ID code: '1LE9' 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 C 702 beta 7 12 10 33 C1' G C 703 beta 29 34 32 55 C1' G C 704 beta 51 56 54 77 C1' A C 705 beta 73 78 76 98 C1' C C 706 beta 94 99 97 117 C1' T C 707 beta 113 118 116 137 C1' T C 708 beta 133 138 136 157 C1' T C 709 beta 153 158 156 177 C1' C C 710 beta 173 178 176 196 C1' C C 711 beta 192 197 195 215 C1' T C 712 beta 211 216 214 236 C1' A D 714 beta 232 237 235 257 C1' G D 715 beta 253 258 256 279 C1' G D 716 beta 275 280 278 301 C1' A D 717 beta 297 302 300 322 C1' A D 718 beta 318 323 321 343 C1' A D 719 beta 339 344 342 364 C1' G D 720 beta 360 365 363 386 C1' T D 721 beta 382 387 385 406 C1' C D 722 beta 402 407 405 425 C1' C D 723 beta 421 426 424 444 C1' C D 724 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 C 702 11 8 32 C2' G C 703 33 30 54 C2' G C 704 55 52 76 C2' A C 705 77 74 97 C2' C C 706 98 95 116 C2' T C 707 117 114 136 C2' T C 708 137 134 156 C2' T C 709 157 154 176 C2' C C 710 177 174 195 C2' C C 711 196 193 214 C2' T C 712 215 212 235 C2' A D 714 236 233 256 C2' G D 715 257 254 278 C2' G D 716 279 276 300 C2' A D 717 301 298 321 C2' A D 718 322 319 342 C2' A D 719 343 340 363 C2' G D 720 364 361 385 C2' T D 721 386 383 405 C2' C D 722 406 403 424 C2' C D 723 425 422 443 C2' C D 724 444 441 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G C 702 OK 6 9 10 30 C3' G C 703 OK 28 31 32 52 C3' G C 704 OK 50 53 54 74 C3' A C 705 OK 72 75 76 95 C3' C C 706 OK 93 96 97 114 C3' T C 707 OK 112 115 116 134 C3' T C 708 OK 132 135 136 154 C3' T C 709 OK 152 155 156 174 C3' C C 710 OK 172 175 176 193 C3' C C 711 OK 191 194 195 212 C3' T C 712 OK 210 213 214 233 C3' A D 714 OK 231 234 235 254 C3' G D 715 OK 252 255 256 276 C3' G D 716 OK 274 277 278 298 C3' A D 717 OK 296 299 300 319 C3' A D 718 OK 317 320 321 340 C3' A D 719 OK 338 341 342 361 C3' G D 720 OK 359 362 363 383 C3' T D 721 OK 381 384 385 403 C3' C D 722 OK 401 404 405 422 C3' C D 723 OK 420 423 424 441 C3' C D 724 OK 439 442 443 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G C 702 OK 8 5 7 28 C4' G C 703 OK 30 27 29 50 C4' G C 704 OK 52 49 51 72 C4' A C 705 OK 74 71 73 93 C4' C C 706 OK 95 92 94 112 C4' T C 707 OK 114 111 113 132 C4' T C 708 OK 134 131 133 152 C4' T C 709 OK 154 151 153 172 C4' C C 710 OK 174 171 173 191 C4' C C 711 OK 193 190 192 210 C4' T C 712 OK 212 209 211 231 C4' A D 714 OK 233 230 232 252 C4' G D 715 OK 254 251 253 274 C4' G D 716 OK 276 273 275 296 C4' A D 717 OK 298 295 297 317 C4' A D 718 OK 319 316 318 338 C4' A D 719 OK 340 337 339 359 C4' G D 720 OK 361 358 360 381 C4' T D 721 OK 383 380 382 401 C4' C D 722 OK 403 400 402 420 C4' C D 723 OK 422 419 421 439 C4' C D 724 OK 441 438 440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G C 702 4 6 27 C5' G C 703 26 28 49 C5' G C 704 48 50 71 C5' A C 705 70 72 92 C5' C C 706 91 93 111 C5' T C 707 110 112 131 C5' T C 708 130 132 151 C5' T C 709 150 152 171 C5' C C 710 170 172 190 C5' C C 711 189 191 209 C5' T C 712 208 210 230 C5' A D 714 229 231 251 C5' G D 715 250 252 273 C5' G D 716 272 274 295 C5' A D 717 294 296 316 C5' A D 718 315 317 337 C5' A D 719 336 338 358 C5' G D 720 357 359 380 C5' T D 721 379 381 400 C5' C D 722 399 401 419 C5' C D 723 418 420 438 C5' C D 724 437 439 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G C 702 distorted distorted 2 3 4 23 P G C 703 distorted distorted 9 24 25 26 45 P G C 704 distorted distorted 31 46 47 48 67 P A C 705 distorted distorted 53 68 69 70 88 P C C 706 distorted distorted 75 89 90 91 107 P T C 707 distorted distorted 96 108 109 110 127 P T C 708 distorted distorted 115 128 129 130 147 P T C 709 distorted distorted 135 148 149 150 167 P C C 710 distorted distorted 155 168 169 170 186 P C C 711 distorted distorted 175 187 188 189 205 P T C 712 distorted distorted 194 206 207 208 226 P A D 714 distorted distorted 227 228 229 247 P G D 715 distorted distorted 234 248 249 250 269 P G D 716 distorted distorted 255 270 271 272 291 P A D 717 distorted distorted 277 292 293 294 312 P A D 718 distorted distorted 299 313 314 315 333 P A D 719 distorted distorted 320 334 335 336 354 P G D 720 distorted distorted 341 355 356 357 376 P T D 721 distorted distorted 362 377 378 379 396 P C D 722 distorted distorted 384 397 398 399 415 P C D 723 distorted distorted 404 416 417 418 434 P C D 724 distorted distorted 423 435 436 437 ---------------------------------------------------------------------------------