ID code: '1JH9' 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 B 700 beta 7 12 10 32 C1' C B 701 beta 28 33 31 51 C1' G B 702 beta 47 52 50 73 C1' A B 703 beta 69 74 72 94 C1' A B 704 beta 90 95 93 115 C1' A B 705 beta 111 116 114 136 C1' A B 706 beta 132 137 135 157 C1' C B 707 beta 153 158 156 176 C1' G B 708 beta 172 177 175 198 C1' T B 709 beta 194 199 197 218 C1' T B 710 beta 214 219 217 238 C1' T B 711 beta 234 239 237 258 C1' T B 712 beta 254 259 257 278 C1' C B 713 beta 274 279 277 297 C1' G B 714 beta 293 298 296 319 C1' T B 715 beta 315 320 318 339 C1' A B 700 beta 335 340 338 360 C1' C B 701 beta 356 361 359 379 C1' G B 702 beta 375 380 378 401 C1' A B 703 beta 397 402 400 422 C1' A B 704 beta 418 423 421 443 C1' A B 705 beta 439 444 442 464 C1' A B 706 beta 460 465 463 485 C1' C B 707 beta 481 486 484 504 C1' G B 708 beta 500 505 503 526 C1' T B 709 beta 522 527 525 546 C1' T B 710 beta 542 547 545 566 C1' T B 711 beta 562 567 565 586 C1' T B 712 beta 582 587 585 606 C1' C B 713 beta 602 607 605 625 C1' G B 714 beta 621 626 624 647 C1' T B 715 beta 643 648 646 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 700 11 8 31 C2' C B 701 32 29 50 C2' G B 702 51 48 72 C2' A B 703 73 70 93 C2' A B 704 94 91 114 C2' A B 705 115 112 135 C2' A B 706 136 133 156 C2' C B 707 157 154 175 C2' G B 708 176 173 197 C2' T B 709 198 195 217 C2' T B 710 218 215 237 C2' T B 711 238 235 257 C2' T B 712 258 255 277 C2' C B 713 278 275 296 C2' G B 714 297 294 318 C2' T B 715 319 316 338 C2' A B 700 339 336 359 C2' C B 701 360 357 378 C2' G B 702 379 376 400 C2' A B 703 401 398 421 C2' A B 704 422 419 442 C2' A B 705 443 440 463 C2' A B 706 464 461 484 C2' C B 707 485 482 503 C2' G B 708 504 501 525 C2' T B 709 526 523 545 C2' T B 710 546 543 565 C2' T B 711 566 563 585 C2' T B 712 586 583 605 C2' C B 713 606 603 624 C2' G B 714 625 622 646 C2' T B 715 647 644 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 700 OK 6 9 10 29 C3' C B 701 OK 27 30 31 48 C3' G B 702 OK 46 49 50 70 C3' A B 703 OK 68 71 72 91 C3' A B 704 OK 89 92 93 112 C3' A B 705 OK 110 113 114 133 C3' A B 706 OK 131 134 135 154 C3' C B 707 OK 152 155 156 173 C3' G B 708 OK 171 174 175 195 C3' T B 709 OK 193 196 197 215 C3' T B 710 OK 213 216 217 235 C3' T B 711 OK 233 236 237 255 C3' T B 712 OK 253 256 257 275 C3' C B 713 OK 273 276 277 294 C3' G B 714 OK 292 295 296 316 C3' T B 715 OK 314 317 318 336 C3' A B 700 OK 334 337 338 357 C3' C B 701 OK 355 358 359 376 C3' G B 702 OK 374 377 378 398 C3' A B 703 OK 396 399 400 419 C3' A B 704 OK 417 420 421 440 C3' A B 705 OK 438 441 442 461 C3' A B 706 OK 459 462 463 482 C3' C B 707 OK 480 483 484 501 C3' G B 708 OK 499 502 503 523 C3' T B 709 OK 521 524 525 543 C3' T B 710 OK 541 544 545 563 C3' T B 711 OK 561 564 565 583 C3' T B 712 OK 581 584 585 603 C3' C B 713 OK 601 604 605 622 C3' G B 714 OK 620 623 624 644 C3' T B 715 OK 642 645 646 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 700 OK 8 5 7 27 C4' C B 701 OK 29 26 28 46 C4' G B 702 OK 48 45 47 68 C4' A B 703 OK 70 67 69 89 C4' A B 704 OK 91 88 90 110 C4' A B 705 OK 112 109 111 131 C4' A B 706 OK 133 130 132 152 C4' C B 707 OK 154 151 153 171 C4' G B 708 OK 173 170 