ID code: '1KSX' 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' A C 4 beta 7 12 10 32 C1' T C 5 beta 28 33 31 52 C1' T C 6 beta 48 53 51 72 C1' G C 7 beta 68 73 71 94 C1' T C 8 beta 90 95 93 114 C1' T C 9 beta 110 115 113 134 C1' G C 10 beta 130 135 133 156 C1' T C 11 beta 152 157 155 176 C1' T C 12 beta 172 177 175 196 C1' A C 13 beta 192 197 195 217 C1' A C 14 beta 213 218 216 238 C1' C C 15 beta 234 239 237 257 C1' A C 16 beta 253 258 256 278 C1' A C 17 beta 274 279 277 299 C1' C C 18 beta 295 300 298 318 C1' A C 19 beta 314 319 317 339 C1' A C 20 beta 335 340 338 360 C1' T C 21 beta 356 361 359 381 C1' A G 4 beta 377 382 380 402 C1' T G 5 beta 398 403 401 422 C1' T G 6 beta 418 423 421 442 C1' G G 7 beta 438 443 441 464 C1' T G 8 beta 460 465 463 484 C1' T G 9 beta 480 485 483 504 C1' G G 10 beta 500 505 503 526 C1' T G 11 beta 522 527 525 546 C1' T G 12 beta 542 547 545 566 C1' A G 13 beta 562 567 565 587 C1' A G 14 beta 583 588 586 608 C1' C G 15 beta 604 609 607 627 C1' A G 16 beta 623 628 626 648 C1' A G 17 beta 644 649 647 669 C1' C G 18 beta 665 670 668 688 C1' A G 19 beta 684 689 687 709 C1' A G 20 beta 705 710 708 730 C1' T G 21 beta 726 731 729 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A C 4 11 8 31 C2' T C 5 32 29 51 C2' T C 6 52 49 71 C2' G C 7 72 69 93 C2' T C 8 94 91 113 C2' T C 9 114 111 133 C2' G C 10 134 131 155 C2' T C 11 156 153 175 C2' T C 12 176 173 195 C2' A C 13 196 193 216 C2' A C 14 217 214 237 C2' C C 15 238 235 256 C2' A C 16 257 254 277 C2' A C 17 278 275 298 C2' C C 18 299 296 317 C2' A C 19 318 315 338 C2' A C 20 339 336 359 C2' T C 21 360 357 380 C2' A G 4 381 378 401 C2' T G 5 402 399 421 C2' T G 6 422 419 441 C2' G G 7 442 439 463 C2' T G 8 464 461 483 C2' T G 9 484 481 503 C2' G G 10 504 501 525 C2' T G 11 526 523 545 C2' T G 12 546 543 565 C2' A G 13 566 563 586 C2' A G 14 587 584 607 C2' C G 15 608 605 626 C2' A G 16 627 624 647 C2' A G 17 648 645 668 C2' C G 18 669 666 687 C2' A G 19 688 685 708 C2' A G 20 709 706 729 C2' T G 21 730 727 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 4 OK 6 9 10 29 C3' T C 5 OK 27 30 31 49 C3' T C 6 OK 47 50 51 69 C3' G C 7 OK 67 70 71 91 C3' T C 8 OK 89 92 93 111 C3' T C 9 OK 109 112 113 131 C3' G C 10 OK 129 132 133 153 C3' T C 11 OK 151 154 155 173 C3' T C 12 OK 171 174 175 193 C3' A C 13 OK 191 194 195 214 C3' A C 14 OK 212 215 216 235 C3' C C 15 OK 233 236 237 254 C3' A C 16 OK 252 255 256 275 C3' A C 17 OK 273 276 277 296 C3' C C 18 OK 294 297 298 315 C3' A C 19 OK 313 316 317 336 C3' A C 20 OK 334 337 338 357 C3' T C 21 OK 355 358 359 378 C3' A G 4 OK 376 379 380 399 C3' T G 5 OK 397 400 401 419 C3' T G 6 OK 417 420 421 439 C3' G G 7 OK 437 440 441 461 C3' T G 8 OK 459 462 463 481 C3' T G 9 OK 479 482 483 501 C3' G G 10 OK 499 502 503 523 C3' T G 11 OK 521 524 525 543 C3' T G 12 OK 541 544 545 563 C3' A G 13 OK 561 564 565 584 C3' A G 14 OK 582 585 586 605 C3' C G 15 OK 603 606 607 624 C3' A G 16 OK 622 625 626 645 C3' A G 17 OK 643 646 647 666 C3' C G 18 OK 664 667 668 685 C3' A G 19 OK 683 686 687 706 C3' A G 20 OK 704 707 708 727 C3' T G 21 OK 725 728 729 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 4 OK 8 5 7 27 C4' T C 5 OK 29 26 28 47 C4' T C 6 OK 49 46 48 67 C4' G C 7 OK 69 66 68 89 C4' T C 8 OK 91 88 90 109 C4' T C 9 OK 111 108 110 129 C4' G C 10 OK 131 128 130 151 C4' T C 11 OK 153 150 152 171 C4' T C 12 OK 173 170 172 191 C4' A C 13 OK 193 190 192 212 C4' A C 