ID code: '1E4P' 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' --------------------------------------------------------------------------------- 10 C1' G A 1 alpha beta 5 28 11 8 44 C1' U A 2 alpha beta 39 59 45 42 74 C1' G A 3 alpha beta 69 92 75 72 108 C1' C A 4 alpha beta 103 123 109 106 139 C1' G A 5 alpha beta 134 157 140 137 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' A A 9 alpha beta 268 290 274 271 306 C1' C A 10 alpha beta 301 321 307 304 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' A A 12 alpha beta 366 388 372 369 404 C1' A A 13 alpha beta 399 421 405 402 437 C1' A A 14 alpha beta 432 454 438 435 470 C1' G A 15 alpha beta 465 488 471 468 504 C1' U A 16 alpha beta 499 519 505 502 534 C1' C A 17 alpha beta 529 549 535 532 565 C1' C A 18 alpha beta 560 580 566 563 596 C1' G A 19 alpha beta 591 614 597 594 630 C1' A A 20 alpha beta 625 647 631 628 663 C1' G A 21 alpha beta 658 681 664 661 697 C1' C A 22 alpha beta 692 712 698 695 728 C1' G A 23 alpha beta 723 746 729 726 762 C1' C A 24 alpha beta 757 777 763 760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8 C2' G A 1 OK OK 10 6 26 9 42 C2' U A 2 OK OK 44 40 57 43 72 C2' G A 3 OK OK 74 70 90 73 106 C2' C A 4 OK OK 108 104 121 107 137 C2' G A 5 OK OK 139 135 155 138 171 C2' A A 6 OK OK 173 169 188 172 204 C2' A A 7 OK OK 206 202 221 205 237 C2' G A 8 OK OK 239 235 255 238 271 C2' A A 9 OK OK 273 269 288 272 304 C2' C A 10 OK OK 306 302 319 305 335 C2' G A 11 OK OK 337 333 353 336 369 C2' A A 12 OK OK 371 367 386 370 402 C2' A A 13 OK OK 404 400 419 403 435 C2' A A 14 OK OK 437 433 452 436 468 C2' G A 15 OK OK 470 466 486 469 502 C2' U A 16 OK OK 504 500 517 503 532 C2' C A 17 OK OK 534 530 547 533 563 C2' C A 18 OK OK 565 561 578 564 594 C2' G A 19 OK OK 596 592 612 595 628 C2' A A 20 OK OK 630 626 645 629 661 C2' G A 21 OK OK 663 659 679 662 695 C2' C A 22 OK OK 697 693 710 696 726 C2' G A 23 OK OK 728 724 744 727 760 C2' C A 24 OK OK 762 758 775 761 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6 C3' G A 1 OK OK 4 25 7 8 40 C3' U A 2 OK OK 38 56 41 42 70 C3' G A 3 OK OK 68 89 71 72 104 C3' C A 4 OK OK 102 120 105 106 135 C3' G A 5 OK OK 133 154 136 137 169 C3' A A 6 OK OK 167 187 170 171 202 C3' A A 7 OK OK 200 220 203 204 235 C3' G A 8 OK OK 233 254 236 237 269 C3' A A 9 OK OK 267 287 270 271 302 C3' C A 10 OK OK 300 318 303 304 333 C3' G A 11 OK OK 331 352 334 335 367 C3' A A 12 OK OK 365 385 368 369 400 C3' A A 13 OK OK 398 418 401 402 433 C3' A A 14 OK OK 431 451 434 435 466 C3' G A 15 OK OK 464 485 467 468 500 C3' U A 16 OK OK 498 516 501 502 530 C3' C A 17 OK OK 528 546 531 532 561 C3' C A 18 OK OK 559 577 562 563 592 C3' G A 19 OK OK 590 611 593 594 626 C3' A A 20 OK OK 624 644 627 628 659 C3' G A 21 OK OK 657 678 660 661 693 C3' C A 22 OK OK 691 709 694 695 724 C3' G A 23 OK OK 722 743 725 726 758 C3' C A 24 OK OK 756 774 759 760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4 C4' G A 1 OK OK 6 24 3 5 38 C4' U A 2 OK OK 40 55 37 39 68 C4' G A 3 OK OK 