ID code: '2PYL' 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 X 1 beta 4 9 7 30 C1' DA X 2 beta 26 31 29 51 C1' DC X 3 beta 47 52 50 70 C1' DT X 4 beta 66 71 69 90 C1' DG X 5 beta 86 91 89 112 C1' DC X 6 beta 108 113 111 131 C1' DT X 7 beta 127 132 130 151 C1' DT X 8 beta 147 152 150 171 C1' DA X 9 beta 167 172 170 192 C1' DC X 10 beta 188 193 191 210 C1' 2DA X 11 beta 207 211 209 229 C1' DA Y 4 beta 225 230 228 250 C1' DC Y 5 beta 246 251 249 269 C1' DA Y 6 beta 265 270 268 290 C1' DT Y 7 beta 286 291 289 310 C1' DG Y 8 beta 306 311 309 332 C1' DT Y 9 beta 328 333 331 352 C1' DA Y 10 beta 348 353 351 373 C1' DA Y 11 beta 369 374 372 394 C1' DG Y 12 beta 390 395 393 416 C1' DC Y 13 beta 412 417 415 435 C1' DA Y 14 beta 431 436 434 456 C1' DG Y 15 beta 452 457 455 478 C1' DT Y 16 beta 474 479 477 498 C1' DC Y 17 beta 494 499 497 5210 C1' TTP A3204 beta 5206 5211 5209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG X 1 8 5 29 C2' DA X 2 30 27 50 C2' DC X 3 51 48 69 C2' DT X 4 70 67 89 C2' DG X 5 90 87 111 C2' DC X 6 112 109 130 C2' DT X 7 131 128 150 C2' DT X 8 151 148 170 C2' DA X 9 171 168 191 C2' DC X 10 192 189 209 C2' 2DA X 11 210 208 228 C2' DA Y 4 229 226 249 C2' DC Y 5 250 247 268 C2' DA Y 6 269 266 289 C2' DT Y 7 290 287 309 C2' DG Y 8 310 307 331 C2' DT Y 9 332 329 351 C2' DA Y 10 352 349 372 C2' DA Y 11 373 370 393 C2' DG Y 12 394 391 415 C2' DC Y 13 416 413 434 C2' DA Y 14 435 432 455 C2' DG Y 15 456 453 477 C2' DT Y 16 478 475 497 C2' DC Y 17 498 495 5209 C2' TTP A3204 5210 5207 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG X 1 OK 3 6 7 27 C3' DA X 2 OK 25 28 29 48 C3' DC X 3 OK 46 49 50 67 C3' DT X 4 OK 65 68 69 87 C3' DG X 5 OK 85 88 89 109 C3' DC X 6 OK 107 110 111 128 C3' DT X 7 OK 126 129 130 148 C3' DT X 8 OK 146 149 150 168 C3' DA X 9 OK 166 169 170 189 C3' DC X 10 OK 187 190 191 208 C3' 2DA X 11 206 209 226 C3' DA Y 4 OK 224 227 228 247 C3' DC Y 5 OK 245 248 249 266 C3' DA Y 6 OK 264 267 268 287 C3' DT Y 7 OK 285 288 289 307 C3' DG Y 8 OK 305 308 309 329 C3' DT Y 9 OK 327 330 331 349 C3' DA Y 10 OK 347 350 351 370 C3' DA Y 11 OK 368 371 372 391 C3' DG Y 12 OK 389 392 393 413 C3' DC Y 13 OK 411 414 415 432 C3' DA Y 14 OK 430 433 434 453 C3' DG Y 15 OK 451 454 455 475 C3' DT Y 16 OK 473 476 477 495 C3' DC Y 17 OK 493 496 497 5207 C3' TTP A3204 OK 5205 5208 5209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG X 1 OK 5 2 4 25 C4' DA X 2 OK 27 24 26 46 C4' DC X 3 OK 48 45 47 65 C4' DT X 4 OK 67 64 66 85 C4' DG X 5 OK 87 84 86 107 C4' DC X 6 OK 109 106 108 126 C4' DT X 7 OK 128 125 127 146 C4' DT X 8 OK 148 145 147 166 C4' DA X 9 OK 168 165 167 187 C4' DC X 10 OK 189 186 188 206 C4' 2DA X 11 OK 208 205 207 224 C4' DA Y 4 OK 226 223 225 245 C4' DC Y 5 OK 247 244 246 264 C4' DA Y 6 OK 266 263 265 285 C4' DT Y 7 OK 287 284 286 305 C4' DG Y 8 OK 307 304 306 327 C4' DT Y 9 OK 329 326 328 347 C4' DA Y 10 OK 349 346 348 368 C4' DA Y 11 OK 370 367 369 389 C4' DG Y 12 OK 391 388 390 411 C4' DC Y 13 OK 413 410 412 430 C4' DA Y 14 OK 432 429 431 451 C4' DG Y 15 OK 453 450 452 473 C4' DT Y 16 OK 475 472 474 493 C4' DC Y 17 OK 495 492 494 5205 C4' TTP A3204 OK 5207 5204 5206 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG X 1 1 3 24 C5' DA X 2 23 25 45 C5' DC X 3 44 46 64 C5' DT X 4 63 65 84 C5' DG X 5 83 85 106 C5' DC X 6 105 107 125 C5' DT X 7 124 126 145 C5' DT X 8 144 146 165 C5' DA X 9 164 166 186 C5' DC X 10 185 187 205 C5' 2DA X 11 204 206 223 C5' DA Y 4 222 224 244 C5' DC Y 5 243 245 263 C5' DA Y 6 262 264 284 C5' DT Y 7 283 285 304 C5' DG Y 8 303 305 326 C5' DT Y 9 325 327 346 C5' DA Y 10 345 347 367 C5' DA Y 11 366 368 388 C5' DG Y 12 387 389 410 C5' DC Y 13 409 411 429 C5' DA Y 14 428 430 450 C5' DG Y 15 449 451 472 C5' DT Y 16 471 473 492 C5' DC Y 17 491 493 5204 C5' TTP A3204 5203 5205 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DA X 2 distorted distorted 6 21 22 23 41 P DC X 3 distorted distorted 28 42 43 44 60 P DT X 4 distorted distorted 49 61 62 63 80 P DG X 5 distorted distorted 68 81 82 83 102 P DC X 6 distorted distorted 88 103 104 105 121 P DT X 7 distorted distorted 110 122 123 124 141 P DT X 8 distorted distorted 129 142 143 144 161 P DA X 9 distorted distorted 149 162 163 164 182 P DC X 10 distorted distorted 169 183 184 185 201 P 2DA X 11 distorted distorted 190 202 203 204 240 P DC Y 5 distorted distorted 227 241 242 243 259 P DA Y 6 distorted distorted 248 260 261 262 280 P DT Y 7 distorted distorted 267 281 282 283 300 P DG Y 8 distorted distorted 288 301 302 303 322 P DT Y 9 distorted distorted 308 323 324 325 342 P DA Y 10 distorted distorted 330 343 344 345 363 P DA Y 11 distorted distorted 350 364 365 366 384 P DG Y 12 distorted distorted 371 385 386 387 406 P DC Y 13 distorted distorted 392 407 408 409 425 P DA Y 14 distorted distorted 414 426 427 428 446 P DG Y 15 distorted distorted 433 447 448 449 468 P DT Y 16 distorted distorted 454 469 470 471 488 P DC Y 17 distorted distorted 476 489 490 491 ---------------------------------------------------------------------------------