ID code: '1X9W' 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' --------------------------------------------------------------------------------- 8 C1' DG C 12 beta 4 9 7 30 C1' DG C 13 beta 26 31 29 52 C1' DT C 14 beta 48 53 51 69 C1' DA C 15 beta 65 70 68 90 C1' DG C 16 beta 86 91 89 112 C1' DT C 17 beta 108 113 111 132 C1' DG C 18 beta 128 133 131 154 C1' DT C 19 beta 150 155 153 174 C1' DG C 20 beta 170 175 173 196 C1' DA C 21 beta 192 197 195 224 C1' 2DT C 22 beta 223 211 220 234 C1' DA D 5 beta 230 235 233 255 C1' DT D 6 beta 251 256 254 275 C1' DC D 7 beta 271 276 274 294 C1' DA D 8 beta 290 295 293 315 C1' DC D 9 beta 311 316 314 334 C1' DA D 10 beta 330 335 333 355 C1' DC D 11 beta 351 356 354 374 C1' DT D 12 beta 370 375 373 394 C1' DA D 13 beta 390 395 393 415 C1' DC D 14 beta 411 416 414 434 C1' DC D 15 beta 430 435 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG C 12 8 5 29 C2' DG C 13 30 27 51 C2' DT C 14 52 49 68 C2' DA C 15 69 66 89 C2' DG C 16 90 87 111 C2' DT C 17 112 109 131 C2' DG C 18 132 129 153 C2' DT C 19 154 151 173 C2' DG C 20 174 171 195 C2' DA C 21 196 193 220 C2' 2DT C 22 224 225 233 C2' DA D 5 234 231 254 C2' DT D 6 255 252 274 C2' DC D 7 275 272 293 C2' DA D 8 294 291 314 C2' DC D 9 315 312 333 C2' DA D 10 334 331 354 C2' DC D 11 355 352 373 C2' DT D 12 374 371 393 C2' DA D 13 394 391 414 C2' DC D 14 415 412 433 C2' DC D 15 434 431 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG C 12 OK 3 6 7 27 C3' DG C 13 OK 25 28 29 49 C3' DT C 14 OK 47 50 51 66 C3' DA C 15 OK 64 67 68 87 C3' DG C 16 OK 85 88 89 109 C3' DT C 17 OK 107 110 111 129 C3' DG C 18 OK 127 130 131 151 C3' DT C 19 OK 149 152 153 171 C3' DG C 20 OK 169 172 173 193 C3' DA C 21 OK 191 194 195 225 C3' 2DT C 22 222 220 231 C3' DA D 5 OK 229 232 233 252 C3' DT D 6 OK 250 253 254 272 C3' DC D 7 OK 270 273 274 291 C3' DA D 8 OK 289 292 293 312 C3' DC D 9 OK 310 313 314 331 C3' DA D 10 OK 329 332 333 352 C3' DC D 11 OK 350 353 354 371 C3' DT D 12 OK 369 372 373 391 C3' DA D 13 OK 389 392 393 412 C3' DC D 14 OK 410 413 414 431 C3' DC D 15 OK 429 432 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG C 12 OK 5 2 4 25 C4' DG C 13 OK 27 24 26 47 C4' DT C 14 OK 49 46 48 64 C4' DA C 15 OK 66 63 65 85 C4' DG C 16 OK 87 84 86 107 C4' DT C 17 OK 109 106 108 127 C4' DG C 18 OK 129 126 128 149 C4' DT C 19 OK 151 148 150 169 C4' DG C 20 OK 171 168 170 191 C4' DA C 21 OK 193 190 192 222 C4' 2DT C 22 OK 225 221 223 229 C4' DA D 5 OK 231 228 230 250 C4' DT D 6 OK 252 249 251 270 C4' DC D 7 OK 272 269 271 289 C4' DA D 8 OK 291 288 290 310 C4' DC D 9 OK 312 309 311 329 C4' DA D 10 OK 331 328 330 350 C4' DC D 11 OK 352 349 351 369 C4' DT D 12 OK 371 368 370 389 C4' DA D 13 OK 391 388 390 410 C4' DC D 14 OK 412 409 411 429 C4' DC D 15 OK 431 428 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG C 12 1 3 24 C5' DG C 13 23 25 46 C5' DT C 14 45 47 63 C5' DA C 15 62 64 84 C5' DG C 16 83 85 106 C5' DT C 17 105 107 126 C5' DG C 18 125 127 148 C5' DT C 19 147 149 168 C5' DG C 20 167 169 190 C5' DA C 21 189 191 221 C5' 2DT C 22 210 222 228 C5' DA D 5 227 229 249 C5' DT D 6 248 250 269 C5' DC D 7 268 270 288 C5' DA D 8 287 289 309 C5' DC D 9 308 310 328 C5' DA D 10 327 329 349 C5' DC D 11 348 350 368 C5' DT D 12 367 369 388 C5' DA D 13 387 389 409 C5' DC D 14 408 410 428 C5' DC D 15 427 429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DG C 13 distorted distorted 6 21 22 23 42 P DT C 14 distorted distorted 28 43 44 45 80 P DG C 16 distorted distorted 67 81 82 83 102 P DT C 17 distorted distorted 88 103 104 105 122 P DG C 18 distorted distorted 110 123 124 125 144 P DT C 19 distorted distorted 130 145 146 147 164 P DG C 20 distorted distorted 152 165 166 167 186 P DA C 21 distorted distorted 172 187 188 189 207 P 2DT C 22 distorted distorted 194 208 209 210 245 P DT D 6 distorted distorted 232 246 247 248 265 P DC D 7 distorted distorted 253 266 267 268 284 P DA D 8 distorted distorted 273 285 286 287 305 P DC D 9 distorted distorted 292 306 307 308 324 P DA D 10 distorted distorted 313 325 326 327 345 P DC D 11 distorted distorted 332 346 347 348 364 P DT D 12 distorted distorted 353 365 366 367 384 P DA D 13 distorted distorted 372 385 386 387 405 P DC D 14 distorted distorted 392 406 407 408 424 P DC D 15 distorted distorted 413 425 426 427 ---------------------------------------------------------------------------------