ID code: '1QE4' 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' --------------------------------------------------------------------------------- 11 C1' G E 4 beta 7 12 10 33 C1' G E 5 beta 29 34 32 55 C1' A E 6 beta 51 56 54 76 C1' A E 7 beta 72 77 75 97 C1' C E 8 beta 93 98 96 116 C1' T E 9 beta 112 117 115 136 C1' A E 10 beta 132 137 135 157 C1' C E 11 beta 153 158 156 176 C1' T E 12 beta 172 177 175 196 C1' G E 13 beta 192 197 195 218 C1' A E 14 beta 214 219 217 239 C1' C E 15 beta 235 240 238 258 C1' G E 16 beta 254 259 257 280 C1' A E 17 beta 276 281 279 301 C1' C E 18 beta 297 302 300 320 C1' G E 19 beta 316 321 319 342 C1' A E 20 beta 338 343 341 363 C1' C E 21 beta 359 364 362 382 C1' G E 22 beta 378 383 381 404 C1' A E 23 beta 400 405 403 426 C1' T D 23 beta 422 427 425 446 C1' C D 22 beta 442 447 445 465 C1' G D 21 beta 461 466 464 487 C1' T D 20 beta 483 488 486 507 C1' C D 19 beta 503 508 506 526 C1' G D 18 beta 522 527 525 548 C1' T D 17 beta 544 549 547 568 C1' C D 16 beta 564 569 567 587 C1' G D 15 beta 583 588 586 609 C1' T D 14 beta 605 610 608 629 C1' C D 13 beta 625 630 628 645 C1' A D 12 beta 641 646 644 666 C1' G D 11 beta 662 667 665 688 C1' T D 10 beta 684 689 687 708 C1' A D 9 beta 704 709 707 729 C1' G D 8 beta 725 730 728 751 C1' T D 7 beta 747 752 750 771 C1' T D 6 beta 767 772 770 791 C1' C D 5 beta 787 792 790 810 C1' C D 4 beta 806 811 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G E 4 11 8 32 C2' G E 5 33 30 54 C2' A E 6 55 52 75 C2' A E 7 76 73 96 C2' C E 8 97 94 115 C2' T E 9 116 113 135 C2' A E 10 136 133 156 C2' C E 11 157 154 175 C2' T E 12 176 173 195 C2' G E 13 196 193 217 C2' A E 14 218 215 238 C2' C E 15 239 236 257 C2' G E 16 258 255 279 C2' A E 17 280 277 300 C2' C E 18 301 298 319 C2' G E 19 320 317 341 C2' A E 20 342 339 362 C2' C E 21 363 360 381 C2' G E 22 382 379 403 C2' A E 23 404 401 425 C2' T D 23 426 423 445 C2' C D 22 446 443 464 C2' G D 21 465 462 486 C2' T D 20 487 484 506 C2' C D 19 507 504 525 C2' G D 18 526 523 547 C2' T D 17 548 545 567 C2' C D 16 568 565 586 C2' G D 15 587 584 608 C2' T D 14 609 606 628 C2' C D 13 629 626 644 C2' A D 12 645 642 665 C2' G D 11 666 663 687 C2' T D 10 688 685 707 C2' A D 9 708 705 728 C2' G D 8 729 726 750 C2' T D 7 751 748 770 C2' T D 6 771 768 790 C2' C D 5 791 788 809 C2' C D 4 810 807 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G E 4 OK 6 9 10 30 C3' G E 5 OK 28 31 32 52 C3' A E 6 OK 50 53 54 73 C3' A E 7 OK 71 74 75 94 C3' C E 8 OK 92 95 96 113 C3' T E 9 OK 111 114 115 133 C3' A E 10 OK 131 134 135 154 C3' C E 11 OK 152 155 156 173 C3' T E 12 OK 171 174 175 193 C3' G E 13 OK 191 194 195 215 C3' A E 14 distorted 213 216 217 236 C3' C E 15 OK 234 237 238 255 C3' G E 16 OK 253 256 257 277 C3' A E 17 distorted 275 278 279 298 C3' C E 18 OK 296 299 300 317 C3' G E 19 OK 315 318 319 339 C3' A E 20 distorted 337 340 341 360 C3' C E 21 OK 358 361 362 379 C3' G E 22 OK 377 380 381 401 C3' A E 23 distorted 399 402 403 423 C3' T D 23 OK 421 424 425 443 C3' C D 22 441 445 462 C3' G D 21 distorted 460 463 464 484 C3' T D 20 OK 482 485 486 504 C3' C D 19 502 506 523 C3' G D 18 distorted 521 524 525 545 C3' T D 17 OK 543 546 547 565 C3' C D 16 563 567 584 C3' G D 15 distorted 582 585 586 606 C3' T D 14 OK 604 607 608 626 C3' C D 13 624 628 642 C3' A D 12 OK 640 643 644 663 C3' G D 11 OK 661 664 665 685 C3' T D 10 OK 683 686 687 705 C3' A D 9 OK 703 706 707 726 C3' G D 8 OK 724 727 728 748 C3' T D 7 OK 746 749 750 768 C3' T D 6 OK 766 769 770 788 C3' C D 5 OK 786 789 790 807 C3' C D 4 OK 805 808 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G E 4 OK 8 5 7 28 C4' G E 5 OK 30 27 29 50 C4' A E 6 OK 52 49 51 71 C4' A E 7 OK 73 70 72 92 C4' C E 8 OK 94 91 93 111 C4' T E 9 OK 113 110 112 131 C4' A E 10 OK 133 130 132 152 C4' C E 11 OK 154 151 153 171 C4' T