ID code: '1NH3' 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' --------------------------------------------------------------------------------- 5 C1' GNG C 11 beta 4 6 17 30 C1' G C 12 beta 26 31 29 52 C1' A C 13 beta 48 53 51 73 C1' A C 14 beta 69 74 72 94 C1' A C 15 beta 90 95 93 115 C1' A C 16 beta 111 116 114 136 C1' A C 17 beta 132 137 135 157 C1' U C 18 beta 153 158 156 176 C1' U C 19 beta 172 177 175 195 C1' U C 20 beta 191 196 194 214 C1' U C 21 beta 210 215 213 233 C1' T C 22 beta 229 234 232 251 C1' A D 101 beta 247 252 250 272 C1' A D 102 beta 268 273 271 293 C1' A D 103 beta 289 294 292 314 C1' A D 104 beta 310 315 313 335 C1' A D 105 beta 331 336 334 356 C1' T D 106 beta 352 357 355 376 C1' U D 107 beta 372 377 375 395 C1' U D 108 beta 391 396 394 414 C1' U D 109 beta 410 415 413 433 C1' U D 110 beta 429 434 432 452 C1' C D 111 beta 448 453 451 472 C1' CAR D 112 beta 467 473 470 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 17 C2' GNG C 11 5 18 29 C2' G C 12 30 27 51 C2' A C 13 52 49 72 C2' A C 14 73 70 93 C2' A C 15 94 91 114 C2' A C 16 115 112 135 C2' A C 17 136 133 156 C2' U C 18 157 154 175 C2' U C 19 176 173 194 C2' U C 20 195 192 213 C2' U C 21 214 211 232 C2' T C 22 233 230 250 C2' A D 101 251 248 271 C2' A D 102 272 269 292 C2' A D 103 293 290 313 C2' A D 104 314 311 334 C2' A D 105 335 332 355 C2' T D 106 356 353 375 C2' U D 107 376 373 394 C2' U D 108 395 392 413 C2' U D 109 414 411 432 C2' U D 110 433 430 451 C2' C D 111 452 449 470 C2' CAR D 112 distorted 472 468 471 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 18 C3' GNG C 11 OK 3 19 17 27 C3' G C 12 OK 25 28 29 49 C3' A C 13 OK 47 50 51 70 C3' A C 14 OK 68 71 72 91 C3' A C 15 OK 89 92 93 112 C3' A C 16 OK 110 113 114 133 C3' A C 17 OK 131 134 135 154 C3' U C 18 OK 152 155 156 173 C3' U C 19 OK 171 174 175 192 C3' U C 20 OK 190 193 194 211 C3' U C 21 OK 209 212 213 230 C3' T C 22 OK 228 231 232 248 C3' A D 101 OK 246 249 250 269 C3' A D 102 OK 267 270 271 290 C3' A D 103 OK 288 291 292 311 C3' A D 104 OK 309 312 313 332 C3' A D 105 OK 330 333 334 353 C3' T D 106 OK 351 354 355 373 C3' U D 107 OK 371 374 375 392 C3' U D 108 OK 390 393 394 411 C3' U D 109 OK 409 412 413 430 C3' U D 110 OK 428 431 432 449 C3' C D 111 OK 447 450 451 468 C3' CAR D 112 OK 466 469 470 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' GNG C 11 OK 18 2 4 25 C4' G C 12 OK 27 24 26 47 C4' A C 13 OK 49 46 48 68 C4' A C 14 OK 70 67 69 89 C4' A C 15 OK 91 88 90 110 C4' A C 16 OK 112 109 111 131 C4' A C 17 OK 133 130 132 152 C4' U C 18 OK 154 151 153 171 C4' U C 19 OK 173 170 172 190 C4' U C 20 OK 192 189 191 209 C4' U C 21 OK 211 208 210 228 C4' T C 22 OK 230 227 229 246 C4' A D 101 OK 248 245 247 267 C4' A D 102 OK 269 266 268 288 C4' A D 103 OK 290 287 289 309 C4' A D 104 OK 311 308 310 330 C4' A D 105 OK 332 329 331 351 C4' T D 106 OK 353 350 352 371 C4' U D 107 OK 373 370 372 390 C4' U D 108 OK 392 389 391 409 C4' U D 109 OK 411 408 410 428 C4' U D 110 OK 430 427 429 447 C4' C D 111 OK 449 446 448 466 C4' CAR D 112 OK 468 465 467 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' GNG C 11 1 3 24 C5' G C 12 23 25 46 C5' A C 13 45 47 67 C5' A C 14 66 68 88 C5' A C 15 87 89 109 C5' A C 16 108 110 130 C5' A C 17 129 131 151 C5' U C 18 150 152 170 C5' U C 19 169 171 189 C5' U C 20 188 190 208 C5' U C 21 207 209 227 C5' T C 22 226 228 245 C5' A D 101 244 246 266 C5' A D 102 265 267 287 C5' A D 103 286 288 308 C5' A D 104 307 309 329 C5' A D 105 328 330 350 C5' T D 106 349 351 370 C5' U D 107 369 371 389 C5' U D 108 388 390 408 C5' U D 109 407 409 427 C5' U D 110 426 428 446 C5' C D 111 445 447 465 C5' CAR D 112 464 466 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G C 12 distorted distorted 19 21 22 23 42 P A C 13 distorted distorted 28 43 44 45 63 P A C 14 distorted distorted 50 64 65 66 84 P A C 15 distorted distorted 71 85 86 87 105 P A C 16 distorted distorted 92 106 107 108 126 P A C 17 distorted distorted 113 127 128 129 147 P U C 18 distorted distorted 134 148 149 150 166 P U C 19 distorted distorted 155 167 168 169 185 P U C 20 distorted distorted 174 186 187 188 204 P U C 21 distorted distorted 193 205 206 207 223 P T C 22 distorted distorted 212 224 225 226 262 P A D 102 distorted distorted 249 263 264 265 283 P A D 103 distorted distorted 270 284 285 286 304 P A D 104 distorted distorted 291 305 306 307 325 P A D 105 distorted distorted 312 326 327 328 346 P T D 106 distorted distorted 333 347 348 349 366 P U D 107 distorted distorted 354 367 368 369 385 P U D 108 distorted distorted 374 386 387 388 404 P U D 109 distorted distorted 393 405 406 407 423 P U D 110 distorted distorted 412 424 425 426 442 P C D 111 distorted distorted 431 443 444 445 461 P CAR D 112 distorted distorted 450 462 463 464 ---------------------------------------------------------------------------------