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Retrieve canonical tRNA tertiary contacts

Source: R/identity.R
tertiary_contacts.Rd

Returns the canonical cloverleaf tertiary interactions that stabilize the L-shape and elbow of the tRNA fold: four base triples and five tertiary base pairs. Numbering follows the Sprinzl convention. Modified bases (m7G46, Psi55, m1A58) are encoded as their unmodified equivalents (G, U, A) so callers can compare against in-vitro transcripts directly.

Usage

tertiary_contacts(organism)

Arguments

organism

Character string specifying the organism name (e.g., "Escherichia coli", "Saccharomyces cerevisiae"). Use identity_organisms() to list supported organisms.

Value

A tibble with one row per contact and columns:

  • contact_id: short label (e.g., "U8-A14-A21", "G15-C48")

  • contact_type: "triple" or "pair"

  • domain: "Bacteria" or "Eukarya"

  • pos1, pos2, pos3: Sprinzl positions (pos3 = NA for pairs)

  • nuc1, nuc2, nuc3: canonical bases (nuc3 = NA for pairs)

  • interaction: geometry label (e.g., "reverse-Hoogsteen", "trans-WC", "Levitt")

  • universal: TRUE for contacts conserved across all domains

  • description: human-readable description

Details

Sources: Westhof & Auffinger (2012) and Giege & Eriani (2023). These tertiary contacts are not aaRS identity elements per se but constrain the tRNA fold and may indirectly affect aminoacylation specificity. Use identity_elements() for aaRS recognition determinants.

References

Westhof E, Auffinger P (2012). "tRNA structure." Encyclopedia of Life Sciences. John Wiley & Sons.

Giege R, Eriani G (2023). "The tRNA identity landscape for aminoacylation and beyond." Nucleic Acids Research, 51(4), 1528–1570. doi:10.1093/nar/gkad007

Examples

tertiary_contacts("Escherichia coli")
#> # A tibble: 9 × 12
#>   contact_id contact_type domain  pos1  pos2  pos3 nuc1  nuc2  nuc3  interaction
#>   <chr>      <chr>        <chr>  <int> <int> <int> <chr> <chr> <chr> <chr>      
#> 1 U8-A14-A21 triple       Bacte…     8    14    21 U     A     A     reverse-Ho…
#> 2 A9-U12-A23 triple       Bacte…     9    12    23 A     U     A     trans-WC   
#> 3 G10-C25-G… triple       Bacte…    10    25    45 G     C     G     trans-WC   
#> 4 C13-G22-G… triple       Bacte…    13    22    46 C     G     G     trans-WC   
#> 5 G15-C48    pair         Bacte…    15    48    NA G     C     NA    Levitt     
#> 6 G18-U55    pair         Bacte…    18    55    NA G     U     NA    trans-WC   
#> 7 G19-C56    pair         Bacte…    19    56    NA G     C     NA    WC         
#> 8 A26-G44    pair         Bacte…    26    44    NA A     G     NA    non-canoni…
#> 9 U54-A58    pair         Bacte…    54    58    NA U     A     NA    reverse-Ho…
#> # ℹ 2 more variables: universal <lgl>, description <chr>

# Just the four classical triples
tc <- tertiary_contacts("Escherichia coli")
tc[tc$contact_type == "triple", ]
#> # A tibble: 4 × 12
#>   contact_id contact_type domain  pos1  pos2  pos3 nuc1  nuc2  nuc3  interaction
#>   <chr>      <chr>        <chr>  <int> <int> <int> <chr> <chr> <chr> <chr>      
#> 1 U8-A14-A21 triple       Bacte…     8    14    21 U     A     A     reverse-Ho…
#> 2 A9-U12-A23 triple       Bacte…     9    12    23 A     U     A     trans-WC   
#> 3 G10-C25-G… triple       Bacte…    10    25    45 G     C     G     trans-WC   
#> 4 C13-G22-G… triple       Bacte…    13    22    46 C     G     G     trans-WC   
#> # ℹ 2 more variables: universal <lgl>, description <chr>