ID code: '2X7N' 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' --------------------------------------------------------------------------------- 12 C1' A A2684 beta 7 13 10 34 C1' C A2685 beta 29 35 32 54 C1' C A2686 beta 49 55 52 74 C1' G A2687 beta 69 75 72 97 C1' U A2688 beta 92 98 95 117 C1' A A2689 beta 112 118 115 139 C1' U A2690 beta 134 140 137 159 C1' A A2691 beta 154 160 157 181 C1' G A2692 alpha 176 182 179 204 C1' U A2693 beta 199 205 202 224 C1' A A2694 beta 219 225 222 246 C1' C A2695 beta 241 247 244 266 C1' G A2696 beta 261 267 264 289 C1' A A2697 beta 284 290 287 311 C1' G A2698 beta 306 312 309 334 C1' A A2699 beta 329 335 332 356 C1' G A2700 beta 351 357 354 379 C1' G A2701 beta 374 380 377 402 C1' A A2702 beta 397 403 400 424 C1' A A2703 beta 419 425 422 446 C1' C A2704 beta 441 447 444 466 C1' U A2705 beta 461 467 464 486 C1' A A2706 beta 481 487 484 508 C1' C A2707 beta 503 509 506 528 C1' G A2708 beta 523 529 526 551 C1' G A2709 beta 546 552 549 574 C1' U A2710 beta 569 575 572 594 C1' U A2711 beta 589 595 592 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A A2684 OK 12 8 11 32 C2' C A2685 OK 34 30 33 52 C2' C A2686 OK 54 50 53 72 C2' G A2687 OK 74 70 73 95 C2' U A2688 OK 97 93 96 115 C2' A A2689 OK 117 113 116 137 C2' U A2690 OK 139 135 138 157 C2' A A2691 OK 159 155 158 179 C2' G A2692 OK 181 177 180 202 C2' U A2693 OK 204 200 203 222 C2' A A2694 OK 224 220 223 244 C2' C A2695 OK 246 242 245 264 C2' G A2696 OK 266 262 265 287 C2' A A2697 OK 289 285 288 309 C2' G A2698 OK 311 307 310 332 C2' A A2699 OK 334 330 333 354 C2' G A2700 OK 356 352 355 377 C2' G A2701 OK 379 375 378 400 C2' A A2702 OK 402 398 401 422 C2' A A2703 OK 424 420 423 444 C2' C A2704 OK 446 442 445 464 C2' U A2705 OK 466 462 465 484 C2' A A2706 OK 486 482 485 506 C2' C A2707 OK 508 504 507 526 C2' G A2708 OK 528 524 527 549 C2' G A2709 OK 551 547 550 572 C2' U A2710 OK 574 570 573 592 C2' U A2711 OK 594 590 593 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A A2684 OK 6 9 10 30 C3' C A2685 OK 28 31 32 50 C3' C A2686 OK 48 51 52 70 C3' G A2687 OK 68 71 72 93 C3' U A2688 OK 91 94 95 113 C3' A A2689 OK 111 114 115 135 C3' U A2690 OK 133 136 137 155 C3' A A2691 OK 153 156 157 177 C3' G A2692 OK 175 178 179 200 C3' U A2693 OK 198 201 202 220 C3' A A2694 OK 218 221 222 242 C3' C A2695 OK 240 243 244 262 C3' G A2696 OK 260 263 264 285 C3' A A2697 OK 283 286 287 307 C3' G A2698 OK 305 308 309 330 C3' A A2699 OK 328 331 332 352 C3' G A2700 OK 350 353 354 375 C3' G A2701 OK 373 376 377 398 C3' A A2702 OK 396 399 400 420 C3' A A2703 OK 418 421 422 442 C3' C A2704 OK 440 443 444 462 C3' U A2705 OK 460 463 464 482 C3' A A2706 OK 480 483 484 504 C3' C A2707 OK 502 505 506 524 C3' G A2708 OK 522 525 526 547 C3' G A2709 OK 545 548 549 570 C3' U A2710 OK 568 571 572 590 C3' U A2711 OK 588 591 592 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A A2684 OK 8 5 7 28 C4' C A2685 OK 30 27 29 48 C4' C A2686 OK 50 47 