ID code: '4NI9' 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 B 1 beta 4 9 7 30 C1' DG B 2 beta 26 31 29 50 C1' OMC B 3 beta 56 42 51 73 C1' DA B 4 beta 69 74 72 94 C1' DG B 5 beta 90 95 93 118 C1' OMG B 6 beta 112 119 115 139 C1' DUZ B 7 beta 154 131 140 168 C1' DUZ B 8 beta 183 160 169 197 C1' UPE B 9 beta 213 189 198 228 C1' DG B 10 beta 224 229 227 250 C1' DG B 11 beta 246 251 249 270 C1' 2JU B 12 beta 271 272 269 305 C1' DA B 13 beta 301 306 304 325 C1' DUZ B 14 beta 340 317 326 354 C1' DUZ B 15 beta 369 346 355 384 C1' A2M B 16 beta 379 386 382 407 C1' DA B 17 beta 403 408 406 428 C1' DC B 18 beta 424 429 427 447 C1' A2M B 19 beta 442 449 445 468 C1' OMC B 20 beta 474 460 469 491 C1' DG B 21 beta 487 492 490 512 C1' DUZ B 22 beta 527 504 513 541 C1' DUZ B 23 beta 556 533 542 571 C1' DA B 24 beta 567 572 570 592 C1' DA B 25 beta 588 593 591 613 C1' DG B 26 beta 609 614 612 634 C1' DUZ B 27 beta 649 626 635 662 C1' OMC B 28 beta 668 654 663 685 C1' DG B 29 beta 681 686 684 706 C1' DUZ B 30 beta 721 698 707 736 C1' DG B 31 beta 732 737 735 758 C1' DG B 32 beta 754 759 757 3011 C1' DG D 1 beta 3007 3012 3010 3033 C1' DG D 2 beta 3029 3034 3032 3053 C1' OMC D 3 beta 3059 3045 3054 3076 C1' DA D 4 beta 3072 3077 3075 3097 C1' DG D 5 beta 3093 3098 3096 3121 C1' OMG D 6 beta 3115 3122 3118 3142 C1' DUZ D 7 beta 3157 3134 3143 3171 C1' DUZ D 8 beta 3186 3163 3172 3200 C1' UPE D 9 beta 3216 3192 3201 3231 C1' DG D 10 beta 3227 3232 3230 3253 C1' DG D 11 beta 3249 3254 3252 3273 C1' 2JU D 12 beta 3274 3275 3272 3308 C1' DA D 13 beta 3304 3309 3307 3328 C1' DUZ D 14 beta 3343 3320 3329 3357 C1' DUZ D 15 beta 3372 3349 3358 3387 C1' A2M D 16 beta 3382 3389 3385 3410 C1' DA D 17 beta 3406 3411 3409 3431 C1' DC D 18 beta 3427 3432 3430 3450 C1' A2M D 19 beta 3445 3452 3448 3471 C1' OMC D 20 beta 3477 3463 3472 3494 C1' DG D 21 beta 3490 3495 3493 3515 C1' DUZ D 22 beta 3530 3507 3516 3544 C1' DUZ D 23 beta 3559 3536 3545 3574 C1' DA D 24 beta 3570 3575 3573 3595 C1' DA D 25 beta 3591 3596 3594 3616 C1' DG D 26 beta 3612 3617 3615 3637 C1' DUZ D 27 beta 3652 3629 3638 3665 C1' OMC D 28 beta 3671 3657 3666 3688 C1' DG D 29 beta 3684 3689 3687 3709 C1' DUZ D 30 beta 3724 3701 3710 3739 C1' DG D 31 beta 3735 3740 3738 3761 C1' DG D 32 beta 3757 3762 3760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG B 1 8 5 29 C2' DG B 2 30 27 51 C2' OMC B 3 OK 50 54 52 72 C2' DA B 4 73 70 93 C2' DG B 5 94 91 115 C2' OMG B 6 OK 118 113 116 140 C2' DUZ B 7 139 150 169 C2' DUZ B 8 168 179 198 C2' UPE B 9 197 208 227 C2' DG B 10 228 225 249 C2' DG B 11 250 247 269 C2' 2JU B 12 270 268 304 C2' DA B 13 305 302 