ID code: '1RRR' 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 305 326 311 308 340 C1' G B 1 alpha beta 335 358 341 338 374 C1' C B 2 alpha beta 369 389 375 372 405 C1' U B 3 alpha beta 400 420 406 403 435 C1' U B 4 alpha beta 430 450 436 433 465 C1' C B 5 alpha beta 460 480 466 463 496 C1' U B 6 alpha beta 491 511 497 494 526 C1' C B 7 alpha beta 521 541 527 524 557 C1' U B 8 alpha beta 552 572 558 555 587 C1' U B 9 alpha beta 582 602 588 585 617 C1' C B 10 alpha beta 612 633 618 615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G B 1 OK OK 340 336 356 339 372 C2' C B 2 OK OK 374 370 387 373 403 C2' U B 3 OK OK 405 401 418 404 433 C2' U B 4 OK OK 435 431 448 434 463 C2' C B 5 OK OK 465 461 478 464 494 C2' U B 6 OK OK 496 492 509 495 524 C2' C B 7 OK OK 526 522 539 525 555 C2' U B 8 OK OK 557 553 570 556 585 C2' U B 9 OK OK 587 583 600 586 615 C2' C B 10 OK OK 617 613 631 616 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 1 OK OK 334 355 337 338 370 C3' C B 2 OK OK 368 386 371 372 401 C3' U B 3 OK OK 399 417 402 403 431 C3' U B 4 OK OK 429 447 432 433 461 C3' C B 5 OK OK 459 477 462 463 492 C3' U B 6 OK OK 490 508 493 494 522 C3' C B 7 OK OK 520 538 523 524 553 C3' U B 8 OK OK 551 569 554 555 583 C3' U B 9 OK OK 581 599 584 585 613 C3' C B 10 OK OK 611 629 614 615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 1 OK OK 336 354 333 335 368 C4' C B 2 OK OK 370 385 367 369 399 C4' U B 3 OK OK 401 416 398 400 429 C4' U B 4 OK OK 431 446 428 430 459 C4' C B 5 OK OK 461 476 458 460 490 C4' U B 6 OK OK 492 507 489 491 520 C4' C B 7 OK OK 522 537 519 521 551 C4' U B 8 OK OK 553 568 550 552 581 C4' U B 9 OK OK 583 598 580 582 611 C4' C B 10 OK OK 613 628 610 612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 1 OK OK 332 352 353 334 367 C5' C B 2 OK OK 366 383 384 368 398 C5' U B 3 OK OK 397 414 415 399 428 C5' U B 4 OK OK 427 444 445 429 458 C5' C B 5 OK OK 457 474 475 459 489 C5' U B 6 OK OK 488 505 506 490 519 C5' C B 7 OK OK 518 535 536 520 550 C5' U B 8 OK OK 549 566 567 551 580 C5' U B 9 OK OK 579 596 597 581 610 C5' C B 10 OK OK 609 626 627 611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 273 300 301 302 363 P C B 2 distorted distorted 337 364 365 366 394 P U B 3 distorted distorted 371 395 396 397 424 P U B 4 distorted distorted 402 425 426 427 454 P C B 5 distorted distorted 432 455 456 457 485 P U B 6 distorted distorted 462 486 487 488 515 P C B 7 distorted distorted 493 516 517 518 546 P U B 8 distorted distorted 523 547 548 549 576 P U B 9 distorted distorted 554 577 578 579 606 P C B 10 distorted distorted 584 607 608 609 ---------------------------------------------------------------------------------