ID code: '1FIU' 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 G 2 beta 7 12 10 33 C1' C G 3 beta 29 34 32 52 C1' G G 4 beta 48 53 51 76 C1' C K 5 beta 72 77 75 95 C1' C K 6 beta 91 96 94 114 C1' G K 7 beta 110 115 113 136 C1' G K 8 beta 132 137 135 158 C1' C K 9 beta 154 159 157 177 C1' G K 10 beta 173 178 176 199 C1' C K 11 beta 195 200 198 219 C1' G H 2 beta 215 220 218 241 C1' C H 3 beta 237 242 240 260 C1' G H 4 beta 256 261 259 284 C1' C L 5 beta 280 285 283 303 C1' C L 6 beta 299 304 302 322 C1' G L 7 beta 318 323 321 344 C1' G L 8 beta 340 345 343 366 C1' C L 9 beta 362 367 365 385 C1' G L 10 beta 381 386 384 407 C1' C L 11 beta 403 408 406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G G 2 11 8 32 C2' C G 3 33 30 51 C2' G G 4 52 49 75 C2' C K 5 76 73 94 C2' C K 6 95 92 113 C2' G K 7 114 111 135 C2' G K 8 136 133 157 C2' C K 9 158 155 176 C2' G K 10 177 174 198 C2' C K 11 199 196 218 C2' G H 2 219 216 240 C2' C H 3 241 238 259 C2' G H 4 260 257 283 C2' C L 5 284 281 302 C2' C L 6 303 300 321 C2' G L 7 322 319 343 C2' G L 8 344 341 365 C2' C L 9 366 363 384 C2' G L 10 385 382 406 C2' C L 11 407 404 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G G 2 OK 6 9 10 30 C3' C G 3 OK 28 31 32 49 C3' G G 4 OK 47 50 51 73 C3' C K 5 OK 71 74 75 92 C3' C K 6 OK 90 93 94 111 C3' G K 7 OK 109 112 113 133 C3' G K 8 OK 131 134 135 155 C3' C K 9 OK 153 156 157 174 C3' G K 10 OK 172 175 176 196 C3' C K 11 OK 194 197 198 216 C3' G H 2 OK 214 217 218 238 C3' C H 3 OK 236 239 240 257 C3' G H 4 OK 255 258 259 281 C3' C L 5 OK 279 282 283 300 C3' C L 6 OK 298 301 302 319 C3' G L 7 OK 317 320 321 341 C3' G L 8 OK 339 342 343 363 C3' C L 9 OK 361 364 365 382 C3' G L 10 OK 380 383 384 404 C3' C L 11 OK 402 405 406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G G 2 OK 8 5 7 28 C4' C G 3 OK 30 27 29 47 C4' G G 4 OK 49 46 48 71 C4' C K 5 OK 73 70 72 90 C4' C K 6 OK 92 89 91 109 C4' G K 7 OK 111 108 110 131 C4' G K 8 OK 133 130 132 153 C4' C K 9 OK 155 152 154 172 C4' G K 10 OK 174 171 173 194 C4' C K 11 OK 196 193 195 214 C4' G H 2 OK 216 213 215 236 C4' C H 3 OK 238 235 237 255 C4' G H 4 OK 257 254 256 279 C4' C L 5 OK 281 278 280 298 C4' C L 6 OK 300 297 299 317 C4' G L 7 OK 319 316 318 339 C4' G L 8 OK 341 338 340 361 C4' C L 9 OK 363 360 362 380 C4' G L 10 OK 382 379 381 402 C4' C L 11 OK 404 401 403 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G G 2 4 6 27 C5' C G 3 26 28 46 C5' G G 4 45 47 70 C5' C K 5 69 71 89 C5' C K 6 88 90 108 C5' G K 7 107 109 130 C5' G K 8 129 131 152 C5' C K 9 151 153 171 C5' G K 10 170 172 193 C5' C K 11 192 194 213 C5' G H 2 212 214 235 C5' C H 3 234 236 254 C5' G H 4 253 255 278 C5' C L 5 277 279 297 C5' C L 6 296 298 316 C5' G L 7 315 317 338 C5' G L 8 337 339 360 C5' C L 9 359 361 379 C5' G L 10 378 380 401 C5' C L 11 400 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G G 2 distorted distorted 2 3 4 23 P C G 3 distorted distorted 9 24 25 26 42 P G G 4 distorted distorted 31 43 44 45 66 P C K 5 OK OK 67 68 69 85 P C K 6 distorted distorted 74 86 87 88 104 P G K 7 distorted distorted 93 105 106 107 126 P G K 8 distorted distorted 112 127 128 129 148 P C K 9 distorted distorted 134 149 150 151 167 P G K 10 distorted distorted 156 168 169 170 189 P C K 11 distorted distorted 175 190 191 192 209 P G H 2 distorted distorted 210 211 212 231 P C H 3 distorted distorted 217 232 233 234 250 P G H 4 distorted distorted 239 251 252 253 274 P C L 5 OK OK 275 276 277 293 P C L 6 distorted distorted 282 294 295 296 312 P G L 7 distorted distorted 301 313 314 315 334 P G L 8 distorted distorted 320 335 336 337 356 P C L 9 distorted distorted 342 357 358 359 375 P G L 10 distorted distorted 364 376 377 378 397 P C L 11 distorted distorted 383 398 399 400 ---------------------------------------------------------------------------------