5 distorted distorted 691 706 707 708 727 P G N 6 distorted distorted 713 728 729 730 749 P A N 7 distorted distorted 735 750 751 752 770 P G N 8 distorted distorted 757 771 772 773 792 P G N 9 distorted distorted 778 793 794 795 814 P G N 10 distorted distorted 800 815 816 817 836 P T N 11 distorted distorted 822 837 838 839 ---------------------------------------------------------------------------------