ID code: '477D' 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' --------------------------------------------------------------------------------- 12 C1' G A 2 beta 8 13 11 34 C1' C A 3 beta 30 35 33 53 C1' G A 4 beta 49 54 52 75 C1' A A 5 beta 71 76 74 96 C1' A A 6 beta 92 97 95 117 C1' T A 7 beta 113 118 116 137 C1' T A 8 beta 133 138 136 157 C1' C A 9 beta 153 158 156 176 C1' G A 10 beta 172 177 175 198 C1' C A 11 beta 194 199 197 241 C1' G B 14 beta 237 242 240 263 C1' C B 15 beta 259 264 262 282 C1' G B 16 beta 278 283 281 304 C1' A B 17 beta 300 305 303 325 C1' A B 18 beta 321 326 324 346 C1' T B 19 beta 342 347 345 366 C1' T B 20 beta 362 367 365 386 C1' C B 21 beta 382 387 385 405 C1' G B 22 beta 401 406 404 427 C1' C B 23 beta 423 428 426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 2 12 9 33 C2' C A 3 34 31 52 C2' G A 4 53 50 74 C2' A A 5 75 72 95 C2' A A 6 96 93 116 C2' T A 7 117 114 136 C2' T A 8 137 134 156 C2' C A 9 157 154 175 C2' G A 10 176 173 197 C2' C A 11 198 195 240 C2' G B 14 241 238 262 C2' C B 15 263 260 281 C2' G B 16 282 279 303 C2' A B 17 304 301 324 C2' A B 18 325 322 345 C2' T B 19 346 343 365 C2' T B 20 366 363 385 C2' C B 21 386 383 404 C2' G B 22 405 402 426 C2' C B 23 427 424 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 2 OK 7 10 11 31 C3' C A 3 OK 29 32 33 50 C3' G A 4 OK 48 51 52 72 C3' A A 5 OK 70 73 74 93 C3' A A 6 OK 91 94 95 114 C3' T A 7 OK 112 115 116 134 C3' T A 8 OK 132 135 136 154 C3' C A 9 OK 152 155 156 173 C3' G A 10 OK 171 174 175 195 C3' C A 11 OK 193 196 197 238 C3' G B 14 OK 236 239 240 260 C3' C B 15 OK 258 261 262 279 C3' G B 16 OK 277 280 281 301 C3' A B 17 OK 299 302 303 322 C3' A B 18 OK 320 323 324 343 C3' T B 19 OK 341 344 345 363 C3' T B 20 OK 361 364 365 383 C3' C B 21 OK 381 384 385 402 C3' G B 22 OK 400 403 404 424 C3' C B 23 OK 422 425 426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 2 OK 9 6 8 29 C4' C A 3 OK 31 28 30 48 C4' G A 4 OK 50 47 49 70 C4' A A 5 OK 72 69 71 91 C4' A A 6 OK 93 90 92 112 C4' T A 7 OK 114 111 113 132 C4' T A 8 OK 134 131 133 152 C4' C A 9 OK 154 151 153 171 C4' G A 10 OK 173 170 172 193 C4' C A 11 OK 195 192 194 236 C4' G B 14 OK 238 235 237 258 C4' C B 15 OK 260 257 259 277 C4' G B 16 OK 279 276 278 299 C4' A B 17 OK 301 298 300 320 C4' A B 18 OK 322 319 321 341 C4' T B 19 OK 343 340 342 361 C4' T B 20 OK 363 360 362 381 C4' C B 21 OK 383 380 382 400 C4' G B 22 OK 402 399 401 422 C4' C B 23 OK 424 421 423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 2 5 7 28 C5' C A 3 27 29 47 C5' G A 4 46 48 69 C5' A A 5 68 70 90 C5' A A 6 89 91 111 C5' T A 7 110 112 131 C5' T A 8 130 132 151 C5' C A 9 150 152 170 C5' G A 10 169 171 192 C5' C A 11 191 193 235 C5' G B 14 234 236 257 C5' C B 15 256 258 276 C5' G B 16 275 277 298 C5' A B 17 297 299 319 C5' A B 18 318 320 340 C5' T B 19 339 341 360 C5' T B 20 359 361 380 C5' C B 21 379 381 399 C5' G B 22 398 400 421 C5' C B 23 420 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 24 P C A 3 distorted distorted 10 25 26 27 43 P G A 4 distorted distorted 32 44 45 46 65 P A A 5 distorted distorted 51 66 67 68 86 P A A 6 distorted distorted 73 87 88 89 107 P T A 7 distorted distorted 94 108 109 110 127 P T A 8 distorted distorted 115 128 129 130 147 P C A 9 distorted distorted 135 148 149 150 166 P G A 10 distorted distorted 155 167 168 169 188 P C A 11 distorted distorted 174 189 190 191 253 P C B 15 distorted distorted 239 254 255 256 272 P G B 16 distorted distorted 261 273 274 275 294 P A B 17 distorted distorted 280 295 296 297 315 P A B 18 distorted distorted 302 316 317 318 336 P T B 19 distorted distorted 323 337 338 339 356 P T B 20 distorted distorted 344 357 358 359 376 P C B 21 distorted distorted 364 377 378 379 395 P G B 22 distorted distorted 384 396 397 398 417 P C B 23 distorted distorted 403 418 419 420 ---------------------------------------------------------------------------------