326 C2' DUZ B 14 325 336 355 C2' DUZ B 15 354 365 382 C2' A2M B 16 OK 384 380 383 406 C2' DA B 17 407 404 427 C2' DC B 18 428 425 445 C2' A2M B 19 OK 447 443 446 469 C2' OMC B 20 OK 468 472 470 490 C2' DG B 21 491 488 513 C2' DUZ B 22 512 523 542 C2' DUZ B 23 541 552 570 C2' DA B 24 571 568 591 C2' DA B 25 592 589 612 C2' DG B 26 613 610 635 C2' DUZ B 27 634 645 663 C2' OMC B 28 OK 662 666 664 684 C2' DG B 29 685 682 707 C2' DUZ B 30 706 717 735 C2' DG B 31 736 733 757 C2' DG B 32 758 755 3010 C2' DG D 1 3011 3008 3032 C2' DG D 2 3033 3030 3054 C2' OMC D 3 OK 3053 3057 3055 3075 C2' DA D 4 3076 3073 3096 C2' DG D 5 3097 3094 3118 C2' OMG D 6 OK 3121 3116 3119 3143 C2' DUZ D 7 3142 3153 3172 C2' DUZ D 8 3171 3182 3201 C2' UPE D 9 3200 3211 3230 C2' DG D 10 3231 3228 3252 C2' DG D 11 3253 3250 3272 C2' 2JU D 12 3273 3271 3307 C2' DA D 13 3308 3305 3329 C2' DUZ D 14 3328 3339 3358 C2' DUZ D 15 3357 3368 3385 C2' A2M D 16 OK 3387 3383 3386 3409 C2' DA D 17 3410 3407 3430 C2' DC D 18 3431 3428 3448 C2' A2M D 19 OK 3450 3446 3449 3472 C2' OMC D 20 OK 3471 3475 3473 3493 C2' DG D 21 3494 3491 3516 C2' DUZ D 22 3515 3526 3545 C2' DUZ D 23 3544 3555 3573 C2' DA D 24 3574 3571 3594 C2' DA D 25 3595 3592 3615 C2' DG D 26 3616 3613 3638 C2' DUZ D 27 3637 3648 3666 C2' OMC D 28 OK 3665 3669 3667 3687 C2' DG D 29 3688 3685 3710 C2' DUZ D 30 3709 3720 3738 C2' DG D 31 3739 3736 3760 C2' DG D 32 3761 3758 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG B 1 OK 3 6 7 27 C3' DG B 2 OK 25 28 29 54 C3' OMC B 3 OK 55 57 51 70 C3' DA B 4 OK 68 71 72 91 C3' DG B 5 OK 89 92 93 113 C3' OMG B 6 OK 111 114 115 150 C3' DUZ B 7 OK 153 151 140 179 C3' DUZ B 8 OK 182 180 169 208 C3' UPE B 9 OK 212 209 198 225 C3' DG B 10 OK 223 226 227 247 C3' DG B 11 OK 245 248 249 268 C3' 2JU B 12 OK 267 294 269 302 C3' DA B 13 OK 300 303 304 336 C3' DUZ B 14 OK 339 337 326 365 C3' DUZ B 15 OK 368 366 355 380 C3' A2M B 16 OK 378 381 382 404 C3' DA B 17 OK 402 405 406 425 C3' DC B 18 OK 423 426 427 443 C3' A2M B 19 OK 441 444 445 472 C3' OMC B 20 OK 473 475 469 488 C3' DG B 21 OK 486 489 490 523 C3' DUZ B 22 OK 526 524 513 552 C3' DUZ B 23 OK 555 553 542 568 C3' DA B 24 OK 566 569 570 589 C3' DA B 25 OK 587 590 591 610 C3' DG B 26 OK 608 611 612 645 C3' DUZ B 27 OK 648 646 635 666 C3' OMC B 28 OK 667 669 663 682 C3' DG B 29 OK 680 683 684 717 C3' DUZ B 30 OK 720 718 707 733 C3' DG B 31 OK 731 734 735 755 C3' DG B 32 OK 753 756 757 3008 C3' DG D 1 OK 3006 3009 3010 3030 C3' DG D 2 OK 3028 3031 3032 3057 C3' OMC D 3 OK 3058 3060 3054 3073 C3' DA D 4 OK 3071 3074 3075 3094 C3' DG D 5 OK 3092 3095 3096 3116 C3' OMG D 6 OK 3114 3117 3118 