14 OK 214 211 213 233 C4' C C 15 OK 235 232 234 252 C4' A C 16 OK 254 251 253 273 C4' A C 17 OK 275 272 274 294 C4' C C 18 OK 296 293 295 313 C4' A C 19 OK 315 312 314 334 C4' A C 20 OK 336 333 335 355 C4' T C 21 OK 357 354 356 376 C4' A G 4 OK 378 375 377 397 C4' T G 5 OK 399 396 398 417 C4' T G 6 OK 419 416 418 437 C4' G G 7 OK 439 436 438 459 C4' T G 8 OK 461 458 460 479 C4' T G 9 OK 481 478 480 499 C4' G G 10 OK 501 498 500 521 C4' T G 11 OK 523 520 522 541 C4' T G 12 OK 543 540 542 561 C4' A G 13 OK 563 560 562 582 C4' A G 14 OK 584 581 583 603 C4' C G 15 OK 605 602 604 622 C4' A G 16 OK 624 621 623 643 C4' A G 17 OK 645 642 644 664 C4' C G 18 OK 666 663 665 683 C4' A G 19 OK 685 682 684 704 C4' A G 20 OK 706 703 705 725 C4' T G 21 OK 727 724 726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 4 4 6 26 C5' T C 5 25 27 46 C5' T C 6 45 47 66 C5' G C 7 65 67 88 C5' T C 8 87 89 108 C5' T C 9 107 109 128 C5' G C 10 127 129 150 C5' T C 11 149 151 170 C5' T C 12 169 171 190 C5' A C 13 189 191 211 C5' A C 14 210 212 232 C5' C C 15 231 233 251 C5' A C 16 250 252 272 C5' A C 17 271 273 293 C5' C C 18 292 294 312 C5' A C 19 311 313 333 C5' A C 20 332 334 354 C5' T C 21 353 355 375 C5' A G 4 374 376 396 C5' T G 5 395 397 416 C5' T G 6 415 417 436 C5' G G 7 435 437 458 C5' T G 8 457 459 478 C5' T G 9 477 479 498 C5' G G 10 497 499 520 C5' T G 11 519 521 540 C5' T G 12 539 541 560 C5' A G 13 559 561 581 C5' A G 14 580 582 602 C5' C G 15 601 603 621 C5' A G 16 620 622 642 C5' A G 17 641 643 663 C5' C G 18 662 664 682 C5' A G 19 681 683 703 C5' A G 20 702 704 724 C5' T G 21 723 725 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 4 distorted distorted 2 3 4 22 P T C 5 distorted distorted 9 23 24 25 42 P T C 6 distorted distorted 30 43 44 45 62 P G C 7 distorted distorted 50 63 64 65 84 P T C 8 distorted distorted 70 85 86 87 104 P T C 9 distorted distorted 92 105 106 107 124 P G C 10 distorted distorted 112 125 126 127 146 P T C 11 distorted distorted 132 147 148 149 166 P T C 12 distorted distorted 154 167 168 169 186 P A C 13 distorted distorted 174 187 188 189 207 P A C 14 distorted distorted 194 208 209 210 228 P C C 15 distorted distorted 215 229 230 231 247 P A C 16 distorted distorted 236 248 249 250 268 P A C 17 distorted distorted 255 269 270 271 289 P C C 18 distorted distorted 276 290 291 292 308 P A C 19 distorted distorted 297 309 310 311 329 P A C 20 distorted distorted 316 330 331 332 350 P T C 21 distorted distorted 337 351 352 353 371 P A G 4 distorted distorted 372 373 374 392 P T G 5 distorted distorted 379 393 394 395 412 P T G 6 distorted distorted 400 413 414 415 432 P G G 7 distorted distorted 420 433 434 435 454 P T G 8 distorted distorted 440 455 456 457 474 P T G 9 distorted distorted 462 475 476 477 494 P G G 10 distorted distorted 482 495 496 497 516 P T G 11 distorted distorted 502 517 518 519 536 P T G 12 distorted distorted 524 537 538 539 556 P A G 13 distorted distorted 544 557 558 559 577 P A G 14 distorted distorted 564 578 579 580 598 P C G 15 distorted distorted 585 599 600 601 617 P A G 16 distorted distorted 606 618 619 620 638 P A G 17 distorted distorted 625 639 640 641 659 P C G 18 distorted distorted 646 660 661 662 678 P A G 19 distorted distorted 667 679 680 681 699 P A G 20 distorted distorted 686 700 701 702 720 P T G 21 distorted distorted 707 721 722 723 ---------------------------------------------------------------------------------