ID code: '5KIF' 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' DA A 1 alpha beta 4 25 9 7 41 C1' DT A 2 alpha beta 37 57 42 40 73 C1' DC A 3 alpha beta 69 88 74 72 103 C1' DC A 4 alpha beta 99 118 104 102 134 C1' G A 5 alpha beta 129 152 135 132 167 C1' DG A 6 alpha beta 163 185 168 166 200 C1' DT A 7 alpha beta 196 216 201 199 232 C1' DA A 8 alpha beta 228 249 233 231 264 C1' DG A 9 alpha beta 260 283 265 263 296 C1' DC B 10 alpha beta 292 311 297 295 327 C1' DT B 11 alpha beta 323 343 328 326 359 C1' DA B 12 alpha beta 355 376 360 358 391 C1' DC B 13 alpha beta 387 406 392 390 421 C1' DC B 14 alpha beta 417 436 422 420 451 C1' DG B 15 alpha beta 447 469 452 450 484 C1' DG B 16 alpha beta 480 502 485 483 517 C1' DA B 17 alpha beta 513 534 518 516 549 C1' DT B 18 alpha beta 545 566 550 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DA A 1 OK OK 8 5 23 24 40 C2' DT A 2 OK OK 41 38 55 56 72 C2' DC A 3 OK OK 73 70 86 87 102 C2' DC A 4 OK OK 103 100 116 117 132 C2' G A 5 OK OK 134 130 150 133 166 C2' DG A 6 OK OK 167 164 183 184 199 C2' DT A 7 OK OK 200 197 214 215 231 C2' DA A 8 OK OK 232 229 247 248 263 C2' DG A 9 OK OK 264 261 281 282 295 C2' DC B 10 OK OK 296 293 309 310 326 C2' DT B 11 OK OK 327 324 341 342 358 C2' DA B 12 OK OK 359 356 374 375 390 C2' DC B 13 OK OK 391 388 404 405 420 C2' DC B 14 OK OK 421 418 434 435 450 C2' DG B 15 OK OK 451 448 467 468 483 C2' DG B 16 OK OK 484 481 500 501 516 C2' DA B 17 OK OK 517 514 532 533 548 C2' DT B 18 OK OK 549 546 564 565 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DA A 1 OK OK 3 22 6 7 38 C3' DT A 2 OK OK 36 54 39 40 70 C3' DC A 3 OK OK 68 85 71 72 100 C3' DC A 4 OK OK 98 115 101 102 130 C3' G A 5 OK OK 128 149 131 132 164 C3' DG A 6 OK OK 162 182 165 166 197 C3' DT A 7 OK OK 195 213 198 199 229 C3' DA A 8 OK OK 227 246 230 231 261 C3' DG A 9 OK OK 259 279 262 263 293 C3' DC B 10 OK OK 291 308 294 295 324 C3' DT B 11 OK OK 322 340 325 326 356 C3' DA B 12 OK OK 354 373 357 358 388 C3' DC B 13 OK OK 386 403 389 390 418 C3' DC B 14 OK OK 416 433 419 420 448 C3' DG B 15 OK OK 446 466 449 450 481 C3' DG B 16 OK OK 479 499 482 483 514 C3' DA B 17 OK OK 512 531 515 516 546 C3' DT B 18 OK OK 544 562 547 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DA A 1 OK OK 5 21 2 4 36 C4' DT A 2 OK OK 38 53 35 37 68 C4' DC A 3 OK OK 70 84 67 69 98 C4' DC A 4 OK OK 100 114 97 99 128 C4' G A 5 OK OK 130 148 127 129 162 C4' DG A 6 OK OK 164 181 161 163 195 C4' DT A 7 OK OK 197 212 194 196 227 C4' DA A 8 OK OK 229 245 226 228 259 C4' DG A 9 OK OK 261 278 258 260 291 C4' DC B 10 OK OK 293 307 290 292 322 C4' DT B 11 OK OK 324 339 321 323 354 C4' DA B 12 OK OK 356 372 353 355 386 C4' DC B 13 OK OK 388 402 385 387 416 C4' DC B 14 OK OK 418 432 415 417 446 C4' DG B 15 OK OK 448 465 445 447 479 C4' DG B 16 OK OK 481 498 478 480 512 C4' DA B 17 OK OK 514 530 511 513 544 C4' DT B 18 OK OK 546 561 543 545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DA A 1 OK OK 1 19 20 3 35 C5' DT A 2 OK OK 34 51 52 36 67 C5' DC A 3 OK OK 66 82 83 68 97 C5' DC A 4 OK OK 96 112 113 98 127 C5' G A 5 OK OK 126 146 147 128 161 C5' DG A 6 OK OK 160 179 180 162 194 C5' DT A 7 OK OK 193 210 211 195 226 C5' DA A 8 OK OK 225 243 244 227 258 C5' DG A 9 OK OK 257 276 277 259 290 C5' DC B 10 OK OK 289 305 306 291 321 C5' DT B 11 OK OK 320 337 338 322 353 C5' DA B 12 OK OK 352 370 371 354 385 C5' DC B 13 OK OK 384 400 401 386 415 C5' DC B 14 OK OK 414 430 431 416 445 C5' DG B 15 OK OK 444 463 464 446 478 C5' DG B 16 OK OK 477 496 497 479 511 C5' DA B 17 OK OK 510 528 529 512 543 C5' DT B 18 OK OK 542 559 560 544 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 31 P DT A 2 distorted distorted 6 32 33 34 63 P DC A 3 distorted distorted 39 64 65 66 93 P DC A 4 distorted distorted 71 94 95 96 123 P G A 5 distorted distorted 101 124 125 126 157 P DG A 6 distorted distorted 131 158 159 160 190 P DT A 7 distorted distorted 165 191 192 193 222 P DA A 8 distorted distorted 198 223 224 225 254 P DG A 9 distorted distorted 230 255 256 257 317 P DT B 11 distorted distorted 294 318 319 320 349 P DA B 12 distorted distorted 325 350 351 352 381 P DC B 13 distorted distorted 357 382 383 384 411 P DC B 14 distorted distorted 389 412 413 414 441 P DG B 15 distorted distorted 419 442 443 444 474 P DG B 16 distorted distorted 449 475 476 477 507 P DA B 17 distorted distorted 482 508 509 510 539 P DT B 18 distorted distorted 515 540 541 542 ---------------------------------------------------------------------------------