3153 C3' DUZ D 7 OK 3156 3154 3143 3182 C3' DUZ D 8 OK 3185 3183 3172 3211 C3' UPE D 9 OK 3215 3212 3201 3228 C3' DG D 10 OK 3226 3229 3230 3250 C3' DG D 11 OK 3248 3251 3252 3271 C3' 2JU D 12 OK 3270 3297 3272 3305 C3' DA D 13 OK 3303 3306 3307 3339 C3' DUZ D 14 OK 3342 3340 3329 3368 C3' DUZ D 15 OK 3371 3369 3358 3383 C3' A2M D 16 OK 3381 3384 3385 3407 C3' DA D 17 OK 3405 3408 3409 3428 C3' DC D 18 OK 3426 3429 3430 3446 C3' A2M D 19 OK 3444 3447 3448 3475 C3' OMC D 20 OK 3476 3478 3472 3491 C3' DG D 21 OK 3489 3492 3493 3526 C3' DUZ D 22 OK 3529 3527 3516 3555 C3' DUZ D 23 OK 3558 3556 3545 3571 C3' DA D 24 OK 3569 3572 3573 3592 C3' DA D 25 OK 3590 3593 3594 3613 C3' DG D 26 OK 3611 3614 3615 3648 C3' DUZ D 27 OK 3651 3649 3638 3669 C3' OMC D 28 OK 3670 3672 3666 3685 C3' DG D 29 OK 3683 3686 3687 3720 C3' DUZ D 30 OK 3723 3721 3710 3736 C3' DG D 31 OK 3734 3737 3738 3758 C3' DG D 32 OK 3756 3759 3760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG B 1 OK 5 2 4 25 C4' DG B 2 OK 27 24 26 55 C4' OMC B 3 OK 54 58 56 68 C4' DA B 4 OK 70 67 69 89 C4' DG B 5 OK 91 88 90 111 C4' OMG B 6 OK 113 110 112 153 C4' DUZ B 7 OK 150 155 154 182 C4' DUZ B 8 OK 179 184 183 212 C4' UPE B 9 OK 208 214 213 223 C4' DG B 10 OK 225 222 224 245 C4' DG B 11 OK 247 244 246 267 C4' 2JU B 12 OK 268 266 271 300 C4' DA B 13 OK 302 299 301 339 C4' DUZ B 14 OK 336 341 340 368 C4' DUZ B 15 OK 365 370 369 378 C4' A2M B 16 OK 380 377 379 402 C4' DA B 17 OK 404 401 403 423 C4' DC B 18 OK 425 422 424 441 C4' A2M B 19 OK 443 440 442 473 C4' OMC B 20 OK 472 476 474 486 C4' DG B 21 OK 488 485 487 526 C4' DUZ B 22 OK 523 528 527 555 C4' DUZ B 23 OK 552 557 556 566 C4' DA B 24 OK 568 565 567 587 C4' DA B 25 OK 589 586 588 608 C4' DG B 26 OK 610 607 609 648 C4' DUZ B 27 OK 645 650 649 667 C4' OMC B 28 OK 666 670 668 680 C4' DG B 29 OK 682 679 681 720 C4' DUZ B 30 OK 717 722 721 731 C4' DG B 31 OK 733 730 732 753 C4' DG B 32 OK 755 752 754 3006 C4' DG D 1 OK 3008 3005 3007 3028 C4' DG D 2 OK 3030 3027 3029 3058 C4' OMC D 3 OK 3057 3061 3059 3071 C4' DA D 4 OK 3073 3070 3072 3092 C4' DG D 5 OK 3094 3091 3093 3114 C4' OMG D 6 OK 3116 3113 3115 3156 C4' DUZ D 7 OK 3153 3158 3157 3185 C4' DUZ D 8 OK 3182 3187 3186 3215 C4' UPE D 9 OK 3211 3217 3216 3226 C4' DG D 10 OK 3228 3225 3227 3248 C4' DG D 11 OK 3250 3247 3249 3270 C4' 2JU D 12 OK 3271 3269 3274 3303 C4' DA D 13 OK 3305 3302 3304 3342 C4' DUZ D 14 OK 3339 3344 3343 3371 C4' DUZ D 15 OK 3368 3373 3372 3381 C4' A2M D 16 OK 3383 3380 3382 3405 C4' DA D 17 OK 3407 3404 3406 3426 C4' DC D 18 OK 3428 3425 3427 3444 C4' A2M D 19 OK 3446 3443 3445 3476 C4' OMC D 20 OK 3475 3479 3477 