Supplement to Analysis of Information Content Present in Portein-DNA Interactions

joint-mi.txt

The full list of mutual information between joint features and DNA-contacting classes. Abbreviations are given below. The file is arranged in 3 space-separated columns which are joint-feature, maximum MI achieved, cutoff distance at which the max was achieved. Abbreviations used for the joint features shown in the below table.

Abbreviation	Num. Values	Feature
sasa2	2	SASA
sasa3	3	SASA
sasa4	4	SASA
sasa20	20	SASA
ipp2	2	IPP
ipp3	3	IPP
ipp4	4	IPP
aa	20	Amino Acids
pn	3	Pos/Neg/Neut Amino acids
ss	3	Secondary Structure
prof5	5	Full profiles
prof10	10	Full profiles
prof20	20	Full profiles
pssmcon5w5	5	Concatenated PSSMs, sliding window size 5
pssmcon10w5	10	Concatenated PSSMs, sliding window size 5
pssmcon20w5	20	Concatenated PSSMs, sliding window size 5
strn5d14s3	5	Structural neighbor counts, within 14 angstroms, sequence distance > 3
strn10d14s3	10	Structural neighbor counts, within 14 angstroms, sequence distance > 3
strn20d14s3	20	Structural neighbor counts, within 14 angstroms, sequence distance > 3
strpssm5d14s3	5	Structural neighbor sums of PSSMs, within 14 angstroms, sequence distance > 3
strpssm10d14s3	10	Structural neighbor sums of PSSMs, within 14 angstroms, sequence distance > 3
strpssm20d14s3	20	Structural neighbor sums of PSSMs, within 14 angstroms, sequence distance > 3
wang5w11	5	pKa, hydropath, moelcular mass used by Wang and Brown (2006)
wang10w11	10	pKa, hydropath, moelcular mass used by Wang and Brown (2006)
wang20w11	20	pKa, hydropath, moelcular mass used by Wang and Brown (2006)
profcon5w5	5	Concatenated profiles, sliding window size 5
profcon10w5	10	Concatenated profiles, sliding window size 5
profcon20w5	20	Concatenated profiles, sliding window size 5
pssm5	5	Position Specific Scoring Matrix only
pssm10	10	Position Specific Scoring Matrix only
pssm20	20	Position Specific Scoring Matrix only

culledids.txt

The full list of PDB files and chains which was used for the dataset. Sequences were extracted directly from the PDB file for each chain and used to ensure this set has less than 30% identity.