ID code: '1OQ0' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' A A 4 alpha beta 106 128 112 109 144 C1' G A 5 alpha beta 139 162 145 142 178 C1' U A 6 alpha beta 173 193 179 176 208 C1' U A 7 alpha beta 203 223 209 206 238 C1' G A 8 alpha beta 233 256 239 236 272 C1' G A 9 alpha beta 267 290 273 270 306 C1' G A 10 alpha beta 301 324 307 304 340 C1' C A 11 alpha beta 335 355 341 338 371 C1' U A 12 alpha beta 366 386 372 369 401 C1' C A 13 alpha beta 396 416 402 399 432 C1' U A 14 alpha beta 427 447 433 430 462 C1' C A 15 alpha beta 457 478 463 460 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' A A 4 OK OK 111 107 126 110 142 C2' G A 5 OK OK 144 140 160 143 176 C2' U A 6 OK OK 178 174 191 177 206 C2' U A 7 OK OK 208 204 221 207 236 C2' G A 8 OK OK 238 234 254 237 270 C2' G A 9 OK OK 272 268 288 271 304 C2' G A 10 OK OK 306 302 322 305 338 C2' C A 11 OK OK 340 336 353 339 369 C2' U A 12 OK OK 371 367 384 370 399 C2' C A 13 OK OK 401 397 414 400 430 C2' U A 14 OK OK 432 428 445 431 460 C2' C A 15 OK OK 462 458 476 461 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' A A 4 OK OK 105 125 108 109 140 C3' G A 5 OK OK 138 159 141 142 174 C3' U A 6 OK OK 172 190 175 176 204 C3' U A 7 OK OK 202 220 205 206 234 C3' G A 8 OK OK 232 253 235 236 268 C3' G A 9 OK OK 266 287 269 270 302 C3' G A 10 OK OK 300 321 303 304 336 C3' C A 11 OK OK 334 352 337 338 367 C3' U A 12 OK OK 365 383 368 369 397 C3' C A 13 OK OK 395 413 398 399 428 C3' U A 14 OK OK 426 444 429 430 458 C3' C A 15 OK OK 456 474 459 460 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' A A 4 OK OK 107 124 104 106 138 C4' G A 5 OK OK 140 158 137 139 172 C4' U A 6 OK OK 174 189 171 173 202 C4' U A 7 OK OK 204 219 201 203 232 C4' G A 8 OK OK 234 252 231 233 266 C4' G A 9 OK OK 268 286 265 267 300 C4' G A 10 OK OK 302 320 299 301 334 C4' C A 11 OK OK 336 351 333 335 365 C4' U A 12 OK OK 367 382 364 366 395 C4' C A 13 OK OK 397 412 394 396 426 C4' U A 14 OK OK 428 443 425 427 456 C4' C A 15 OK OK 458 473 455 457 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' A A 4 OK OK 103 122 123 105 137 C5' G A 5 OK OK 136 156 157 138 171 C5' U A 6 OK OK 170 187 188 172 201 C5' U A 7 OK OK 200 217 218 202 231 C5' G A 8 OK OK 230 250 251 232 265 C5' G A 9 OK OK 264 284 285 266 299 C5' G A 10 OK OK 298 318 319 300 333 C5' C A 11 OK OK 332 349 350 334 364 C5' U A 12 OK OK 363 380 381 365 394 C5' C A 13 OK OK 393 410 411 395 425 C5' U A 14 OK OK 424 441 442 426 455 C5' C A 15 OK OK 454 471 472 456 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P A A 4 distorted distorted 74 101 102 103 133 P G A 5 distorted distorted 108 134 135 136 167 P U A 6 distorted distorted 141 168 169 170 197 P U A 7 distorted distorted 175 198 199 200 227 P G A 8 distorted distorted 205 228 229 230 261 P G A 9 distorted distorted 235 262 263 264 295 P G A 10 distorted distorted 269 296 297 298 329 P C A 11 distorted distorted 303 330 331 332 360 P U A 12 distorted distorted 337 361 362 363 390 P C A 13 distorted distorted 368 391 392 393 421 P U A 14 distorted distorted 398 422 423 424 451 P C A 15 distorted distorted 429 452 453 454 ---------------------------------------------------------------------------------