3489 C4' DG D 21 OK 3491 3488 3490 3529 C4' DUZ D 22 OK 3526 3531 3530 3558 C4' DUZ D 23 OK 3555 3560 3559 3569 C4' DA D 24 OK 3571 3568 3570 3590 C4' DA D 25 OK 3592 3589 3591 3611 C4' DG D 26 OK 3613 3610 3612 3651 C4' DUZ D 27 OK 3648 3653 3652 3670 C4' OMC D 28 OK 3669 3673 3671 3683 C4' DG D 29 OK 3685 3682 3684 3723 C4' DUZ D 30 OK 3720 3725 3724 3734 C4' DG D 31 OK 3736 3733 3735 3756 C4' DG D 32 OK 3758 3755 3757 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG B 1 1 3 24 C5' DG B 2 23 25 58 C5' OMC B 3 59 55 67 C5' DA B 4 66 68 88 C5' DG B 5 87 89 110 C5' OMG B 6 109 111 155 C5' DUZ B 7 156 153 184 C5' DUZ B 8 185 182 214 C5' UPE B 9 215 212 222 C5' DG B 10 221 223 244 C5' DG B 11 243 245 266 C5' 2JU B 12 265 267 299 C5' DA B 13 298 300 341 C5' DUZ B 14 342 339 370 C5' DUZ B 15 371 368 377 C5' A2M B 16 376 378 401 C5' DA B 17 400 402 422 C5' DC B 18 421 423 440 C5' A2M B 19 439 441 476 C5' OMC B 20 477 473 485 C5' DG B 21 484 486 528 C5' DUZ B 22 529 526 557 C5' DUZ B 23 558 555 565 C5' DA B 24 564 566 586 C5' DA B 25 585 587 607 C5' DG B 26 606 608 650 C5' DUZ B 27 651 648 670 C5' OMC B 28 671 667 679 C5' DG B 29 678 680 722 C5' DUZ B 30 723 720 730 C5' DG B 31 729 731 752 C5' DG B 32 751 753 3005 C5' DG D 1 3004 3006 3027 C5' DG D 2 3026 3028 3061 C5' OMC D 3 3062 3058 3070 C5' DA D 4 3069 3071 3091 C5' DG D 5 3090 3092 3113 C5' OMG D 6 3112 3114 3158 C5' DUZ D 7 3159 3156 3187 C5' DUZ D 8 3188 3185 3217 C5' UPE D 9 3218 3215 3225 C5' DG D 10 3224 3226 3247 C5' DG D 11 3246 3248 3269 C5' 2JU D 12 3268 3270 3302 C5' DA D 13 3301 3303 3344 C5' DUZ D 14 3345 3342 3373 C5' DUZ D 15 3374 3371 3380 C5' A2M D 16 3379 3381 3404 C5' DA D 17 3403 3405 3425 C5' DC D 18 3424 3426 3443 C5' A2M D 19 3442 3444 3479 C5' OMC D 20 3480 3476 3488 C5' DG D 21 3487 3489 3531 C5' DUZ D 22 3532 3529 3560 C5' DUZ D 23 3561 3558 3568 C5' DA D 24 3567 3569 3589 C5' DA D 25 3588 3590 3610 C5' DG D 26 3609 3611 3653 C5' DUZ D 27 3654 3651 3673 C5' OMC D 28 3674 3670 3682 C5' DG D 29 3681 3683 3725 C5' DUZ D 30 3726 3723 3733 C5' DG D 31 3732 3734 3755 C5' DG D 32 3754 3756 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DG B 2 distorted distorted 6 21 22 23 60 P OMC B 3 OK OK 28 61 62 59 63 P DA B 4 distorted distorted 57 64 65 66 84 P DG B 5 distorted distorted 71 85 86 87 106 P OMG B 6 OK OK 92 107 108 109 130 P DUZ B 7 distorted distorted 114 157 158 156 159 P DUZ B 8 OK OK 151 186 187 185 188 P UPE B 9 distorted distorted 180 216 217 215 218 P DG B 10 distorted distorted 209 219 220 221 240 P DG B 11 distorted distorted 226 241 242 243 262 P 2JU B 12 distorted distorted 248 263 264 265 295 P DA