ID code: '1JK1' 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' --------------------------------------------------------------------------------- 11 C1' G B 2 beta 7 12 10 33 C1' C B 3 beta 29 34 32 52 C1' G B 4 beta 48 53 51 74 C1' T B 5 beta 70 75 73 94 C1' G B 6 beta 90 95 93 116 C1' G B 7 beta 112 117 115 138 C1' G B 8 beta 134 139 137 160 C1' C B 9 beta 156 161 159 179 C1' G B 10 beta 175 180 178 201 C1' G B 11 beta 197 202 200 224 C1' C C 52 beta 220 225 223 243 C1' C C 53 beta 239 244 242 262 C1' G C 54 beta 258 263 261 284 C1' C C 55 beta 280 285 283 303 C1' C C 56 beta 299 304 302 322 C1' C C 57 beta 318 323 321 341 C1' A C 58 beta 337 342 340 362 C1' C C 59 beta 358 363 361 381 C1' G C 60 beta 377 382 380 403 C1' C C 61 beta 399 404 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 2 11 8 32 C2' C B 3 33 30 51 C2' G B 4 52 49 73 C2' T B 5 74 71 93 C2' G B 6 94 91 115 C2' G B 7 116 113 137 C2' G B 8 138 135 159 C2' C B 9 160 157 178 C2' G B 10 179 176 200 C2' G B 11 201 198 223 C2' C C 52 224 221 242 C2' C C 53 243 240 261 C2' G C 54 262 259 283 C2' C C 55 284 281 302 C2' C C 56 303 300 321 C2' C C 57 322 319 340 C2' A C 58 341 338 361 C2' C C 59 362 359 380 C2' G C 60 381 378 402 C2' C C 61 403 400 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 2 OK 6 9 10 30 C3' C B 3 OK 28 31 32 49 C3' G B 4 OK 47 50 51 71 C3' T B 5 OK 69 72 73 91 C3' G B 6 OK 89 92 93 113 C3' G B 7 OK 111 114 115 135 C3' G B 8 OK 133 136 137 157 C3' C B 9 OK 155 158 159 176 C3' G B 10 OK 174 177 178 198 C3' G B 11 OK 196 199 200 221 C3' C C 52 OK 219 222 223 240 C3' C C 53 OK 238 241 242 259 C3' G C 54 OK 257 260 261 281 C3' C C 55 OK 279 282 283 300 C3' C C 56 OK 298 301 302 319 C3' C C 57 OK 317 320 321 338 C3' A C 58 OK 336 339 340 359 C3' C C 59 OK 357 360 361 378 C3' G C 60 OK 376 379 380 400 C3' C C 61 OK 398 401 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 2 OK 8 5 7 28 C4' C B 3 OK 30 27 29 47 C4' G B 4 OK 49 46 48 69 C4' T B 5 OK 71 68 70 89 C4' G B 6 OK 91 88 90 111 C4' G B 7 OK 113 110 112 133 C4' G B 8 OK 135 132 134 155 C4' C B 9 OK 157 154 156 174 C4' G B 10 OK 176 173 175 196 C4' G B 11 OK 198 195 197 219 C4' C C 52 OK 221 218 220 238 C4' C C 53 OK 240 237 239 257 C4' G C 54 OK 259 256 258 279 C4' C C 55 OK 281 278 280 298 C4' C C 56 OK 300 297 299 317 C4' C C 57 OK 319 316 318 336 C4' A C 58 OK 338 335 337 357 C4' C C 59 OK 359 356 358 376 C4' G C 60 OK 378 375 377 398 C4' C C 61 OK 400 397 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 2 4 6 27 C5' C B 3 26 28 46 C5' G B 4 45 47 68 C5' T B 5 67 69 88 C5' G B 6 87 89 110 C5' G B 7 109 111 132 C5' G B 8 131 133 154 C5' C B 9 153 155 173 C5' G B 10 172 174 195 C5' G B 11 194 196 218 C5' C C 52 217 219 237 C5' C C 53 236 238 256 C5' G C 54 255 257 278 C5' C C 55 277 279 297 C5' C C 56 296 298 316 C5' C C 57 315 317 335 C5' A C 58 334 336 356 C5' C C 59 355 357 375 C5' G C 60 374 376 397 C5' C C 61 396 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 2 distorted distorted 2 3 4 23 P C B 3 distorted distorted 9 24 25 26 42 P G B 4 distorted distorted 31 43 44 45 64 P T B 5 distorted distorted 50 65 66 67 84 P G B 6 distorted distorted 72 85 86 87 106 P G B 7 distorted distorted 92 107 108 109 128 P G B 8 distorted distorted 114 129 130 131 150 P C B 9 distorted distorted 136 151 152 153 169 P G B 10 distorted distorted 158 170 171 172 191 P G B 11 distorted distorted 177 192 193 194 214 P C C 52 distorted distorted 215 216 217 233 P C C 53 distorted distorted 222 234 235 236 252 P G C 54 distorted distorted 241 253 254 255 274 P C C 55 distorted distorted 260 275 276 277 293 P C C 56 distorted distorted 282 294 295 296 312 P C C 57 distorted distorted 301 313 314 315 331 P A C 58 distorted distorted 320 332 333 334 352 P C C 59 distorted distorted 339 353 354 355 371 P G C 60 distorted distorted 360 372 373 374 393 P C C 61 distorted distorted 379 394 395 396 ---------------------------------------------------------------------------------