ID code: '1RRD' 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 43 C1' A A 2 alpha beta 38 60 44 41 76 C1' A A 3 alpha beta 71 93 77 74 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' A A 7 alpha beta 205 227 211 208 243 C1' A A 8 alpha beta 238 260 244 241 276 C1' G A 9 alpha beta 271 294 277 274 310 C1' C A 10 alpha beta 305 326 311 308 339 C1' DG B 1 alpha beta 335 357 340 338 372 C1' DC B 2 alpha beta 368 387 373 371 402 C1' DT B 3 alpha beta 398 418 403 401 434 C1' DT B 4 alpha beta 430 450 435 433 466 C1' DC B 5 alpha beta 462 481 467 465 496 C1' DT B 6 alpha beta 492 512 497 495 528 C1' DC B 7 alpha beta 524 543 529 527 558 C1' DT B 8 alpha beta 554 574 559 557 590 C1' DT B 9 alpha beta 586 606 591 589 622 C1' DC B 10 alpha beta 618 638 623 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' A A 2 OK OK 43 39 58 42 74 C2' A A 3 OK OK 76 72 91 75 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 174 C2' G A 6 OK OK 176 172 192 175 208 C2' A A 7 OK OK 210 206 225 209 241 C2' A A 8 OK OK 243 239 258 242 274 C2' G A 9 OK OK 276 272 292 275 308 C2' C A 10 OK OK 310 306 324 309 338 C2' DG B 1 OK OK 339 336 355 356 371 C2' DC B 2 OK OK 372 369 385 386 401 C2' DT B 3 OK OK 402 399 416 417 433 C2' DT B 4 OK OK 434 431 448 449 465 C2' DC B 5 OK OK 466 463 479 480 495 C2' DT B 6 OK OK 496 493 510 511 527 C2' DC B 7 OK OK 528 525 541 542 557 C2' DT B 8 OK OK 558 555 572 573 589 C2' DT B 9 OK OK 590 587 604 605 621 C2' DC B 10 OK OK 622 619 636 637 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' A A 2 OK OK 37 57 40 41 72 C3' A A 3 OK OK 70 90 73 74 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' G A 6 OK OK 170 191 173 174 206 C3' A A 7 OK OK 204 224 207 208 239 C3' A A 8 OK OK 237 257 240 241 272 C3' G A 9 OK OK 270 291 273 274 306 C3' C A 10 OK OK 304 322 307 308 336 C3' DG B 1 OK OK 334 354 337 338 369 C3' DC B 2 OK OK 367 384 370 371 399 C3' DT B 3 OK OK 397 415 400 401 431 C3' DT B 4 OK OK 429 447 432 433 463 C3' DC B 5 OK OK 461 478 464 465 493 C3' DT B 6 OK OK 491 509 494 495 525 C3' DC B 7 OK OK 523 540 526 527 555 C3' DT B 8 OK OK 553 571 556 557 587 C3' DT B 9 OK OK 585 603 588 589 619 C3' DC B 10 OK OK 617 634 620 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' A A 2 OK OK 39 56 36 38 70 C4' A A 3 OK OK 72 89 69 71 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 170 C4' G A 6 OK OK 172 190 169 171 204 C4' A A 7 OK OK 206 223 203 205 237 C4' A A 8 OK OK 239 256 236 238 270 C4' G A 9 OK OK 272 290 269 271 304 C4' C A 10 OK OK 306 321 303 305 334 C4' DG B 1 OK OK 336 353 333 335 367 C4' DC B 2 OK OK 369 383 366 368 397 C4' DT B 3 OK OK 399 414 396 398 429 C4' DT B 4 OK OK 431 446 428 430 461 C4' DC B 5 OK OK 463 477 460 462 491 C4' DT B 6 OK OK 493 508 490 492 523 C4' DC B 7 OK OK 525 539 522 524 553 C4' DT B 8 OK OK 555 570 552 554 585 C4' DT B 9 OK OK 587 602 584 586 617 C4' DC B 10 OK OK 619 633 616 618 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 distorted OK 1 21 22 3 36 C5' A A 2 OK OK 35 54 55 37 69 C5' A A 3 OK OK 68 87 88 70 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 169 C5' G A 6 OK OK 168 188 189 170 203 C5' A A 7 OK OK 202 221 222 204 236 C5' A A 8 OK OK 235 254 255 237 269 C5' G A 9 OK OK 268 288 289 270 303 C5' C A 10 OK OK 302 319 320 304 333 C5' DG B 1 OK OK 332 351 352 334 366 C5' DC B 2 OK OK 365 381 382 367 396 C5' DT B 3 OK OK 395 412 413 397 428 C5' DT B 4 OK OK 427 444 445 429 460 C5' DC B 5 OK OK 459 475 476 461 490 C5' DT B 6 OK OK 489 506 507 491 522 C5' DC B 7 OK OK 521 537 538 523 552 C5' DT B 8 OK OK 551 568 569 553 584 C5' DT B 9 OK OK 583 600 601 585 616 C5' DC B 10 OK OK 615 631 632 617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P A A 2 distorted distorted 6 33 34 35 65 P A A 3 distorted distorted 40 66 67 68 98 P G A 4 distorted distorted 73 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P G A 6 distorted distorted 140 166 167 168 199 P A A 7 distorted distorted 173 200 201 202 232 P A A 8 distorted distorted 207 233 234 235 265 P G A 9 distorted distorted 240 266 267 268 299 P C A 10 distorted distorted 273 300 301 302 362 P DC B 2 distorted distorted 337 363 364 365 392 P DT B 3 distorted distorted 370 393 394 395 424 P DT B 4 distorted distorted 400 425 426 427 456 P DC B 5 distorted distorted 432 457 458 459 486 P DT B 6 distorted distorted 464 487 488 489 518 P DC B 7 distorted distorted 494 519 520 521 548 P DT B 8 distorted distorted 526 549 550 551 580 P DT B 9 distorted distorted 556 581 582 583 612 P DC B 10 distorted distorted 588 613 614 615 ---------------------------------------------------------------------------------