ID code: '2QH4' 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 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' A A 8 alpha beta 235 257 241 238 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' U A 10 alpha beta 302 322 308 305 337 C1' U A 11 alpha beta 332 352 338 335 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' U A 13 alpha beta 395 415 401 398 430 C1' G A 14 alpha beta 425 448 431 428 464 C1' U A 15 alpha beta 459 479 465 462 494 C1' G A 16 alpha beta 489 512 495 492 528 C1' C A 17 alpha beta 523 543 529 526 559 C1' C A 18 alpha beta 554 575 560 557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' C A 5 OK OK 142 138 155 141 171 C2' A A 6 OK OK 173 169 188 172 204 C2' G A 7 OK OK 206 202 222 205 238 C2' A A 8 OK OK 240 236 255 239 271 C2' G A 9 OK OK 273 269 289 272 305 C2' U A 10 OK OK 307 303 320 306 335 C2' U A 11 OK OK 337 333 350 336 365 C2' A A 12 OK OK 367 363 382 366 398 C2' U A 13 OK OK 400 396 413 399 428 C2' G A 14 OK OK 430 426 446 429 462 C2' U A 15 OK OK 464 460 477 463 492 C2' G A 16 OK OK 494 490 510 493 526 C2' C A 17 OK OK 528 524 541 527 557 C2' C A 18 OK OK 559 555 573 558 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' C A 5 OK OK 136 154 139 140 169 C3' A A 6 OK OK 167 187 170 171 202 C3' G A 7 OK OK 200 221 203 204 236 C3' A A 8 OK OK 234 254 237 238 269 C3' G A 9 OK OK 267 288 270 271 303 C3' U A 10 OK OK 301 319 304 305 333 C3' U A 11 OK OK 331 349 334 335 363 C3' A A 12 OK OK 361 381 364 365 396 C3' U A 13 OK OK 394 412 397 398 426 C3' G A 14 OK OK 424 445 427 428 460 C3' U A 15 OK OK 458 476 461 462 490 C3' G A 16 OK OK 488 509 491 492 524 C3' C A 17 OK OK 522 540 525 526 555 C3' C A 18 OK OK 553 571 556 557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' C A 5 OK OK 138 153 135 137 167 C4' A A 6 OK OK 169 186 166 168 200 C4' G A 7 OK OK 202 220 199 201 234 C4' A A 8 OK OK 236 253 233 235 267 C4' G A 9 OK OK 269 287 266 268 301 C4' U A 10 OK OK 303 318 300 302 331 C4' U A 11 OK OK 333 348 330 332 361 C4' A A 12 OK OK 363 380 360 362 394 C4' U A 13 OK OK 396 411 393 395 424 C4' G A 14 OK OK 426 444 423 425 458 C4' U A 15 OK OK 460 475 457 459 488 C4' G A 16 OK OK 490 508 487 489 522 C4' C A 17 OK OK 524 539 521 523 553 C4' C A 18 OK OK 555 570 552 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' C A 5 OK OK 134 151 152 136 166 C5' A A 6 OK OK 165 184 185 167 199 C5' G A 7 OK OK 198 218 219 200 233 C5' A A 8 OK OK 232 251 252 234 266 C5' G A 9 OK OK 265 285 286 267 300 C5' U A 10 OK OK 299 316 317 301 330 C5' U A 11 OK OK 329 346 347 331 360 C5' A A 12 OK OK 359 378 379 361 393 C5' U A 13 OK OK 392 409 410 394 423 C5' G A 14 OK OK 422 442 443 424 457 C5' U A 15 OK OK 456 473 474 458 487 C5' G A 16 OK OK 486 506 507 488 521 C5' C A 17 OK OK 520 537 538 522 552 C5' C A 18 OK OK 551 568 569 553 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P C A 5 distorted distorted 106 132 133 134 162 P A A 6 distorted distorted 139 163 164 165 195 P G A 7 distorted distorted 170 196 197 198 229 P A A 8 distorted distorted 203 230 231 232 262 P G A 9 distorted distorted 237 263 264 265 296 P U A 10 distorted distorted 270 297 298 299 326 P U A 11 distorted distorted 304 327 328 329 356 P A A 12 distorted distorted 334 357 358 359 389 P U A 13 distorted distorted 364 390 391 392 419 P G A 14 distorted distorted 397 420 421 422 453 P U A 15 distorted distorted 427 454 455 456 483 P G A 16 distorted distorted 461 484 485 486 517 P C A 17 distorted distorted 491 518 519 520 548 P C A 18 distorted distorted 525 549 550 551 ---------------------------------------------------------------------------------