ID code: '1LE5' 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' G G 3 beta 29 34 32 55 C1' G G 4 beta 51 56 54 77 C1' A G 5 beta 73 78 76 98 C1' A G 6 beta 94 99 97 119 C1' A G 7 beta 115 120 118 140 C1' T G 8 beta 136 141 139 160 C1' T G 9 beta 156 161 159 180 C1' C G 10 beta 176 181 179 199 C1' C G 11 beta 195 200 198 218 C1' T G 12 beta 214 219 217 239 C1' A H 14 beta 235 240 238 260 C1' G H 15 beta 256 261 259 282 C1' G H 16 beta 278 283 281 304 C1' A H 17 beta 300 305 303 325 C1' A H 18 beta 321 326 324 346 C1' T H 19 beta 342 347 345 366 C1' T H 20 beta 362 367 365 386 C1' T H 21 beta 382 387 385 406 C1' C H 22 beta 402 407 405 425 C1' C H 23 beta 421 426 424 444 C1' C H 24 beta 440 445 443 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G G 3 33 30 54 C2' G G 4 55 52 76 C2' A G 5 77 74 97 C2' A G 6 98 95 118 C2' A G 7 119 116 139 C2' T G 8 140 137 159 C2' T G 9 160 157 179 C2' C G 10 180 177 198 C2' C G 11 199 196 217 C2' T G 12 218 215 238 C2' A H 14 239 236 259 C2' G H 15 260 257 281 C2' G H 16 282 279 303 C2' A H 17 304 301 324 C2' A H 18 325 322 345 C2' T H 19 346 343 365 C2' T H 20 366 363 385 C2' T H 21 386 383 405 C2' C H 22 406 403 424 C2' C H 23 425 422 443 C2' C H 24 444 441 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G G 2 OK 6 9 10 30 C3' G G 3 OK 28 31 32 52 C3' G G 4 OK 50 53 54 74 C3' A G 5 OK 72 75 76 95 C3' A G 6 OK 93 96 97 116 C3' A G 7 OK 114 117 118 137 C3' T G 8 OK 135 138 139 157 C3' T G 9 OK 155 158 159 177 C3' C G 10 OK 175 178 179 196 C3' C G 11 OK 194 197 198 215 C3' T G 12 OK 213 216 217 236 C3' A H 14 OK 234 237 238 257 C3' G H 15 OK 255 258 259 279 C3' G H 16 OK 277 280 281 301 C3' A H 17 OK 299 302 303 322 C3' A H 18 OK 320 323 324 343 C3' T H 19 OK 341 344 345 363 C3' T H 20 OK 361 364 365 383 C3' T H 21 OK 381 384 385 403 C3' C H 22 OK 401 404 405 422 C3' C H 23 OK 420 423 424 441 C3' C H 24 OK 439 442 443 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G G 2 OK 8 5 7 28 C4' G G 3 OK 30 27 29 50 C4' G G 4 OK 52 49 51 72 C4' A G 5 OK 74 71 73 93 C4' A G 6 OK 95 92 94 114 C4' A G 7 OK 116 113 115 135 C4' T G 8 OK 137 134 136 155 C4' T G 9 OK 157 154 156 175 C4' C G 10 OK 177 174 176 194 C4' C G 11 OK 196 193 195 213 C4' T G 12 OK 215 212 214 234 C4' A H 14 OK 236 233 235 255 C4' G H 15 OK 257 254 256 277 C4' G H 16 OK 279 276 278 299 C4' A H 17 OK 301 298 300 320 C4' A H 18 OK 322 319 321 341 C4' T H 19 OK 343 340 342 361 C4' T H 20 OK 363 360 362 381 C4' T H 21 OK 383 380 382 401 C4' C H 22 OK 403 400 402 420 C4' C H 23 OK 422 419 421 439 C4' C H 24 OK 441 438 440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G G 2 4 6 27 C5' G G 3 26 28 49 C5' G G 4 48 50 71 C5' A G 5 70 72 92 C5' A G 6 91 93 113 C5' A G 7 112 114 134 C5' T G 8 133 135 154 C5' T G 9 153 155 174 C5' C G 10 173 175 193 C5' C G 11 192 194 212 C5' T G 12 211 213 233 C5' A H 14 232 234 254 C5' G H 15 253 255 276 C5' G H 16 275 277 298 C5' A H 17 297 299 319 C5' A H 18 318 320 340 C5' T H 19 339 341 360 C5' T H 20 359 361 380 C5' T H 21 379 381 400 C5' C H 22 399 401 419 C5' C H 23 418 420 438 C5' C H 24 437 439 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G G 2 distorted distorted 2 3 4 23 P G G 3 distorted distorted 9 24 25 26 45 P G G 4 distorted distorted 31 46 47 48 67 P A G 5 distorted distorted 53 68 69 70 88 P A G 6 distorted distorted 75 89 90 91 109 P A G 7 distorted distorted 96 110 111 112 130 P T G 8 distorted distorted 117 131 132 133 150 P T G 9 distorted distorted 138 151 152 153 170 P C G 10 distorted distorted 158 171 172 173 189 P C G 11 distorted distorted 178 190 191 192 208 P T G 12 distorted distorted 197 209 210 211 229 P A H 14 distorted distorted 230 231 232 250 P G H 15 distorted distorted 237 251 252 253 272 P G H 16 distorted distorted 258 273 274 275 294 P A H 17 distorted distorted 280 295 296 297 315 P A H 18 distorted distorted 302 316 317 318 336 P T H 19 distorted distorted 323 337 338 339 356 P T H 20 distorted distorted 344 357 358 359 376 P T H 21 distorted distorted 364 377 378 379 396 P C H 22 distorted distorted 384 397 398 399 415 P C H 23 distorted distorted 404 416 417 418 434 P C H 24 distorted distorted 423 435 436 437 ---------------------------------------------------------------------------------