User:Jessica Sheehe/Sandbox 1: Difference between revisions
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XI. Other Interesting Structural Features | |||
[[Image:Capping residue.png|400px|left|thumb| Capping Residue, Asp316 is acting as a capping residue at the N-terminus of helix F in PKG-Ia (PDB 3SHR). The oxygen of Asp316 (N cap) main chain is hydrogen bonding with the backbone nitrogen of Ser319 (N3) and the backbone of Phe320 (N4) with bond distances of 3.1Å and 3.0Å respectively. According to Seale and colleagues, this N-capping motif is called a capping box. The cap is generally inaccessible to solvent. N’ (Ile315) and N4 (Phe320) residues are usually hydrophobic. N1 (Arg317) and N2 (Asp318) side chains are exposed to solvent. If N2 is an Asp, it will make an additional hydrogen bond to the side chain of the cap; this bond measures 3.1Å. (PDB 3SHR)]] | |||
[[Image:Beta turn.png|400px|center|thumb| A beta-turn between Lys151 and Val154 of PKG-Ia (PDB 3SHR). The carbonyl of Lys151(i) is hydrogen bonded to the amide of Val154 (i+3) measuring 3.2Å. The distance between alpha carbons measures 5.0Å. This beta-turn can be classified as a type II beta-turn because the CO group of n+1 (Glu152) is pointing in the same direction as the side chain of n+2 (Gly153); additionally n+2 must be glycine for a type II turn. ]] | |||
[[Image:Amphipathic Helix E.png|400px|right|thumb| Amphipathic Helix E, The hydrophobic face of PKG-Ia, helix E associates with hydrophobic residues in the interior (PDB 3SHR).]] | |||
[[Image:Cation-pi interaction.png|400px|left|thumb| A cation-pi interaction between Tyr246 and Arg249 in cGMP-dependent protein kinase Ia was identified (PDB 3SHR). Distance between the amine of the arginine and the center of the tyrosine ring measures approximately 5.6Å. Average cation-pi distance was determined by averaging the distances from the amide of the arginine to the shortest and furthest points on the tyrosine ring. The electrostatic interaction energy measures -4.53 kcal/mol and the van der Waals interaction energy measures -3.35 kcal/mol as determined by http://capturecaltech.edu. (PDB 3SHR).]] | |||
