FR3D annotations of PDB files

The directory http://rna.bgsu.edu/FR3D/AnalyzedStructures/All contains FR3D annotations of all RNA-containing PDB files.  It is updated every few months.  All files are tab delimited with a variable number of comment lines beginning with #, and one header line.  The first comment line indicates the FR3D classification version and the versions of Dangle and Suitename used for backbone conformations.  To facilitate mapping pairwise annotations of the 3D structure to sequence alignments, the chains and sequences within those chains are provided in the next comment lines.  Note that the nucleotide sequence omits any nucleotide that FR3D skips.  FR3D skips modified nucleotides and nucleotides with incomplete base coordinates in the PDB file. The header line explains the format of the data.  Each line of the rest of the file has this format:

PDB ID of the file TAB
Pairwise interaction between 1 and 2 TAB
Nucleotide 1 base
Nucleotide 1 number from PDB file TAB
Nucleotide 1 chain TAB
Nucleotide 1 position in its chain TAB
Nucleotide 2 base
Nucleotide 2 number from PDB file TAB
Nucleotide 2 chain TAB
Nucleotide 2 position in its chain

Thus, each nucleotide is referred to in two ways:  the nucleotide number found in the PDB file, which can have non-numeric characters such as 190G, and the position in the nucleotide sequence of the chain in which the nucleotide occurs, starting at 1.

The file FR3D_AnalyzedStructures_All.zip contains all of the annotations from all files.

What follows is an explanation of what data appears in each file.  The annotation of PDB file 1S72.pdb is used as a template.  PDB IDs always have uppercase letters.

Basepair annotations

Basepairs are listed in 1S72_basepairs_FR3D.txt.  Basepair annotation follows the scheme of Leontis-Westhof.  Three letter codes are used such as cWW, tHS, etc.  c refers to cis, t refers to trans, W refers to the Watson-Crick edge, H refers to the Hoogsteen (CH) edge, and S refers to the sugar edge of the base.  There is one exception; bif refers to a bifurcated basepair, see Table 13 in Leontis-Stombaugh-Westhof 2002.  Each basepair is listed twice to account for the two orders in which the basepair can be listed.  For example,

1S72	tSH	G	23	0	14	A	520	0	509
1S72	tHS	A	520	0	509	G	23	0	14

The first line says that nucleotide 23 uses its sugar edge in a trans interaction with the Hoogsteen edge of nucleotide 520, both in chain 0 in 1S72.  The second line says that nucleotide 520 uses its Hoogsteen edge in a trans interaction with the sugar edge of nucleotide 23, both in chain 0 of 1S72.  These nucleotides are found in positions 14 and 509, respectively, in chain 0 of 1S72.  Lowercase w, h, and s indicate the asymmetry in interactions where the same edge is used by each nucleotide, for example:

1S72	cSs	A	161	0	150	C	769	0	756
1S72	csS	A	439	0	428	C	153	0	142
Refer to the cis Sugar Edge-Sugar Edge link on this page to understand the difference between AC cSs and AC csS basepairs. Basepairing interactions were studied in the papers:

FR3D annotations of basepairs were described in the paper:

Stacking annotations

Stacking interactions are listed in 1S72_stacking_FR3D.txt.  The possible annotations are s35, s53, s33, and s55.  s refers to stacking, while 3 and 5 refer to the two faces of the base.  The 3 face is the one which faces toward the 3' end of the chain in a normal helix; the 5 face faces toward the 5' end.  s35 means that the 3 face of the first base is stacked on the 5 face of the second nucleotide.  This is the normal stacking found in a helix.  As with basepairs, each stacking interaction is listed twice.  For example,

1S72	s35	G	20	0	11	G	21	0	12
1S72	s53	G	21	0	12	G	20	0	11

FR3D annotations of base stacking were described in the paper:

Base-phosphate interactions

Base-phosphate interactions are listed in 1S72_base_phosphate_FR3D.txt.  Each interaction is listed only once.  For example,

1S72	W_4BPh	G	23	0	14	A	519	0	508

indicates that nucleotide 23 of chain 0 of 1S72 has a hydrogen bond donor on the Watson-Crick edge (W) in a hydrogen bond with a phosphate oxygen of nucleotide 519 in chain 0.  In particular, the hydrogen bond is of type 4BPh, which is a particular way in which the Watson-Crick edge can participate in a base-phosphate interaction. The edge can be W, H, S, or, for the base-phosphate interaction 2BPh made by A, the edge is denoted SW because it is intermediate between the sugar and Watson-Crick edges.  Base-phosphate interactions are characterized in the paper:

Backbone conformations

Backbone conformations between two nucleotides that are connected by the sugar-phosphate backbone are listed in 1S72_backbone_conformation_FR3D.txt.  They are only listed once, with the lower nucleotide number occurring first.  They are calculated by Suitename and Dangle, produced by the Richardson group.  The filename says FR3D for two reasons:  the implementation of Suitename and Dangle may not be up to date, and because FR3D skips nucleotides with backbone atoms but no base atoms, and so the list of backbone conformations will be limited by FR3D compared to what Suitename and Dangle can do.  The output looks like this:

1S72	1a	G	20	0	11	G	21	0	12

says that the backbone between nucleotides 20 and 21 has backbone conformation 1a.  Backbone conformations were characterized in the paper:

Backbone connectivity

Backbone connectivity is listed in the file 1S72_backbone_connectivity_FR3D.txt.  It is determined by examining the distance between the O2 and O3 atoms of a lower-numbered nucleotide and the P atom of the next nucleotide.  When the O3 atom is within 2 Angstroms of the P and the O2 is farther, the backbone connectivity is annotated as c35.  When the O2 atom is within 2 Angstroms and the O3 atom is farther, the backbone connectivity is annotated as c25.  Each connection is listed twice, thus:

1S72	c35	G	20	0	11	G	21	0	12
1S72	c53	G	21	0	12	G	20	0	11
both indicate that nucleotides 20 and 21 in chain 0 of 1S72 are connected in the usual way. FR3D skips modified nucleotides and nucleotides with no base, so it may indicate more backbone breaks than actually exist in the PDB file.

All interactions together

The file 1S72_interactions_FR3D.txt lists all interactions described above in a single file.  The file FR3D_AnalyzedStructures_All.zip contains all of the annotations from all files.

Near interactions

The file 1S72_near_interactions_FR3D.txt lists pairs which do not meet the strict classification limits to be included in the basepair, stacking, or base-phosphate categories listed above, but which are close enough that they may indeed be instances of the indicated interaction, but were not annotated that way due to poor resolution, poor modeling, or overly restrictive classification limits in FR3D.  They are annotated by adding the letter "n" before the annotation; thus, for example, ncWW, ns35, and Wn4BPh.  Allowing for this amount of flexibility in annotation of pairwise interactions can be useful, but it dramatically increases the number of pairwise annotations to be considered.

Last updated 2009-08-26 / Return to the FR3D home page /