ID code: '1EKD' 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' G A 4 alpha beta 104 127 110 107 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' C A 7 alpha beta 202 222 208 205 238 C1' C A 8 alpha beta 233 254 239 236 268 C1' G B 1 alpha beta 263 286 269 266 303 C1' G B 2 alpha beta 298 321 304 301 337 C1' C B 3 alpha beta 332 352 338 335 368 C1' G B 4 alpha beta 363 386 369 366 402 C1' U B 5 alpha beta 397 417 403 400 432 C1' G B 6 alpha beta 427 450 433 430 466 C1' C B 7 alpha beta 461 481 467 464 497 C1' C B 8 alpha beta 492 513 498 495 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 109 105 125 108 141 C2' U A 5 OK OK 143 139 156 142 171 C2' G A 6 OK OK 173 169 189 172 205 C2' C A 7 OK OK 207 203 220 206 236 C2' C A 8 OK OK 238 234 252 237 266 C2' G B 1 OK OK 268 264 284 267 301 C2' G B 2 OK OK 303 299 319 302 335 C2' C B 3 OK OK 337 333 350 336 366 C2' G B 4 OK OK 368 364 384 367 400 C2' U B 5 OK OK 402 398 415 401 430 C2' G B 6 OK OK 432 428 448 431 464 C2' C B 7 OK OK 466 462 479 465 495 C2' C B 8 OK OK 497 493 511 496 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 103 124 106 107 139 C3' U A 5 OK OK 137 155 140 141 169 C3' G A 6 OK OK 167 188 170 171 203 C3' C A 7 OK OK 201 219 204 205 234 C3' C A 8 OK OK 232 250 235 236 264 C3' G B 1 OK OK 262 283 265 266 299 C3' G B 2 OK OK 297 318 300 301 333 C3' C B 3 OK OK 331 349 334 335 364 C3' G B 4 OK OK 362 383 365 366 398 C3' U B 5 OK OK 396 414 399 400 428 C3' G B 6 OK OK 426 447 429 430 462 C3' C B 7 OK OK 460 478 463 464 493 C3' C B 8 OK OK 491 509 494 495 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 105 123 102 104 137 C4' U A 5 OK OK 139 154 136 138 167 C4' G A 6 OK OK 169 187 166 168 201 C4' C A 7 OK OK 203 218 200 202 232 C4' C A 8 OK OK 234 249 231 233 262 C4' G B 1 OK OK 264 282 261 263 297 C4' G B 2 OK OK 299 317 296 298 331 C4' C B 3 OK OK 333 348 330 332 362 C4' G B 4 OK OK 364 382 361 363 396 C4' U B 5 OK OK 398 413 395 397 426 C4' G B 6 OK OK 428 446 425 427 460 C4' C B 7 OK OK 462 477 459 461 491 C4' C B 8 OK OK 493 508 490 492 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 101 121 122 103 136 C5' U A 5 OK OK 135 152 153 137 166 C5' G A 6 OK OK 165 185 186 167 200 C5' C A 7 OK OK 199 216 217 201 231 C5' C A 8 OK OK 230 247 248 232 261 C5' G B 1 OK OK 260 280 281 262 296 C5' G B 2 OK OK 295 315 316 297 330 C5' C B 3 OK OK 329 346 347 331 361 C5' G B 4 OK OK 360 380 381 362 395 C5' U B 5 OK OK 394 411 412 396 425 C5' G B 6 OK OK 424 444 445 426 459 C5' C B 7 OK OK 458 475 476 460 490 C5' C B 8 OK OK 489 506 507 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 99 100 101 132 P U A 5 distorted distorted 106 133 134 135 162 P G A 6 distorted distorted 140 163 164 165 196 P C A 7 distorted distorted 170 197 198 199 227 P C A 8 distorted distorted 204 228 229 230 292 P G B 2 distorted distorted 265 293 294 295 326 P C B 3 distorted distorted 300 327 328 329 357 P G B 4 distorted distorted 334 358 359 360 391 P U B 5 distorted distorted 365 392 393 394 421 P G B 6 distorted distorted 399 422 423 424 455 P C B 7 distorted distorted 429 456 457 458 486 P C B 8 distorted distorted 463 487 488 489 ---------------------------------------------------------------------------------