ID code: '5TDJ' 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' C A 1 beta 4 10 7 29 C1' C A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' G A 6 beta 110 116 113 138 C1' C A 7 beta 133 139 136 158 C1' C A 8 beta 153 159 156 178 C1' G A 9 beta 173 179 176 201 C1' G A 10 beta 196 202 199 222 C1' C B 1 beta 217 223 220 242 C1' C B 2 beta 237 243 240 262 C1' G B 3 beta 257 263 260 285 C1' G B 4 beta 280 286 283 308 C1' C B 5 beta 303 309 306 328 C1' G B 6 beta 323 329 326 351 C1' C B 7 beta 346 352 349 371 C1' C B 8 beta 366 372 369 391 C1' G B 9 beta 386 392 389 414 C1' G B 10 beta 409 415 412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' C A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' G A 6 OK 115 111 114 136 C2' C A 7 OK 138 134 137 156 C2' C A 8 OK 158 154 157 176 C2' G A 9 OK 178 174 177 199 C2' G A 10 OK 201 197 200 220 C2' C B 1 OK 222 218 221 240 C2' C B 2 OK 242 238 241 260 C2' G B 3 OK 262 258 261 283 C2' G B 4 OK 285 281 284 306 C2' C B 5 OK 308 304 307 326 C2' G B 6 OK 328 324 327 349 C2' C B 7 OK 351 347 350 369 C2' C B 8 OK 371 367 370 389 C2' G B 9 OK 391 387 390 412 C2' G B 10 OK 414 410 413 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' C A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' G A 6 OK 109 112 113 134 C3' C A 7 OK 132 135 136 154 C3' C A 8 OK 152 155 156 174 C3' G A 9 OK 172 175 176 197 C3' G A 10 OK 195 198 199 218 C3' C B 1 OK 216 219 220 238 C3' C B 2 OK 236 239 240 258 C3' G B 3 OK 256 259 260 281 C3' G B 4 OK 279 282 283 304 C3' C B 5 OK 302 305 306 324 C3' G B 6 OK 322 325 326 347 C3' C B 7 OK 345 348 349 367 C3' C B 8 OK 365 368 369 387 C3' G B 9 OK 385 388 389 410 C3' G B 10 OK 408 411 412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' C A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' G A 6 OK 111 108 110 132 C4' C A 7 OK 134 131 133 152 C4' C A 8 OK 154 151 153 172 C4' G A 9 OK 174 171 173 195 C4' G A 10 OK 197 194 196 216 C4' C B 1 OK 218 215 217 236 C4' C B 2 OK 238 235 237 256 C4' G B 3 OK 258 255 257 279 C4' G B 4 OK 281 278 280 302 C4' C B 5 OK 304 301 303 322 C4' G B 6 OK 324 321 323 345 C4' C B 7 OK 347 344 346 365 C4' C B 8 OK 367 364 366 385 C4' G B 9 OK 387 384 386 408 C4' G B 10 OK 410 407 409 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' C A 2 21 23 42 C5' G A 3 41 43 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' G A 6 107 109 131 C5' C A 7 130 132 151 C5' C A 8 150 152 171 C5' G A 9 170 172 194 C5' G A 10 193 195 215 C5' C B 1 214 216 235 C5' C B 2 234 236 255 C5' G B 3 254 256 278 C5' G B 4 277 279 301 C5' C B 5 300 302 321 C5' G B 6 320 322 344 C5' C B 7 343 345 364 C5' C B 8 363 365 384 C5' G B 9 383 385 407 C5' G B 10 406 408 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P G A 4 distorted distorted 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P G A 6 distorted distorted 105 106 107 127 P C A 7 distorted distorted 112 128 129 130 147 P C A 8 distorted distorted 135 148 149 150 167 P G A 9 distorted distorted 155 168 169 170 190 P G A 10 distorted distorted 175 191 192 193 231 P C B 2 distorted distorted 219 232 233 234 251 P G B 3 distorted distorted 239 252 253 254 274 P G B 4 distorted distorted 275 276 277 297 P C B 5 distorted distorted 282 298 299 300 317 P G B 6 distorted distorted 318 319 320 340 P C B 7 distorted distorted 325 341 342 343 360 P C B 8 distorted distorted 348 361 362 363 380 P G B 9 distorted distorted 368 381 382 383 403 P G B 10 distorted distorted 388 404 405 406 ---------------------------------------------------------------------------------