ID code: '1FLO' 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' A E -16 beta 7 12 10 32 C1' A E -15 beta 28 33 31 53 C1' G E -14 beta 49 54 52 75 C1' T E -13 beta 71 76 74 95 C1' T E -12 beta 91 96 94 115 C1' C E -11 beta 111 116 114 134 C1' C E -10 beta 130 135 133 153 C1' T E -9 beta 149 154 152 173 C1' A E -8 beta 169 174 172 194 C1' T E -7 beta 190 195 193 214 C1' T E -6 beta 210 215 213 234 C1' C E -5 beta 230 235 233 254 C1' G F 5 beta 250 255 253 276 C1' A F 6 beta 272 277 275 297 C1' A F 7 beta 293 298 296 318 C1' T F 8 beta 314 319 317 338 C1' A F 9 beta 334 339 337 359 C1' G F 10 beta 355 360 358 381 C1' G F 11 beta 377 382 380 403 C1' A F 12 beta 399 404 402 424 C1' A F 13 beta 420 425 423 445 C1' C F 14 beta 441 446 444 464 C1' T F 15 beta 460 465 463 484 C1' T F 16 beta 480 485 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A E -16 11 8 31 C2' A E -15 32 29 52 C2' G E -14 53 50 74 C2' T E -13 75 72 94 C2' T E -12 95 92 114 C2' C E -11 115 112 133 C2' C E -10 134 131 152 C2' T E -9 153 150 172 C2' A E -8 173 170 193 C2' T E -7 194 191 213 C2' T E -6 214 211 233 C2' C E -5 234 231 253 C2' G F 5 254 251 275 C2' A F 6 276 273 296 C2' A F 7 297 294 317 C2' T F 8 318 315 337 C2' A F 9 338 335 358 C2' G F 10 359 356 380 C2' G F 11 381 378 402 C2' A F 12 403 400 423 C2' A F 13 424 421 444 C2' C F 14 445 442 463 C2' T F 15 464 461 483 C2' T F 16 484 481 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A E -16 OK 6 9 10 29 C3' A E -15 OK 27 30 31 50 C3' G E -14 OK 48 51 52 72 C3' T E -13 OK 70 73 74 92 C3' T E -12 OK 90 93 94 112 C3' C E -11 OK 110 113 114 131 C3' C E -10 OK 129 132 133 150 C3' T E -9 OK 148 151 152 170 C3' A E -8 OK 168 171 172 191 C3' T E -7 OK 189 192 193 211 C3' T E -6 OK 209 212 213 231 C3' C E -5 OK 229 232 233 251 C3' G F 5 OK 249 252 253 273 C3' A F 6 OK 271 274 275 294 C3' A F 7 OK 292 295 296 315 C3' T F 8 OK 313 316 317 335 C3' A F 9 OK 333 336 337 356 C3' G F 10 OK 354 357 358 378 C3' G F 11 OK 376 379 380 400 C3' A F 12 OK 398 401 402 421 C3' A F 13 OK 419 422 423 442 C3' C F 14 OK 440 443 444 461 C3' T F 15 OK 459 462 463 481 C3' T F 16 OK 479 482 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A E -16 OK 8 5 7 27 C4' A E -15 OK 29 26 28 48 C4' G E -14 OK 50 47 49 70 C4' T E -13 OK 72 69 71 90 C4' T E -12 OK 92 89 91 110 C4' C E -11 OK 112 109 111 129 C4' C E -10 OK 131 128 130 148 C4' T E -9 OK 150 147 149 168 C4' A E -8 OK 170 167 169 189 C4' T E -7 OK 191 188 190 209 C4' T E -6 OK 211 208 210 229 C4' C E -5 OK 231 228 230 249 C4' G F 5 OK 251 248 250 271 C4' A F 6 OK 273 270 272 292 C4' A F 7 OK 294 291 293 313 C4' T F 8 OK 315 312 314 333 C4' A F 9 OK 335 332 334 354 C4' G F 10 OK 356 353 355 376 C4' G F 11 OK 378 375 377 398 C4' A F 12 OK 400 397 399 419 C4' A F 13 OK 421 418 420 440 C4' C F 14 OK 442 439 441 459 C4' T F 15 OK 461 458 460 479 C4' T F 16 OK 481 478 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A E -16 4 6 26 C5' A E -15 25 27 47 C5' G E -14 46 48 69 C5' T E -13 68 70 89 C5' T E -12 88 90 109 C5' C E -11 108 110 128 C5' C E -10 127 129 147 C5' T E -9 146 148 167 C5' A E -8 166 168 188 C5' T E -7 187 189 208 C5' T E -6 207 209 228 C5' C E -5 227 229 248 C5' G F 5 247 249 270 C5' A F 6 269 271 291 C5' A F 7 290 292 312 C5' T F 8 311 313 332 C5' A F 9 331 333 353 C5' G F 10 352 354 375 C5' G F 11 374 376 397 C5' A F 12 396 398 418 C5' A F 13 417 419 439 C5' C F 14 438 440 458 C5' T F 15 457 459 478 C5' T F 16 477 479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A E -16 distorted distorted 2 3 4 22 P A E -15 distorted distorted 9 23 24 25 43 P G E -14 distorted distorted 30 44 45 46 65 P T E -13 distorted distorted 51 66 67 68 85 P T E -12 distorted distorted 73 86 87 88 105 P C E -11 distorted distorted 93 106 107 108 124 P C E -10 distorted distorted 113 125 126 127 143 P T E -9 distorted distorted 132 144 145 146 163 P A E -8 distorted distorted 151 164 165 166 184 P T E -7 distorted distorted 171 185 186 187 204 P T E -6 distorted distorted 192 205 206 207 224 P C E -5 distorted distorted 212 225 226 227 244 P G F 5 distorted distorted 245 246 247 266 P A F 6 distorted distorted 252 267 268 269 287 P A F 7 distorted distorted 274 288 289 290 308 P T F 8 distorted distorted 295 309 310 311 328 P A F 9 distorted distorted 316 329 330 331 349 P G F 10 distorted distorted 336 350 351 352 371 P G F 11 distorted distorted 357 372 373 374 393 P A F 12 distorted distorted 379 394 395 396 414 P A F 13 distorted distorted 401 415 416 417 435 P C F 14 distorted distorted 422 436 437 438 454 P T F 15 distorted distorted 443 455 456 457 474 P T F 16 distorted distorted 462 475 476 477 ---------------------------------------------------------------------------------