ID code: '1F2I' 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' A C3001 beta 4 9 7 29 C1' T C3002 beta 25 30 28 49 C1' G C3003 beta 45 50 48 71 C1' G C3004 beta 67 72 70 93 C1' G C3005 beta 89 94 92 115 C1' C C3006 beta 111 116 114 134 C1' G C3007 beta 130 135 133 156 C1' C C3008 beta 152 157 155 175 C1' G C3009 beta 171 176 174 197 C1' C C3010 beta 193 198 196 216 C1' C C3011 beta 212 217 215 235 C1' C C3012 beta 231 236 234 254 C1' A C3013 beta 250 255 253 275 C1' T C3014 beta 271 276 274 293 C1' A D4001 beta 289 294 292 314 C1' T D4002 beta 310 315 313 334 C1' G D4003 beta 330 335 333 356 C1' G D4004 beta 352 357 355 378 C1' G D4005 beta 374 379 377 400 C1' C D4006 beta 396 401 399 419 C1' G D4007 beta 415 420 418 441 C1' C D4008 beta 437 442 440 460 C1' G D4009 beta 456 461 459 482 C1' C D4010 beta 478 483 481 501 C1' C D4011 beta 497 502 500 520 C1' C D4012 beta 516 521 519 539 C1' A D4013 beta 535 540 538 560 C1' T D4014 beta 556 561 559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C3001 8 5 28 C2' T C3002 29 26 48 C2' G C3003 49 46 70 C2' G C3004 71 68 92 C2' G C3005 93 90 114 C2' C C3006 115 112 133 C2' G C3007 134 131 155 C2' C C3008 156 153 174 C2' G C3009 175 172 196 C2' C C3010 197 194 215 C2' C C3011 216 213 234 C2' C C3012 235 232 253 C2' A C3013 254 251 274 C2' T C3014 275 272 292 C2' A D4001 293 290 313 C2' T D4002 314 311 333 C2' G D4003 334 331 355 C2' G D4004 356 353 377 C2' G D4005 378 375 399 C2' C D4006 400 397 418 C2' G D4007 419 416 440 C2' C D4008 441 438 459 C2' G D4009 460 457 481 C2' C D4010 482 479 500 C2' C D4011 501 498 519 C2' C D4012 520 517 538 C2' A D4013 539 536 559 C2' T D4014 560 557 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C3001 OK 3 6 7 26 C3' T C3002 OK 24 27 28 46 C3' G C3003 OK 44 47 48 68 C3' G C3004 OK 66 69 70 90 C3' G C3005 OK 88 91 92 112 C3' C C3006 OK 110 113 114 131 C3' G C3007 OK 129 132 133 153 C3' C C3008 OK 151 154 155 172 C3' G C3009 OK 170 173 174 194 C3' C C3010 OK 192 195 196 213 C3' C C3011 OK 211 214 215 232 C3' C C3012 OK 230 233 234 251 C3' A C3013 OK 249 252 253 272 C3' T C3014 OK 270 273 274 290 C3' A D4001 OK 288 291 292 311 C3' T D4002 OK 309 312 313 331 C3' G D4003 OK 329 332 333 353 C3' G D4004 OK 351 354 355 375 C3' G D4005 OK 373 376 377 397 C3' C D4006 OK 395 398 399 416 C3' G D4007 OK 414 417 418 438 C3' C D4008 OK 436 439 440 457 C3' G D4009 OK 455 458 459 479 C3' C D4010 OK 477 480 481 498 C3' C D4011 OK 496 499 500 517 C3' C D4012 OK 515 518 519 536 C3' A D4013 OK 534 537 538 557 C3' T D4014 OK 555 558 559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C3001 OK 5 2 4 24 C4' T C3002 OK 26 23 25 44 C4' G C3003 OK 46 43 45 66 C4' G C3004 OK 68 65 67 88 C4' G C3005 OK 90 87 89 110 C4' C C3006 OK 112 109 111 129 C4' G C3007 OK 131 128 130 151 C4' C C3008 OK 153 150 152 170 C4' G C3009 OK 172 169 171 192 C4' C C3010 OK 194 191 193 211 C4' C C3011 OK 213 210 212 230 C4' C C3012 OK 232 229 231 249 C4' A C3013 OK 251 248 250 270 C4' T C3014 OK 272 269 271 288 C4' A D4001 OK 290 287 289 309 C4' T D4002 OK 311 308 310 329 C4' G D4003 OK 331 328 330 351 C4' G D4004 OK 353 350 352 373 C4' G D4005 OK 375 372 374 395 C4' C D4006 OK 397 394 396 414 C4' G D4007 OK 416 413 415 436 C4' C D4008 OK 438 435 437 455 C4' G D4009 OK 457 454 456 477 C4' C D4010 OK 479 476 478 496 C4' C D4011 OK 498 495 497 515 C4' C D4012 OK 517 514 516 534 C4' A D4013 OK 536 533 535 555 C4' T D4014 OK 557 554 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C3001 1 3 23 C5' T C3002 22 24 43 C5' G C3003 42 44 65 C5' G C3004 64 66 87 C5' G C3005 86 88 109 C5' C C3006 108 110 128 C5' G C3007 127 129 150 C5' C C3008 149 151 169 C5' G C3009 168 170 191 C5' C C3010 190 192 210 C5' C C3011 209 211 229 C5' C C3012 228 230 248 C5' A C3013 247 249 269 C5' T C3014 268 270 287 C5' A D4001 286 288 308 C5' T D4002 307 309 328 C5' G D4003 327 329 350 C5' G D4004 349 351 372 C5' G D4005 371 373 394 C5' C D4006 393 395 413 C5' G D4007 412 414 435 C5' C D4008 434 436 454 C5' G D4009 453 455 476 C5' C D4010 475 477 495 C5' C D4011 494 496 514 C5' C D4012 513 515 533 C5' A D4013 532 534 554 C5' T D4014 553 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P T C3002 distorted distorted 6 20 21 22 39 P G C3003 distorted distorted 27 40 41 42 61 P G C3004 distorted distorted 47 62 63 64 83 P G C3005 distorted distorted 69 84 85 86 105 P C C3006 distorted distorted 91 106 107 108 124 P G C3007 distorted distorted 113 125 126 127 146 P C C3008 distorted distorted 132 147 148 149 165 P G C3009 distorted distorted 154 166 167 168 187 P C C3010 distorted distorted 173 188 189 190 206 P C C3011 distorted distorted 195 207 208 209 225 P C C3012 distorted distorted 214 226 227 228 244 P A C3013 distorted distorted 233 245 246 247 265 P T C3014 distorted distorted 252 266 267 268 304 P T D4002 distorted distorted 291 305 306 307 324 P G D4003 distorted distorted 312 325 326 327 346 P G D4004 distorted distorted 332 347 348 349 368 P G D4005 distorted distorted 354 369 370 371 390 P C D4006 distorted distorted 376 391 392 393 409 P G D4007 distorted distorted 398 410 411 412 431 P C D4008 distorted distorted 417 432 433 434 450 P G D4009 distorted distorted 439 451 452 453 472 P C D4010 distorted distorted 458 473 474 475 491 P C D4011 distorted distorted 480 492 493 494 510 P C D4012 distorted distorted 499 511 512 513 529 P A D4013 distorted distorted 518 530 531 532 550 P T D4014 distorted distorted 537 551 552 553 ---------------------------------------------------------------------------------