Primary Citation PubMed: 10089404
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Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective.
(2010) BMC Bioinformatics 11
PubMed: 20462403 | PubMedCentral: PMC2882391 | DOI: 10.1186/1471-2105-11-244
We also note that although the two chain Es in 2BTC and in 2PTC are identical chains, the specific residues involved in are not the same due to the low similarity between their partner chains.
PDB entries 1EJA :B 1TAB :I 1TGS :I 2BTC :I 2PTC :I 1BTH :P 1EJA :A A B - - - - - 1TAB :E 83 E I - - - - 1TGS :Z 83 100 Z I - - - 2BTC :E 83 100 100 E I - - 2PTC :E 83 100 100 100 E I 100 1BTH :H 37 36 36 36 36 H P The italic half is for the sequence similarity among these inhibitors, while the bold-face half is for the sequence similarity among trypsins/trypsinogen; '-' means no significant sequence alignment.
Chain E of 1TAB , chain Z of 1TGS , chain E of 2BTC and chain E of 2PTC are identical chains.
Residue SER in 2BTC is in the position 217, while it is in the position 195 in 2PTC .
PDB entry First Chains Second Chains 1EJA -A:B GLN192-SER195-SER214-TRP215-GLY216 CYS33-LYS34 1TAB -E:I GLN192-SER214-TRP215-GLY216-SER217 CYS24-LYS26 1TGS -Z:I GLN192-SER214-TRP215-GLY216-SER217 CYS16-LYS18 2BTC -E:I GLN192-SER214-TRP215-GLY216-SER217 CYS503-LYS505 2PTC -E:I GLN192-SER195-SER214-TRP215-GLY216 CYS14-LYS15 1BTH -H:P GLN192-SER195-SER214-TRP215-GLY216 CYS14-LYS15 We take these examples to highlight that the uniqueness of DWE bicliques matches to different interfacial properties of the three types of protein interactions in terms of polarity, hydrophobicity, the composition of residues and residue pairs in protein interfaces.
For example, 1TGS is about 'three-dimensional structure of the complex between pancreatic secretory inhibitor (kazal type) and trypsinogen', and 2BTC is about 'bovine trypsin in complex with squash seed inhibitor (cucurbita pepo trypsin inhibitor II)'.
Publication Year: 2010
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