In Chimera, amino acid residues are automatically assigned an attribute named kdHydrophobicity, with values according to the hydrophobicity scale of Kyte and Doolittle. Each of the 20 most common amino acids has its specific chemical characteristics and its unique role in protein structure and function. On the other hand, polarity is not always straightforward to assign. Water molecules may also be involved in the stabilization of protein structures by making hydrogen bonds with the main chain and side chain groups in proteins and even linking different protein groups to each other. Serine (Ser) and threonine (Thr) are polar since both carry a hydroxyl group, asparagine (Asn) and glutamine (Gln) carry a polar amide group. For discussion of OH−π, and CH−O type of hydrogen bonds see: Scheiner et al., 2002.The hydrophobic amino acids include alanine (Ala, A), valine (Val, V), leucine (Leu, L), isoleucine (Ile, I), proline (Pro, P), phenylalanine (Phe, F) and cysteine (Cys). In proteins essentially all groups capable of forming H-bonds (both main chain and side chain, independently of whether the residues are within a secondary structure or some other type of structure) are usually H-bonded to each other or to water molecules. The key difference between hydrophobic and hydrophilic amino acids is that the hydrophobic amino acids are nonpolar whereas the hydrophilic amino acids are polar.. Amino acids are the building blocks of proteins. Shown at the right is the structure of serine. Also in this chapter:Introductiontorsion angles helices & sheetsprotein motifsprotein foldsprotein domainsprotein databasesprotein databank PDB, Structural bioinformatics, protein crystallography, sequence analysis & homolog modeling. water) environment. In a protein, hydrophobic amino acids are likely to be found in the interior, whereas hydrophilic amino acids are likely to be in contact with the aqueous environment. Below is a listing of the 20 amino acids grouped by their "R" group properties. The 20 different types of amino acids, depending on their physicochemical properties, can be grouped into three major classes: hydrophobic, hydrophilic, and charged. Here are the nonpolar amino acids: The vertical axis shows the fraction of highly buried residues, while the horizontal axis shows the amino acid names in one-letter code. The anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic, and charged residues separately for a large number of proteins were studied. In addition, the side chains of histidine, tyrosine, phenylalanine and tryptophan are also able to form weak hydrogen bonds of the types, OH−π, and CH−O, by other words using electron clouds within their ring structures. Hydrophobicity scales are values that define the relative hydrophobicity or hydrophilicity of amino acid residues. For a hydrogen bond to be formed, two electronegative atoms (for example in the case of an alpha-helix the amide N, and the carbonyl O) have to interact with the same hydrogen. The charged amino acids are easy to assign, they include two basic residues, lysine (Lys) and arginine (Arg) both having positive charge at neutral pH values, and two acidic, aspartate (Asp) and glutamate (Glu) both carrying negative charge at neutral pH. Glycine (Gly), being one of the common amino acids, does not have a side chain. E-mail: [email protected]. In addition, water is often found to be involved in ligand binding to proteins, mediating ligand interactions with polar or charged side chain- or main chain atoms. Due to their electronic structure, water molecules may accept 2 hydrogen bonds, and donate 2, thus being simultaneously engaged in a total of 4 hydrogen bonds. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. However, the pKa may be modulated by the environment inside the protein in a way that the side chain may give away a proton and become neutral, or accept a proton, becoming charged. It has two –NH group with a pKa value of around 6. For example, based on the propensity of the side chain to be in contact with water, amino acids can be classified as hydrophobic (low propensity to be in contact with water), polar and charged (energetically favorable contact with water). They don’t gratefully interact with (dissolve in) water. This ability makes histidine useful within enzyme active sites. For example, based on the propensity of the side chain to be in contact with water, amino acids can be classified as hydrophobic (low propensity to be in contact with water), polar and charged (energetically favorable contact with water). These residues are often found close to the surface of proteins. They don’t gratefully interact with (dissolve in) water. The hydrogen is covalently attached to one of the atoms (called the hydrogen-bond donor), but interacts electrostatically with the other atom (the hydrogen bond acceptor, O). The nine amino acids that have hydrophobic side chains are glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), phenylalanine (Phe), methionine (Met), and tryptophan (Trp). The other scales in the following table are not assigned automatically, but input files to assign them with Define Attribute are linked below.