ID code: '2LA9' 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' G A 3 alpha beta 73 96 79 76 112 C1' G A 4 alpha beta 107 130 113 110 146 C1' A A 5 alpha beta 141 163 147 144 179 C1' C A 6 alpha beta 174 194 180 177 210 C1' U A 7 alpha beta 205 225 211 208 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' U A 9 alpha beta 269 289 275 272 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' A A 11 alpha beta 332 354 338 335 370 C1' A A 12 alpha beta 365 387 371 368 400 C1' PSU A 13 alpha beta 406 415 396 401 433 C1' C A 14 alpha beta 428 448 434 431 464 C1' C A 15 alpha beta 459 479 465 462 495 C1' C A 16 alpha beta 490 510 496 493 526 C1' C A 17 alpha beta 521 542 527 524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' G A 4 OK OK 112 108 128 111 144 C2' A A 5 OK OK 146 142 161 145 177 C2' C A 6 OK OK 179 175 192 178 208 C2' U A 7 OK OK 210 206 223 209 238 C2' G A 8 OK OK 240 236 256 239 272 C2' U A 9 OK OK 274 270 287 273 302 C2' A A 10 OK OK 304 300 319 303 335 C2' A A 11 OK OK 337 333 352 336 368 C2' A A 12 OK OK 370 366 385 369 401 C2' PSU A 13 OK OK 400 403 416 402 431 C2' C A 14 OK OK 433 429 446 432 462 C2' C A 15 OK OK 464 460 477 463 493 C2' C A 16 OK OK 495 491 508 494 524 C2' C A 17 OK OK 526 522 540 525 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' G A 4 OK OK 106 127 109 110 142 C3' A A 5 OK OK 140 160 143 144 175 C3' C A 6 OK OK 173 191 176 177 206 C3' U A 7 OK OK 204 222 207 208 236 C3' G A 8 OK OK 234 255 237 238 270 C3' U A 9 OK OK 268 286 271 272 300 C3' A A 10 OK OK 298 318 301 302 333 C3' A A 11 OK OK 331 351 334 335 366 C3' A A 12 OK OK 364 384 367 368 403 C3' PSU A 13 OK OK 404 418 405 401 429 C3' C A 14 OK OK 427 445 430 431 460 C3' C A 15 OK OK 458 476 461 462 491 C3' C A 16 OK OK 489 507 492 493 522 C3' C A 17 OK OK 520 538 523 524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' G A 4 OK OK 108 126 105 107 140 C4' A A 5 OK OK 142 159 139 141 173 C4' C A 6 OK OK 175 190 172 174 204 C4' U A 7 OK OK 206 221 203 205 234 C4' G A 8 OK OK 236 254 233 235 268 C4' U A 9 OK OK 270 285 267 269 298 C4' A A 10 OK OK 300 317 297 299 331 C4' A A 11 OK OK 333 350 330 332 364 C4' A A 12 OK OK 366 383 363 365 404 C4' PSU A 13 OK OK 403 419 407 406 427 C4' C A 14 OK OK 429 444 426 428 458 C4' C A 15 OK OK 460 475 457 459 489 C4' C A 16 OK OK 491 506 488 490 520 C4' C A 17 OK OK 522 537 519 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' G A 4 OK OK 104 124 125 106 139 C5' A A 5 OK OK 138 157 158 140 172 C5' C A 6 OK OK 171 188 189 173 203 C5' U A 7 OK OK 202 219 220 204 233 C5' G A 8 OK OK 232 252 253 234 267 C5' U A 9 OK OK 266 283 284 268 297 C5' A A 10 OK OK 296 315 316 298 330 C5' A A 11 OK OK 329 348 349 331 363 C5' A A 12 OK OK 362 381 382 364 407 C5' PSU A 13 OK OK 408 420 421 404 426 C5' C A 14 OK OK 425 442 443 427 457 C5' C A 15 OK OK 456 473 474 458 488 C5' C A 16 OK OK 487 504 505 489 519 C5' C A 17 OK OK 518 535 536 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P G A 4 distorted distorted 75 102 103 104 135 P A A 5 distorted distorted 109 136 137 138 168 P C A 6 distorted distorted 143 169 170 171 199 P U A 7 distorted distorted 176 200 201 202 229 P G A 8 distorted distorted 207 230 231 232 263 P U A 9 distorted distorted 237 264 265 266 293 P A A 10 distorted distorted 271 294 295 296 326 P A A 11 distorted distorted 301 327 328 329 359 P A A 12 distorted distorted 334 360 361 362 409 P PSU A 13 distorted distorted 367 410 411 408 422 P C A 14 distorted distorted 405 423 424 425 453 P C A 15 distorted distorted 430 454 455 456 484 P C A 16 distorted distorted 461 485 486 487 515 P C A 17 distorted distorted 492 516 517 518 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