ID code: '1E3O' 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' --------------------------------------------------------------------------------- 15 C1' A A 201 beta 14 1 11 35 C1' T A 202 beta 34 22 31 57 C1' G A 203 beta 56 42 53 76 C1' C A 204 beta 75 64 72 93 C1' A A 205 beta 92 79 89 117 C1' T A 206 beta 116 104 113 139 C1' G A 207 beta 138 124 135 156 C1' A A 208 beta 155 142 152 182 C1' G A 209 beta 181 167 178 204 C1' G A 210 beta 203 189 200 221 C1' A A 211 beta 220 207 217 240 C1' T B 201 beta 239 227 236 259 C1' C B 202 beta 258 247 255 278 C1' C B 203 beta 277 266 274 298 C1' T B 204 beta 297 285 294 317 C1' C B 205 beta 316 305 313 334 C1' A B 206 beta 333 320 330 358 C1' T B 207 beta 357 345 354 380 C1' G B 208 beta 379 365 376 399 C1' C B 209 beta 398 387 395 416 C1' A B 210 beta 415 402 412 440 C1' T B 211 beta 439 427 436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A A 201 15 16 31 C2' T A 202 35 36 53 C2' G A 203 57 58 72 C2' C A 204 76 77 89 C2' A A 205 93 94 113 C2' T A 206 117 118 135 C2' G A 207 139 140 152 C2' A A 208 156 157 178 C2' G A 209 182 183 200 C2' G A 210 204 205 217 C2' A A 211 221 222 236 C2' T B 201 240 241 255 C2' C B 202 259 260 274 C2' C B 203 278 279 294 C2' T B 204 298 299 313 C2' C B 205 317 318 330 C2' A B 206 334 335 354 C2' T B 207 358 359 376 C2' G B 208 380 381 395 C2' C B 209 399 400 412 C2' A B 210 416 417 436 C2' T B 211 440 441 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 16 C3' A A 201 OK 13 17 11 36 C3' T A 202 OK 33 37 31 58 C3' G A 203 OK 55 59 53 77 C3' C A 204 OK 74 78 72 94 C3' A A 205 OK 91 95 89 118 C3' T A 206 OK 115 119 113 140 C3' G A 207 OK 137 141 135 157 C3' A A 208 OK 154 158 152 183 C3' G A 209 OK 180 184 178 205 C3' G A 210 OK 202 206 200 222 C3' A A 211 OK 219 223 217 241 C3' T B 201 OK 238 242 236 260 C3' C B 202 OK 257 261 255 279 C3' C B 203 OK 276 280 274 299 C3' T B 204 OK 296 300 294 318 C3' C B 205 OK 315 319 313 335 C3' A B 206 OK 332 336 330 359 C3' T B 207 OK 356 360 354 381 C3' G B 208 OK 378 382 376 400 C3' C B 209 OK 397 401 395 417 C3' A B 210 OK 414 418 412 441 C3' T B 211 OK 438 442 436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 13 C4' A A 201 OK 16 12 14 33 C4' T A 202 OK 36 32 34 55 C4' G A 203 OK 58 54 56 74 C4' C A 204 OK 77 73 75 91 C4' A A 205 OK 94 90 92 115 C4' T A 206 OK 118 114 116 137 C4' G A 207 OK 140 136 138 154 C4' A A 208 OK 157 153 155 180 C4' G A 209 OK 183 179 181 202 C4' G A 210 OK 205 201 203 219 C4' A A 211 OK 222 218 220 238 C4' T B 201 OK 241 237 239 257 C4' C B 202 OK 260 256 258 276 C4' C B 203 OK 279 275 277 296 C4' T B 204 OK 299 295 297 315 C4' C B 205 OK 318 314 316 332 C4' A B 206 OK 335 331 333 356 C4' T B 207 OK 359 355 357 378 C4' G B 208 OK 381 377 379 397 C4' C B 209 OK 400 396 398 414 C4' A B 210 OK 417 413 415 438 C4' T B 211 OK 441 437 439 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 12 C5' A A 201 13 32 C5' T A 202 21 33 54 C5' G A 203 41 55 73 C5' C A 204 63 74 90 C5' A A 205 99 91 114 C5' T A 206 103 115 136 C5' G A 207 123 137 153 C5' A A 208 162 154 179 C5' G A 209 166 180 201 C5' G A 210 188 202 218 C5' A A 211 224 219 237 C5' T B 201 226 238 256 C5' C B 202 246 257 275 C5' C B 203 265 276 295 C5' T B 204 284 296 314 C5' C B 205 304 315 331 C5' A B 206 340 332 355 C5' T B 207 344 356 377 C5' G B 208 364 378 396 C5' C B 209 386 397 413 C5' A B 210 422 414 437 C5' T B 211 426 438 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P T A 202 distorted distorted 17 19 20 21 38 P G A 203 distorted distorted 37 39 40 41 60 P C A 204 distorted distorted 59 61 62 63 96 P A A 205 distorted distorted 78 97 98 99 100 P T A 206 distorted distorted 95 101 102 103 120 P G A 207 distorted distorted 119 121 122 123 159 P A A 208 distorted distorted 141 160 161 162 163 P G A 209 distorted distorted 158 164 165 166 185 P G A 210 distorted distorted 184 186 187 188 243 P C B 202 distorted distorted 242 244 245 246 262 P C B 203 distorted distorted 261 263 264 265 281 P T B 204 distorted distorted 280 282 283 284 301 P C B 205 distorted distorted 300 302 303 304 337 P A B 206 distorted distorted 319 338 339 340 341 P T B 207 distorted distorted 336 342 343 344 361 P G B 208 distorted distorted 360 362 363 364 383 P C B 209 distorted distorted 382 384 385 386 419 P A B 210 distorted distorted 401 420 421 422 423 P T B 211 distorted distorted 418 424 425 426 ---------------------------------------------------------------------------------