Data downloads: raw data for the manuscript

PDB files:

control 1: 5 pairs of non-allosteric protein structures

control 2: nine pairs of allosteric structures in the same biochemical (I or A) state

bench: 51 allosteric proteins

The PDB files given are those used in the calculations, which may be different than the files you download directly from the PDB. Biological unit coordinates rather than asymmetric unit coordinates are used, and in some cases the numbers of HETATM (substrate and effector) groups have been changed.

Use Table II in the manuscript to find the PDB files appropriate to a protein. The four-letter codes match, but sometimes an extension (e.g. _AB) is used to indicate that only certain chains in the original file were used.

Raw motion data:

Calculated values by six measures of motion (see Figure 1 of the manuscript) for all residues in all subunit types of all proteins in the three sets listed above.

The format for the filenames is:
PDB1-PDB2.ccData
where PDB1 and PDB2 are the codes corresponding to the pair PDBs for which motions were calculated.

Columns in ccData files:

CAdisp: Δ_α

scrms: ΔSC

scflip: Θ_αβ

dphi, dpsi, maxdihed: Δφ, Δψ, max(|Δφ|,|Δψ|)

dchi1, dchi2, maxdchi: Δχ₁, Δχ₂, max(|Δχ₁|,|Δχ₂|)

fI, fA, fmax: ƒ_Ι, ƒ_Α, max(ƒ_Ι, ƒ_Α)

ss1, ss2: secondary structure determined by dssp in I and A states, respectively. All helix types have been corrected to 'H' and all non 'H' or 'E' types have been corrected to 'L' (loop).

asa1, asa2, asaavg: percent all-atom solvent-accessible surface area (ASA) determined by naccess in I, A, and average of I and A state values, respectively.

burial: B (buried) for residues with < 30% ASA, E (exposed) for residues with ≤ 30% ASA

asasc1, asasc2, asascavg: percent side-chain ASA

asabb1, asabb2, asabbavg: percent backbone ASA

Sequence alignment view data:

Moving and non-moving residues mapped onto the sequences of all proteins in the allosteric set, corresponding to the view in figure 2 of the manuscript.

Enzymes, signaling proteins, and DNA-binding proteins view of raw motion data and interactive sequence alignment view of this data for each of the 51 proteins in the allosteric set.

In the sequence alignment input form of a sequence alignment view page, you can manually set thresholds for each of the six motion measures. The default values shown are taken from Table IV of the manuscript.