49 68 C4' G A2687 OK 70 67 69 91 C4' U A2688 OK 93 90 92 111 C4' A A2689 OK 113 110 112 133 C4' U A2690 OK 135 132 134 153 C4' A A2691 OK 155 152 154 175 C4' G A2692 OK 177 174 176 198 C4' U A2693 OK 200 197 199 218 C4' A A2694 OK 220 217 219 240 C4' C A2695 OK 242 239 241 260 C4' G A2696 OK 262 259 261 283 C4' A A2697 OK 285 282 284 305 C4' G A2698 OK 307 304 306 328 C4' A A2699 OK 330 327 329 350 C4' G A2700 OK 352 349 351 373 C4' G A2701 OK 375 372 374 396 C4' A A2702 OK 398 395 397 418 C4' A A2703 OK 420 417 419 440 C4' C A2704 OK 442 439 441 460 C4' U A2705 OK 462 459 461 480 C4' A A2706 OK 482 479 481 502 C4' C A2707 OK 504 501 503 522 C4' G A2708 OK 524 521 523 545 C4' G A2709 OK 547 544 546 568 C4' U A2710 OK 570 567 569 588 C4' U A2711 OK 590 587 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A A2684 4 6 27 C5' C A2685 26 28 47 C5' C A2686 46 48 67 C5' G A2687 66 68 90 C5' U A2688 89 91 110 C5' A A2689 109 111 132 C5' U A2690 131 133 152 C5' A A2691 151 153 174 C5' G A2692 173 175 197 C5' U A2693 196 198 217 C5' A A2694 216 218 239 C5' C A2695 238 240 259 C5' G A2696 258 260 282 C5' A A2697 281 283 304 C5' G A2698 303 305 327 C5' A A2699 326 328 349 C5' G A2700 348 350 372 C5' G A2701 371 373 395 C5' A A2702 394 396 417 C5' A A2703 416 418 439 C5' C A2704 438 440 459 C5' U A2705 458 460 479 C5' A A2706 478 480 501 C5' C A2707 500 502 521 C5' G A2708 520 522 544 C5' G A2709 543 545 567 C5' U A2710 566 568 587 C5' U A2711 586 588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A A2684 distorted distorted 2 3 4 23 P C A2685 distorted distorted 9 24 25 26 43 P C A2686 distorted distorted 31 44 45 46 63 P G A2687 distorted distorted 51 64 65 66 86 P U A2688 distorted distorted 71 87 88 89 106 P A A2689 distorted distorted 94 107 108 109 128 P U A2690 distorted distorted 114 129 130 131 148 P A A2691 distorted distorted 136 149 150 151 170 P G A2692 distorted distorted 156 171 172 173 193 P U A2693 distorted distorted 178 194 195 196 213 P A A2694 distorted distorted 201 214 215 216 235 P C A2695 distorted distorted 221 236 237 238 255 P G A2696 distorted distorted 243 256 257 258 278 P A A2697 distorted distorted 263 279 280 281 300 P G A2698 distorted distorted 286 301 302 303 323 P A A2699 distorted distorted 308 324 325 326 345 P G A2700 distorted distorted 331 346 347 348 368 P G A2701 distorted distorted 353 369 370 371 391 P A A2702 distorted distorted 376 392 393 394 413 P A A2703 distorted distorted 399 414 415 416 435 P C A2704 distorted distorted 421 436 437 438 455 P U A2705 distorted distorted 443 456 457 458 475 P A A2706 distorted distorted 463 476 477 478 497 P C A2707 distorted distorted 483 498 499 500 517 P G A2708 distorted distorted 505 518 519 520 540 P G A2709 distorted distorted 525 541 542 543 563 P U A2710 distorted distorted 548 564 565 566 583 P U A2711 distorted distorted 571 584 585 586 ---------------------------------------------------------------------------------