172 193 C4' T B 709 OK 195 192 194 213 C4' T B 710 OK 215 212 214 233 C4' T B 711 OK 235 232 234 253 C4' T B 712 OK 255 252 254 273 C4' C B 713 OK 275 272 274 292 C4' G B 714 OK 294 291 293 314 C4' T B 715 OK 316 313 315 334 C4' A B 700 OK 336 333 335 355 C4' C B 701 OK 357 354 356 374 C4' G B 702 OK 376 373 375 396 C4' A B 703 OK 398 395 397 417 C4' A B 704 OK 419 416 418 438 C4' A B 705 OK 440 437 439 459 C4' A B 706 OK 461 458 460 480 C4' C B 707 OK 482 479 481 499 C4' G B 708 OK 501 498 500 521 C4' T B 709 OK 523 520 522 541 C4' T B 710 OK 543 540 542 561 C4' T B 711 OK 563 560 562 581 C4' T B 712 OK 583 580 582 601 C4' C B 713 OK 603 600 602 620 C4' G B 714 OK 622 619 621 642 C4' T B 715 OK 644 641 643 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 700 4 6 26 C5' C B 701 25 27 45 C5' G B 702 44 46 67 C5' A B 703 66 68 88 C5' A B 704 87 89 109 C5' A B 705 108 110 130 C5' A B 706 129 131 151 C5' C B 707 150 152 170 C5' G B 708 169 171 192 C5' T B 709 191 193 212 C5' T B 710 211 213 232 C5' T B 711 231 233 252 C5' T B 712 251 253 272 C5' C B 713 271 273 291 C5' G B 714 290 292 313 C5' T B 715 312 314 333 C5' A B 700 332 334 354 C5' C B 701 353 355 373 C5' G B 702 372 374 395 C5' A B 703 394 396 416 C5' A B 704 415 417 437 C5' A B 705 436 438 458 C5' A B 706 457 459 479 C5' C B 707 478 480 498 C5' G B 708 497 499 520 C5' T B 709 519 521 540 C5' T B 710 539 541 560 C5' T B 711 559 561 580 C5' T B 712 579 581 600 C5' C B 713 599 601 619 C5' G B 714 618 620 641 C5' T B 715 640 642 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 700 distorted distorted 2 3 4 22 P C B 701 distorted distorted 9 23 24 25 41 P G B 702 distorted distorted 30 42 43 44 63 P A B 703 distorted distorted 49 64 65 66 84 P A B 704 distorted distorted 71 85 86 87 105 P A B 705 distorted distorted 92 106 107 108 126 P A B 706 distorted distorted 113 127 128 129 147 P C B 707 distorted distorted 134 148 149 150 166 P G B 708 distorted distorted 155 167 168 169 188 P T B 709 distorted distorted 174 189 190 191 208 P T B 710 distorted distorted 196 209 210 211 228 P T B 711 distorted distorted 216 229 230 231 248 P T B 712 distorted distorted 236 249 250 251 268 P C B 713 distorted distorted 256 269 270 271 287 P G B 714 distorted distorted 276 288 289 290 309 P T B 715 distorted distorted 295 310 311 312 329 P A B 700 distorted distorted 330 331 332 350 P C B 701 distorted distorted 337 351 352 353 369 P G B 702 distorted distorted 358 370 371 372 391 P A B 703 distorted distorted 377 392 393 394 412 P A B 704 distorted distorted 399 413 414 415 433 P A B 705 distorted distorted 420 434 435 436 454 P A B 706 distorted distorted 441 455 456 457 475 P C B 707 distorted distorted 462 476 477 478 494 P G B 708 distorted distorted 483 495 496 497 516 P T B 709 distorted distorted 502 517 518 519 536 P T B 710 distorted distorted 524 537 538 539 556 P T B 711 distorted distorted 544 557 558 559 576 P T B 712 distorted distorted 564 577 578 579 596 P C B 713 distorted distorted 584 597 598 599 615 P G B 714 distorted distorted 604 616 617 618 637 P T B 715 distorted distorted 623 638 639 640 ---------------------------------------------------------------------------------