Identification of C-H...N/O H-honds using 3DNA

Recently, I came across an interesting article by Kiliszek et al., titled "Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases". In addition to its biological implications, this paper uses 3DNA to deal with non-canonical-base-pair-containing helical structures in a sensible way:

The helical parameters were calculated using 3DNA (29). Sequence-independent measures were used, based on vectors connecting the C1' atoms of the paired residues, to avoid computational artefacts arising from non-canonical base pairing.

Another significant point, which is the focus of this post, is the observation that "All the adenosines are in the anti-conformation and the only interaction within each A-A pair is a single C2-H2...N1 hydrogen bond." (Figure below) Given the 0.95 Å ultrahigh resolution of structure 3nj6/na0608, it is likely that this type of A-A is real.


The find_pair program in the currently distributed versions of 3DNA (v2.0 and before), however, does not identify this A-A pair (thus the corresponding NDB list of "Base Pair Step Parameters" is incomplete) for the following two reasons:

1. No H-bond exists between N/O base atoms – currently a requirement for a base-pair.
2. By default, only N/O atoms are used in defining H-bonds (see tag hb_atoms in file "misc_3dna.par"). Nevertheless, by adding C as a possible atom in forming H-bond, and manually editing find_pair generated input file to analyze, 3DNA structural parameters can be calculated as usual.
   

I have updated find_pair in 3DNA to identify such C-H...N/O H-bond automatically (see below for entry 3nj6). Upon further refinements and validations, future releases of 3DNA will have this functionality available.

    1   95  #    1 | ...1>A:...1_:[..G]G-----C[..C]:..10_:A<...2
    2   94  #    2 | ...1>A:...2_:[..G]G-----C[..C]:...9_:A<...2
    3   93  #    3 | ...1>A:...3_:[..C]C-----G[..G]:...8_:A<...2
    4   92  #    4 | ...1>A:...4_:[..A]A-**--A[..A]:...7_:A<...2
    5   91  #    5 | ...1>A:...5_:[..G]G-----C[..C]:...6_:A<...2
    6   90  #    6 | ...1>A:...6_:[..C]C-----G[..G]:...5_:A<...2
    7   89  #    7 | ...1>A:...7_:[..A]A-**--A[..A]:...4_:A<...2
    8   88  #    8 | ...1>A:...8_:[..G]G-----C[..C]:...3_:A<...2
    9   87  #    9 | ...1>A:...9_:[..C]C-----G[..G]:...2_:A<...2
   10   86  #   10 | ...1>A:..10_:[..C]C-----G[..G]:...1_:A<...2
##### Criteria: 4.00  0.00  15.00  2.50  65.00  4.50  7.50   [ O N C]
##### 2 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (10): 1 - 10