ID code: '2K65' 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 13 alpha beta 4 27 10 7 44 C1' G A 14 alpha beta 39 62 45 42 78 C1' C A 15 alpha beta 73 93 79 76 109 C1' A A 16 alpha beta 104 126 110 107 142 C1' C A 17 alpha beta 137 157 143 140 173 C1' U A 18 alpha beta 168 188 174 171 203 C1' G A 19 alpha beta 198 222 204 201 236 C1' C B 59 alpha beta 231 251 237 234 268 C1' A B 60 alpha beta 263 285 269 266 301 C1' G B 61 alpha beta 296 319 302 299 335 C1' U B 62 alpha beta 330 350 336 333 365 C1' G B 63 alpha beta 360 383 366 363 399 C1' U B 64 alpha beta 394 414 400 397 429 C1' C B 65 alpha beta 424 445 430 427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 13 OK OK 9 5 25 8 42 C2' G A 14 OK OK 44 40 60 43 76 C2' C A 15 OK OK 78 74 91 77 107 C2' A A 16 OK OK 109 105 124 108 140 C2' C A 17 OK OK 142 138 155 141 171 C2' U A 18 OK OK 173 169 186 172 201 C2' G A 19 OK OK 203 199 220 202 234 C2' C B 59 OK OK 236 232 249 235 266 C2' A B 60 OK OK 268 264 283 267 299 C2' G B 61 OK OK 301 297 317 300 333 C2' U B 62 OK OK 335 331 348 334 363 C2' G B 63 OK OK 365 361 381 364 397 C2' U B 64 OK OK 399 395 412 398 427 C2' C B 65 OK OK 429 425 443 428 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 13 OK OK 3 24 6 7 40 C3' G A 14 OK OK 38 59 41 42 74 C3' C A 15 OK OK 72 90 75 76 105 C3' A A 16 OK OK 103 123 106 107 138 C3' C A 17 OK OK 136 154 139 140 169 C3' U A 18 OK OK 167 185 170 171 199 C3' G A 19 OK OK 197 218 200 201 232 C3' C B 59 OK OK 230 248 233 234 264 C3' A B 60 OK OK 262 282 265 266 297 C3' G B 61 OK OK 295 316 298 299 331 C3' U B 62 OK OK 329 347 332 333 361 C3' G B 63 OK OK 359 380 362 363 395 C3' U B 64 OK OK 393 411 396 397 425 C3' C B 65 OK OK 423 441 426 427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 13 OK OK 5 23 2 4 38 C4' G A 14 OK OK 40 58 37 39 72 C4' C A 15 OK OK 74 89 71 73 103 C4' A A 16 OK OK 105 122 102 104 136 C4' C A 17 OK OK 138 153 135 137 167 C4' U A 18 OK OK 169 184 166 168 197 C4' G A 19 OK OK 199 217 196 198 230 C4' C B 59 OK OK 232 247 229 231 262 C4' A B 60 OK OK 264 281 261 263 295 C4' G B 61 OK OK 297 315 294 296 329 C4' U B 62 OK OK 331 346 328 330 359 C4' G B 63 OK OK 361 379 358 360 393 C4' U B 64 OK OK 395 410 392 394 423 C4' C B 65 OK OK 425 440 422 424 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 13 OK OK 1 21 22 3 37 C5' G A 14 OK OK 36 56 57 38 71 C5' C A 15 OK OK 70 87 88 72 102 C5' A A 16 OK OK 101 120 121 103 135 C5' C A 17 OK OK 134 151 152 136 166 C5' U A 18 OK OK 165 182 183 167 196 C5' G A 19 OK OK 195 215 216 197 229 C5' C B 59 OK OK 228 245 246 230 261 C5' A B 60 OK OK 260 279 280 262 294 C5' G B 61 OK OK 293 313 314 295 328 C5' U B 62 OK OK 327 344 345 329 358 C5' G B 63 OK OK 357 377 378 359 392 C5' U B 64 OK OK 391 408 409 393 422 C5' C B 65 OK OK 421 438 439 423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 14 distorted distorted 6 34 35 36 67 P C A 15 distorted distorted 41 68 69 70 98 P A A 16 distorted distorted 75 99 100 101 131 P C A 17 distorted distorted 106 132 133 134 162 P U A 18 distorted distorted 139 163 164 165 192 P G A 19 distorted distorted 170 193 194 195 257 P A B 60 distorted distorted 233 258 259 260 290 P G B 61 distorted distorted 265 291 292 293 324 P U B 62 distorted distorted 298 325 326 327 354 P G B 63 distorted distorted 332 355 356 357 388 P U B 64 distorted distorted 362 389 390 391 418 P C B 65 distorted distorted 396 419 420 421 ---------------------------------------------------------------------------------