B 13 distorted distorted 294 296 297 298 316 P DUZ B 14 distorted distorted 303 343 344 342 345 P DUZ B 15 distorted distorted 337 372 373 371 374 P A2M B 16 distorted distorted 366 375 396 376 397 P DA B 17 distorted distorted 381 398 399 400 418 P DC B 18 distorted distorted 405 419 420 421 437 P A2M B 19 OK OK 426 438 459 439 478 P OMC B 20 distorted distorted 444 479 480 477 481 P DG B 21 distorted distorted 475 482 483 484 503 P DUZ B 22 OK OK 489 530 531 529 532 P DUZ B 23 OK OK 524 559 560 558 561 P DA B 24 distorted distorted 553 562 563 564 582 P DA B 25 distorted distorted 569 583 584 585 603 P DG B 26 distorted distorted 590 604 605 606 625 P DUZ B 27 distorted distorted 611 652 653 651 672 P OMC B 28 distorted distorted 646 673 674 671 675 P DG B 29 distorted distorted 669 676 677 678 697 P DUZ B 30 distorted distorted 683 724 725 723 726 P DG B 31 distorted distorted 718 727 728 729 748 P DG B 32 distorted distorted 734 749 750 751 3023 P DG D 2 distorted distorted 3009 3024 3025 3026 3063 P OMC D 3 distorted distorted 3031 3064 3065 3062 3066 P DA D 4 distorted distorted 3060 3067 3068 3069 3087 P DG D 5 distorted distorted 3074 3088 3089 3090 3109 P OMG D 6 distorted distorted 3095 3110 3111 3112 3133 P DUZ D 7 distorted distorted 3117 3160 3161 3159 3162 P DUZ D 8 distorted distorted 3154 3189 3190 3188 3191 P UPE D 9 distorted distorted 3183 3219 3220 3218 3221 P DG D 10 distorted distorted 3212 3222 3223 3224 3243 P DG D 11 distorted distorted 3229 3244 3245 3246 3265 P 2JU D 12 distorted distorted 3251 3266 3267 3268 3298 P DA D 13 distorted distorted 3297 3299 3300 3301 3319 P DUZ D 14 OK OK 3306 3346 3347 3345 3348 P DUZ D 15 OK OK 3340 3375 3376 3374 3377 P A2M D 16 OK OK 3369 3378 3399 3379 3400 P DA D 17 distorted distorted 3384 3401 3402 3403 3421 P DC D 18 distorted distorted 3408 3422 3423 3424 3440 P A2M D 19 distorted distorted 3429 3441 3462 3442 3481 P OMC D 20 OK OK 3447 3482 3483 3480 3484 P DG D 21 distorted distorted 3478 3485 3486 3487 3506 P DUZ D 22 distorted distorted 3492 3533 3534 3532 3535 P DUZ D 23 distorted distorted 3527 3562 3563 3561 3564 P DA D 24 distorted distorted 3556 3565 3566 3567 3585 P DA D 25 distorted distorted 3572 3586 3587 3588 3606 P DG D 26 distorted distorted 3593 3607 3608 3609 3628 P DUZ D 27 OK OK 3614 3655 3656 3654 3675 P OMC D 28 OK OK 3649 3676 3677 3674 3678 P DG D 29 distorted distorted 3672 3679 3680 3681 3700 P DUZ D 30 distorted distorted 3686 3727 3728 3726 3729 P DG D 31 distorted distorted 3721 3730 3731 3732 3751 P DG D 32 distorted distorted 3737 3752 3753 3754 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