Amino acids hydrophobic nature

Host defense peptide hydrophobicity (H) is defined as the proportion of hydrophobic amino acids within a peptide. Typically, these peptides are comprised of >30% hydrophobic residues and this governs the ability of a host defense peptide to partition into the lipid bilayer, an essential requirement for antimicrobial peptide-membrane interactions. Typically, the hydrophobic and hydrophilic amino acids of natural peptides are segregated to create specific regions or domains that allow for optimal interaction with microbial membranes. This likely represents evolutionary optimization to maximize the selectivity of these defense molecules. It has been established that increasing antimicrobial peptide hydrophobicity above a specific threshold correlates... 

The amino acids are usually divided into three different classes defined hy the chemical nature of the side chain. The first class comprises those with strictly hydrophobic side chains Ala (A), Val (V), Leu (L), He (1), Phe (F), Pro (P), and Met (M). The four charged residues, Asp (D), Glu (E), Lys (K), and Arg (R), form the second class. The third class comprises those with polar side chains Ser (S), Thr (T), Cys (C), Asn (N), Gin (Q), His (H), Tyr (Y), and Trp (W). The amino acid glycine (G), which has only a hydrogen atom as a side chain and so is the simplest of the 20 amino acids, has special properties and is usually considered either to form a fourth class or to belong to the first class. 

The 20 natural amino acids differ from each other by the nature of their sidechains. Differences involve overall size, hydrophobic or hydrophilic character and, perhaps most importantly, ionization state. While the sidechains are normally written in terms of neutral structures, some may also exist in either protonated or deprotonated forms depending on pH. 

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