ID code: '2ES5' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' G A 6 alpha beta 173 196 179 176 212 C1' G A 7 alpha beta 207 230 213 210 246 C1' C A 8 alpha beta 241 261 247 244 277 C1' U A 9 alpha beta 272 292 278 275 307 C1' C A 10 alpha beta 302 322 308 305 338 C1' U A 11 alpha beta 333 353 339 336 368 C1' G A 12 alpha beta 363 386 369 366 402 C1' G A 13 alpha beta 397 420 403 400 436 C1' C A 14 alpha beta 431 451 437 434 467 C1' A A 15 alpha beta 462 484 468 465 500 C1' G A 16 alpha beta 495 518 501 498 534 C1' C A 17 alpha beta 529 549 535 532 565 C1' U A 18 alpha beta 560 580 566 563 595 C1' U A 19 alpha beta 590 610 596 593 625 C1' U A 20 alpha beta 620 640 626 623 655 C1' U A 21 alpha beta 650 670 656 653 685 C1' C A 22 alpha beta 680 700 686 683 716 C1' C A 23 alpha beta 711 732 717 714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' G A 6 OK OK 178 174 194 177 210 C2' G A 7 OK OK 212 208 228 211 244 C2' C A 8 OK OK 246 242 259 245 275 C2' U A 9 OK OK 277 273 290 276 305 C2' C A 10 OK OK 307 303 320 306 336 C2' U A 11 OK OK 338 334 351 337 366 C2' G A 12 OK OK 368 364 384 367 400 C2' G A 13 OK OK 402 398 418 401 434 C2' C A 14 OK OK 436 432 449 435 465 C2' A A 15 OK OK 467 463 482 466 498 C2' G A 16 OK OK 500 496 516 499 532 C2' C A 17 OK OK 534 530 547 533 563 C2' U A 18 OK OK 565 561 578 564 593 C2' U A 19 OK OK 595 591 608 594 623 C2' U A 20 OK OK 625 621 638 624 653 C2' U A 21 OK OK 655 651 668 654 683 C2' C A 22 OK OK 685 681 698 684 714 C2' C A 23 OK OK 716 712 730 715 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' G A 6 OK OK 172 193 175 176 208 C3' G A 7 OK OK 206 227 209 210 242 C3' C A 8 OK OK 240 258 243 244 273 C3' U A 9 OK OK 271 289 274 275 303 C3' C A 10 OK OK 301 319 304 305 334 C3' U A 11 OK OK 332 350 335 336 364 C3' G A 12 OK OK 362 383 365 366 398 C3' G A 13 OK OK 396 417 399 400 432 C3' C A 14 OK OK 430 448 433 434 463 C3' A A 15 OK OK 461 481 464 465 496 C3' G A 16 OK OK 494 515 497 498 530 C3' C A 17 OK OK 528 546 531 532 561 C3' U A 18 OK OK 559 577 562 563 591 C3' U A 19 OK OK 589 607 592 593 621 C3' U A 20 OK OK 619 637 622 623 651 C3' U A 21 OK OK 649 667 652 653 681 C3' C A 22 OK OK 679 697 682 683 712 C3' C A 23 OK OK 710 728 713 714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' G A 6 OK OK 174 192 171 173 206 C4' G A 7 OK OK 208 226 205 207 240 C4' C A 8 OK OK 242 257 239 241 271 C4' U A 9 OK OK 273 288 270 272 301 C4' C A 10 OK OK 303 318 300 302 332 C4' U A 11 OK OK 334 349 331 333 362 C4' G A 12 OK OK 364 382 361 363 396 C4' G A 13 OK OK 398 416 395 397 430 C4' C A 14 OK OK 432 447 429 431 461 C4' A A 15 OK OK 463 480 460 462 494 C4' G A 16 OK OK 496 514 493 495 528 C4' C A 17 OK OK 530 545 527 529 559 C4' U A 18 OK OK 561 576 558 560 589 C4' U A 19 OK OK 591 606 588 590 619 C4' U A 20 OK OK 621 636 618 620 649 C4' U A 21 OK OK 651 666 648 650 679 C4' C A 22 OK OK 681 696 678 680 710 C4' C A 23 OK OK 712 727 709 711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' G A 6 OK OK 170 190 191 172 205 C5' G A 7 OK OK 204 224 225 206 239 C5' C A 8 OK OK 238 255 256 240 270 C5' U A 9 OK OK 269 286 287 271 300 C5' C A 10 OK OK 299 316 317 301 331 C5' U A 11 OK OK 330 347 348 332 361 C5' G A 12 OK OK 360 380 381 362 395 C5' G A 13 OK OK 394 414 415 396 429 C5' C A 14 OK OK 428 445 446 430 460 C5' A A 15 OK OK 459 478 479 461 493 C5' G A 16 OK OK 492 512 513 494 527 C5' C A 17 OK OK 526 543 544 528 558 C5' U A 18 OK OK 557 574 575 559 588 C5' U A 19 OK OK 587 604 605 589 618 C5' U A 20 OK OK 617 634 635 619 648 C5' U A 21 OK OK 647 664 665 649 678 C5' C A 22 OK OK 677 694 695 679 709 C5' C A 23 OK OK 708 725 726 710 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P G A 6 distorted distorted 142 168 169 170 201 P G A 7 distorted distorted 175 202 203 204 235 P C A 8 distorted distorted 209 236 237 238 266 P U A 9 distorted distorted 243 267 268 269 296 P C A 10 distorted distorted 274 297 298 299 327 P U A 11 distorted distorted 304 328 329 330 357 P G A 12 distorted distorted 335 358 359 360 391 P G A 13 distorted distorted 365 392 393 394 425 P C A 14 distorted distorted 399 426 427 428 456 P A A 15 distorted distorted 433 457 458 459 489 P G A 16 distorted distorted 464 490 491 492 523 P C A 17 distorted distorted 497 524 525 526 554 P U A 18 distorted distorted 531 555 556 557 584 P U A 19 distorted distorted 562 585 586 587 614 P U A 20 distorted distorted 592 615 616 617 644 P U A 21 distorted distorted 622 645 646 647 674 P C A 22 distorted distorted 652 675 676 677 705 P C A 23 distorted distorted 682 706 707 708 ---------------------------------------------------------------------------------