ID code: '8PSH' 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 A 1 alpha beta 4 26 9 7 40 C1' SC A 2 alpha beta 44 55 32 41 72 C1' GS A 3 alpha beta 68 90 73 71 105 C1' PST A 4 alpha beta 101 121 106 104 135 C1' SC A 5 alpha beta 139 150 127 136 167 C1' AS A 6 alpha beta 163 184 168 166 199 C1' GS A 7 alpha beta 195 217 200 198 232 C1' GS A 8 alpha beta 228 251 233 231 265 C1' C B 9 alpha beta 260 280 266 263 297 C1' C B 10 alpha beta 292 312 298 295 328 C1' U B 11 alpha beta 323 343 329 326 358 C1' G B 12 alpha beta 353 376 359 356 392 C1' A B 13 alpha beta 387 409 393 390 425 C1' C B 14 alpha beta 420 440 426 423 456 C1' G B 15 alpha beta 451 474 457 454 490 C1' C B 16 alpha beta 485 506 491 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 OK OK 8 5 24 25 41 C2' SC A 2 OK OK 40 42 56 57 71 C2' GS A 3 OK OK 72 69 88 89 104 C2' PST A 4 OK OK 105 102 119 120 136 C2' SC A 5 OK OK 135 137 151 152 166 C2' AS A 6 OK OK 167 164 182 183 198 C2' GS A 7 OK OK 199 196 215 216 231 C2' GS A 8 OK OK 232 229 249 250 263 C2' C B 9 OK OK 265 261 278 264 295 C2' C B 10 OK OK 297 293 310 296 326 C2' U B 11 OK OK 328 324 341 327 356 C2' G B 12 OK OK 358 354 374 357 390 C2' A B 13 OK OK 392 388 407 391 423 C2' C B 14 OK OK 425 421 438 424 454 C2' G B 15 OK OK 456 452 472 455 488 C2' C B 16 OK OK 490 486 504 489 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK OK 3 23 6 7 42 C3' SC A 2 OK OK 43 58 45 41 69 C3' GS A 3 OK OK 67 87 70 71 102 C3' PST A 4 OK OK 100 118 103 104 137 C3' SC A 5 OK OK 138 153 140 136 164 C3' AS A 6 OK OK 162 181 165 166 196 C3' GS A 7 OK OK 194 214 197 198 229 C3' GS A 8 OK OK 227 247 230 231 261 C3' C B 9 OK OK 259 277 262 263 293 C3' C B 10 OK OK 291 309 294 295 324 C3' U B 11 OK OK 322 340 325 326 354 C3' G B 12 OK OK 352 373 355 356 388 C3' A B 13 OK OK 386 406 389 390 421 C3' C B 14 OK OK 419 437 422 423 452 C3' G B 15 OK OK 450 471 453 454 486 C3' C B 16 OK OK 484 502 487 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK OK 5 22 2 4 43 C4' SC A 2 OK OK 42 59 46 44 67 C4' GS A 3 OK OK 69 86 66 68 100 C4' PST A 4 OK OK 102 117 99 101 138 C4' SC A 5 OK OK 137 154 141 139 162 C4' AS A 6 OK OK 164 180 161 163 194 C4' GS A 7 OK OK 196 213 193 195 227 C4' GS A 8 OK OK 229 246 226 228 259 C4' C B 9 OK OK 261 276 258 260 291 C4' C B 10 OK OK 293 308 290 292 322 C4' U B 11 OK OK 324 339 321 323 352 C4' G B 12 OK OK 354 372 351 353 386 C4' A B 13 OK OK 388 405 385 387 419 C4' C B 14 OK OK 421 436 418 420 450 C4' G B 15 OK OK 452 470 449 451 484 C4' C B 16 OK OK 486 501 483 485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 OK OK 1 20 21 3 46 C5' SC A 2 OK OK 47 60 61 43 66 C5' GS A 3 OK OK 65 84 85 67 99 C5' PST A 4 OK OK 98 115 116 100 141 C5' SC A 5 OK OK 142 155 156 138 161 C5' AS A 6 OK OK 160 178 179 162 193 C5' GS A 7 OK OK 192 211 212 194 226 C5' GS A 8 OK OK 225 244 245 227 258 C5' C B 9 OK OK 257 274 275 259 290 C5' C B 10 OK OK 289 306 307 291 321 C5' U B 11 OK OK 320 337 338 322 351 C5' G B 12 OK OK 350 370 371 352 385 C5' A B 13 OK OK 384 403 404 386 418 C5' C B 14 OK OK 417 434 435 419 449 C5' G B 15 OK OK 448 468 469 450 483 C5' C B 16 OK OK 482 499 500 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 48 P SC A 2 6 49 47 62 P GS A 3 45 63 65 95 P PST A 4 70 96 98 143 P SC A 5 103 144 142 157 P AS A 6 140 158 160 189 P GS A 7 165 190 192 222 P GS A 8 197 223 225 286 P C B 10 distorted distorted 262 287 288 289 317 P U B 11 distorted distorted 294 318 319 320 347 P G B 12 distorted distorted 325 348 349 350 381 P A B 13 distorted distorted 355 382 383 384 414 P C B 14 distorted distorted 389 415 416 417 445 P G B 15 distorted distorted 422 446 447 448 479 P C B 16 distorted distorted 453 480 481 482 ---------------------------------------------------------------------------------