ID code: '1AJL' 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 2 alpha beta 4 27 10 7 44 C1' G A 3 alpha beta 39 62 45 42 78 C1' U A 4 alpha beta 73 93 79 76 108 C1' A A 5 alpha beta 103 125 109 106 141 C1' A A 6 alpha beta 136 158 142 139 174 C1' U A 7 alpha beta 169 189 175 172 204 C1' A A 8 alpha beta 199 221 205 202 237 C1' A A 9 alpha beta 232 254 238 235 270 C1' G A 10 alpha beta 265 288 271 268 304 C1' C A 11 alpha beta 299 319 305 302 335 C1' U A 12 alpha beta 330 350 336 333 365 C1' C A 13 alpha beta 360 381 366 363 395 C1' G B 18 alpha beta 390 413 396 393 430 C1' A B 19 alpha beta 425 447 431 428 463 C1' G B 20 alpha beta 458 481 464 461 497 C1' U B 21 alpha beta 492 512 498 495 527 C1' A B 22 alpha beta 522 544 528 525 560 C1' C B 23 alpha beta 555 575 561 558 591 C1' C B 24 alpha beta 586 607 592 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 2 OK OK 9 5 25 8 42 C2' G A 3 OK OK 44 40 60 43 76 C2' U A 4 OK OK 78 74 91 77 106 C2' A A 5 OK OK 108 104 123 107 139 C2' A A 6 OK OK 141 137 156 140 172 C2' U A 7 OK OK 174 170 187 173 202 C2' A A 8 OK OK 204 200 219 203 235 C2' A A 9 OK OK 237 233 252 236 268 C2' G A 10 OK OK 270 266 286 269 302 C2' C A 11 OK OK 304 300 317 303 333 C2' U A 12 OK OK 335 331 348 334 363 C2' C A 13 OK OK 365 361 379 364 393 C2' G B 18 OK OK 395 391 411 394 428 C2' A B 19 OK OK 430 426 445 429 461 C2' G B 20 OK OK 463 459 479 462 495 C2' U B 21 OK OK 497 493 510 496 525 C2' A B 22 OK OK 527 523 542 526 558 C2' C B 23 OK OK 560 556 573 559 589 C2' C B 24 OK OK 591 587 605 590 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 2 OK OK 3 24 6 7 40 C3' G A 3 OK OK 38 59 41 42 74 C3' U A 4 OK OK 72 90 75 76 104 C3' A A 5 OK OK 102 122 105 106 137 C3' A A 6 OK OK 135 155 138 139 170 C3' U A 7 OK OK 168 186 171 172 200 C3' A A 8 OK OK 198 218 201 202 233 C3' A A 9 OK OK 231 251 234 235 266 C3' G A 10 OK OK 264 285 267 268 300 C3' C A 11 OK OK 298 316 301 302 331 C3' U A 12 OK OK 329 347 332 333 361 C3' C A 13 OK OK 359 377 362 363 391 C3' G B 18 OK OK 389 410 392 393 426 C3' A B 19 OK OK 424 444 427 428 459 C3' G B 20 OK OK 457 478 460 461 493 C3' U B 21 OK OK 491 509 494 495 523 C3' A B 22 OK OK 521 541 524 525 556 C3' C B 23 OK OK 554 572 557 558 587 C3' C B 24 OK OK 585 603 588 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 2 OK OK 5 23 2 4 38 C4' G A 3 OK OK 40 58 37 39 72 C4' U A 4 OK OK 74 89 71 73 102 C4' A A 5 OK OK 104 121 101 103 135 C4' A A 6 OK OK 137 154 134 136 168 C4' U A 7 OK OK 170 185 167 169 198 C4' A A 8 OK OK 200 217 197 199 231 C4' A A 9 OK OK 233 250 230 232 264 C4' G A 10 OK OK 266 284 263 265 298 C4' C A 11 OK OK 300 315 297 299 329 C4' U A 12 OK OK 331 346 328 330 359 C4' C A 13 OK OK 361 376 358 360 389 C4' G B 18 OK OK 391 409 388 390 424 C4' A B 19 OK OK 426 443 423 425 457 C4' G B 20 OK OK 459 477 456 458 491 C4' U B 21 OK OK 493 508 490 492 521 C4' A B 22 OK OK 523 540 520 522 554 C4' C B 23 OK OK 556 571 553 555 585 C4' C B 24 OK OK 587 602 584 586 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 2 OK OK 1 21 22 3 37 C5' G A 3 OK OK 36 56 57 38 71 C5' U A 4 OK OK 70 87 88 72 101 C5' A A 5 OK OK 100 119 120 102 134 C5' A A 6 OK OK 133 152 153 135 167 C5' U A 7 OK OK 166 183 184 168 197 C5' A A 8 OK OK 196 215 216 198 230 C5' A A 9 OK OK 229 248 249 231 263 C5' G A 10 OK OK 262 282 283 264 297 C5' C A 11 OK OK 296 313 314 298 328 C5' U A 12 OK OK 327 344 345 329 358 C5' C A 13 OK OK 357 374 375 359 388 C5' G B 18 OK OK 387 407 408 389 423 C5' A B 19 OK OK 422 441 442 424 456 C5' G B 20 OK OK 455 475 476 457 490 C5' U B 21 OK OK 489 506 507 491 520 C5' A B 22 OK OK 519 538 539 521 553 C5' C B 23 OK OK 552 569 570 554 584 C5' C B 24 OK OK 583 600 601 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 3 distorted distorted 6 34 35 36 67 P U A 4 distorted distorted 41 68 69 70 97 P A A 5 distorted distorted 75 98 99 100 130 P A A 6 distorted distorted 105 131 132 133 163 P U A 7 distorted distorted 138 164 165 166 193 P A A 8 distorted distorted 171 194 195 196 226 P A A 9 distorted distorted 201 227 228 229 259 P G A 10 distorted distorted 234 260 261 262 293 P C A 11 distorted distorted 267 294 295 296 324 P U A 12 distorted distorted 301 325 326 327 354 P C A 13 distorted distorted 332 355 356 357 419 P A B 19 distorted distorted 392 420 421 422 452 P G B 20 distorted distorted 427 453 454 455 486 P U B 21 distorted distorted 460 487 488 489 516 P A B 22 distorted distorted 494 517 518 519 549 P C B 23 distorted distorted 524 550 551 552 580 P C B 24 distorted distorted 557 581 582 583 ---------------------------------------------------------------------------------