70 88 67 69 102 C4' C A 4 OK OK 104 119 101 103 133 C4' G A 5 OK OK 135 153 132 134 167 C4' A A 6 OK OK 169 186 166 168 200 C4' A A 7 OK OK 202 219 199 201 233 C4' G A 8 OK OK 235 253 232 234 267 C4' A A 9 OK OK 269 286 266 268 300 C4' C A 10 OK OK 302 317 299 301 331 C4' G A 11 OK OK 333 351 330 332 365 C4' A A 12 OK OK 367 384 364 366 398 C4' A A 13 OK OK 400 417 397 399 431 C4' A A 14 OK OK 433 450 430 432 464 C4' G A 15 OK OK 466 484 463 465 498 C4' U A 16 OK OK 500 515 497 499 528 C4' C A 17 OK OK 530 545 527 529 559 C4' C A 18 OK OK 561 576 558 560 590 C4' G A 19 OK OK 592 610 589 591 624 C4' A A 20 OK OK 626 643 623 625 657 C4' G A 21 OK OK 659 677 656 658 691 C4' C A 22 OK OK 693 708 690 692 722 C4' G A 23 OK OK 724 742 721 723 756 C4' C A 24 OK OK 758 773 755 757 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3 C5' G A 1 OK OK 2 22 23 4 37 C5' U A 2 OK OK 36 53 54 38 67 C5' G A 3 OK OK 66 86 87 68 101 C5' C A 4 OK OK 100 117 118 102 132 C5' G A 5 OK OK 131 151 152 133 166 C5' A A 6 OK OK 165 184 185 167 199 C5' A A 7 distorted distorted 198 217 218 200 232 C5' G A 8 distorted distorted 231 251 252 233 266 C5' A A 9 OK OK 265 284 285 267 299 C5' C A 10 OK OK 298 315 316 300 330 C5' G A 11 distorted distorted 329 349 350 331 364 C5' A A 12 OK OK 363 382 383 365 397 C5' A A 13 distorted distorted 396 415 416 398 430 C5' A A 14 OK OK 429 448 449 431 463 C5' G A 15 OK OK 462 482 483 464 497 C5' U A 16 OK OK 496 513 514 498 527 C5' C A 17 OK OK 526 543 544 528 558 C5' C A 18 OK OK 557 574 575 559 589 C5' G A 19 distorted distorted 588 608 609 590 623 C5' A A 20 distorted distorted 622 641 642 624 656 C5' G A 21 OK OK 655 675 676 657 690 C5' C A 22 OK OK 689 706 707 691 721 C5' G A 23 OK OK 720 740 741 722 755 C5' C A 24 OK OK 754 771 772 756 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 2 33 P U A 2 distorted distorted 7 34 35 36 63 P G A 3 distorted distorted 41 64 65 66 97 P C A 4 distorted distorted 71 98 99 100 128 P G A 5 distorted distorted 105 129 130 131 162 P A A 6 distorted distorted 136 163 164 165 195 P A A 7 distorted distorted 170 196 197 198 228 P G A 8 distorted distorted 203 229 230 231 262 P A A 9 distorted distorted 236 263 264 265 295 P C A 10 distorted distorted 270 296 297 298 326 P G A 11 distorted distorted 303 327 328 329 360 P A A 12 distorted distorted 334 361 362 363 393 P A A 13 distorted distorted 368 394 395 396 426 P A A 14 distorted distorted 401 427 428 429 459 P G A 15 distorted distorted 434 460 461 462 493 P U A 16 distorted distorted 467 494 495 496 523 P C A 17 distorted distorted 501 524 525 526 554 P C A 18 distorted distorted 531 555 556 557 585 P G A 19 distorted distorted 562 586 587 588 619 P A A 20 distorted distorted 593 620 621 622 652 P G A 21 distorted distorted 627 653 654 655 686 P C A 22 distorted distorted 660 687 688 689 717 P G A 23 distorted distorted 694 718 719 720 751 P C A 24 distorted distorted 725 752 753 754 ---------------------------------------------------------------------------------