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Figure 4 | BMC Bioinformatics

Figure 4

From: Oligomeric protein structure networks: insights into protein-protein interactions

Figure 4

Examples of Arginine and Tyrosine hubs and their interactions. (a) Arginine hubs in the interface of 5-aminolevulinic acid dehydratase tetramer (1B4K) at Imin = 4%. The protein tetramer is shown in cartoon representation with each monomer colored differently. Arg 17 (C), Arg 14 (C) and Arg 198 (B) form hubs, which interact with other residues (including other Arginines) belonging to different chains, thus forming a connected network of amino acid cluster at the interface. All the Arginine residues are shown in ball and stick representation and are colored according to the atom types (carbon in cyan, oxygen in red and nitrogen in blue) and the other residues are shown in bond representations and are colored according to the different residue types. The residue names and numbers are indicated along with the chains to which they belong. (b) Tyrosine hub in the interface of the shaker potassium channel (1A68) obtained at Imin = 4%. The protein backbone is shown in cartoon representation with the monomers colored differently. The interface hub residue (Tyr 123 D) and the residues with which it interacts (Arg 130 D, Ser 127 D, Gln 126 D, Val 141 C, Asn 114 C) are shown in van der Waal's representation. The residue numbers, names and the chain identifiers are given. The Tyrosine hydroxyl is involved in a short-strong hydrogen bond with the Arginine side-chain with a donor-acceptor distance of 2.52 Å. The Tyrosine and the Arginine residues involved in the short hydrogen bond are colored according to atom type (carbon in cyan, nitrogen in blue and oxygen in red) and the other residues are colored differently based on their residue types.

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