E 12 OK 173 170 172 191 C4' G E 13 OK 193 190 192 213 C4' A E 14 OK 215 212 214 234 C4' C E 15 OK 236 233 235 253 C4' G E 16 OK 255 252 254 275 C4' A E 17 OK 277 274 276 296 C4' C E 18 OK 298 295 297 315 C4' G E 19 OK 317 314 316 337 C4' A E 20 OK 339 336 338 358 C4' C E 21 OK 360 357 359 377 C4' G E 22 OK 379 376 378 399 C4' A E 23 OK 401 398 400 421 C4' T D 23 OK 423 420 422 441 C4' C D 22 OK 443 440 442 460 C4' G D 21 OK 462 459 461 482 C4' T D 20 OK 484 481 483 502 C4' C D 19 OK 504 501 503 521 C4' G D 18 OK 523 520 522 543 C4' T D 17 OK 545 542 544 563 C4' C D 16 OK 565 562 564 582 C4' G D 15 OK 584 581 583 604 C4' T D 14 OK 606 603 605 624 C4' C D 13 OK 626 623 625 640 C4' A D 12 OK 642 639 641 661 C4' G D 11 OK 663 660 662 683 C4' T D 10 OK 685 682 684 703 C4' A D 9 OK 705 702 704 724 C4' G D 8 OK 726 723 725 746 C4' T D 7 OK 748 745 747 766 C4' T D 6 OK 768 765 767 786 C4' C D 5 OK 788 785 787 805 C4' C D 4 OK 807 804 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G E 4 4 6 27 C5' G E 5 26 28 49 C5' A E 6 48 50 70 C5' A E 7 69 71 91 C5' C E 8 90 92 110 C5' T E 9 109 111 130 C5' A E 10 129 131 151 C5' C E 11 150 152 170 C5' T E 12 169 171 190 C5' G E 13 189 191 212 C5' A E 14 211 213 233 C5' C E 15 232 234 252 C5' G E 16 251 253 274 C5' A E 17 273 275 295 C5' C E 18 294 296 314 C5' G E 19 313 315 336 C5' A E 20 335 337 357 C5' C E 21 356 358 376 C5' G E 22 375 377 398 C5' A E 23 397 399 420 C5' T D 23 419 421 440 C5' C D 22 439 441 459 C5' G D 21 458 460 481 C5' T D 20 480 482 501 C5' C D 19 500 502 520 C5' G D 18 519 521 542 C5' T D 17 541 543 562 C5' C D 16 561 563 581 C5' G D 15 580 582 603 C5' T D 14 602 604 623 C5' C D 13 622 624 639 C5' A D 12 638 640 660 C5' G D 11 659 661 682 C5' T D 10 681 683 702 C5' A D 9 701 703 723 C5' G D 8 722 724 745 C5' T D 7 744 746 765 C5' T D 6 764 766 785 C5' C D 5 784 786 804 C5' C D 4 803 805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G E 4 distorted distorted 2 3 4 23 P G E 5 distorted distorted 9 24 25 26 45 P A E 6 distorted distorted 31 46 47 48 66 P A E 7 distorted distorted 53 67 68 69 87 P C E 8 distorted distorted 74 88 89 90 106 P T E 9 distorted distorted 95 107 108 109 126 P A E 10 distorted distorted 114 127 128 129 147 P C E 11 distorted distorted 134 148 149 150 166 P T E 12 distorted distorted 155 167 168 169 186 P G E 13 distorted distorted 187 188 189 208 P A E 14 distorted distorted 194 209 210 211 229 P C E 15 distorted distorted 230 231 232 248 P G E 16 distorted distorted 249 250 251 270 P A E 17 distorted distorted 256 271 272 273 291 P C E 18 distorted distorted 292 293 294 310 P G E 19 distorted distorted 311 312 313 332 P A E 20 distorted distorted 318 333 334 335 353 P C E 21 distorted distorted 354 355 356 372 P G E 22 distorted distorted 373 374 375 394 P A E 23 distorted distorted 380 395 396 397 416 P T D 23 distorted distorted 417 418 419 436 P C D 22 distorted distorted 424 437 438 439 455 P G D 21 distorted distorted 444 456 457 458 477 P T D 20 distorted distorted 478 479 480 497 P C D 19 distorted distorted 485 498 499 500 516 P G D 18 distorted distorted 505 517 518 519 538 P T D 17 distorted distorted 524 539 540 541 558 P C D 16 distorted distorted 546 559 560 561 577 P G D 15 distorted distorted 566 578 579 580 599 P T D 14 distorted distorted 600 601 602 619 P C D 13 distorted distorted 607 620 621 622 656 P G D 11 distorted distorted 643 657 658 659 678 P T D 10 distorted distorted 664 679 680 681 698 P A D 9 distorted distorted 686 699 700 701 719 P G D 8 distorted distorted 706 720 721 722 741 P T D 7 distorted distorted 727 742 743 744 761 P T D 6 distorted distorted 749 762 763 764 781 P C D 5 distorted distorted 769 782 783 784 800 P C D 4 distorted distorted 789 801 802 803 ---------------------------------------------------------------------------------