Sorting these datas from the table, we can find out some relationships out of it. The relationships are listed by the orders of the table columns.

1. Val-Ile-Thr
2. Gly-Ser-Asn
3. Ala-Ser-Asn
4. Ser-Thr-Asn-Lys
5. Asn-Asp
6. Gln-Glu
7. Lys-Arg

    These relationships indicate the structural similarities and functional similarities of those residues. The last three are the most obvious ones. Asparagine and aspartic acid have alomst identical structures but one amino group, so do glutamine and glutamic acid. Lysine and arginine are both long-branched, and arginine has two additional amino groups than lysine. Other relationships such as Val-Ile-Thr also have these similarities. These groups are either one carbonyl group differences or hydroxyl group different.
    Accroding to  these cludes we can infer that point mutations of DNA sequences result amino acids sequence mutations, for example, (Asn-AAU/AAC and Ser-AGU/AGC) these two residues share similar genetic codes but only the second A/U difference. Yet, these mutations are somehow tolerate dur to their structural and functional similarities. Therefore, these mutations give the evolutional varieties and mantain their functional properties.

    As the evolution proceed and mutation occurs, protein sequences change in various regions. However, proteins which have similar functions have conserved sequence homologies in their functional and structural domains. Thus, by the sequence homology analysis, we can predict one unkown protein's function by its homology with other proteins. Also, the sequence homology analysis provides informations about protein structure. This can also apply to the structure modeling and prediction.

Chiral centre is defined as the carbon which is compeletly bonded with four different groups. For instance, the C gamma atom of amino acids is bonded with one acyl group(COO^-), one amino group(NH₃⁺), one H atom and its side chain.

(b) Which amino acids have chiral centres that are not alpha-carbon atoms?
 

C beta atoms of threonine and isoleucine are the chiral centres shown as the following figures.
 

Threonine  Isoleucine

 
 

(c) Which amino acid is this one ? Is it a D-amino acid ?

This is a D-Threonine by the CORN law.
 

(a) Why the gauche(+) is the most abundant conformation of chi1?
The C gamma group position determines the conformations of gauche(+), gauche(-), and trans. Because the C gamma group experiences the exclusive forces of the amino group and the acyl group due to the electronegativity of C, N and O, therefore the C gamma group tends to locate in the least exclusive site. As we can see in the conformation figure, the C gamma group in the gauche(+) conformation is closer to the amino group, NH₃⁺, and distant from the acyl group, COO^-. The C gamma group often has OH group which is in favor of the NH₃⁺ and is repulsive to the COO^- .

(b) What is the gauche(+) conformation ?

(c) Why aliphatic amino acids which are bifurcated at C_b, ie valine and isoleucine, do not adopt the trans conformation very often ?

    Aliphatic amino acids which are bifurcated at C_b, ie valine and isoleucine, do not adopt the trans conformation very often as this involves one of the Cg atoms being in the unfavourable gauche(-)'position'.
    In general, side chains tend to adopt the same three torsion angles (+/-60 and 180 degrees) about chi2 since these correspond to staggered conformations. However, for residues with an sp2 hydridised gamma atom such as Phe, Tyr, etc., chi2 rarely equals 180 degrees because this would involve an eclipsed conformation. For these side chains the chi2 angle is usually close to +/-90 degrees as this minimizes close contacts. For residues such as Asp and Asn the chi2 angles are strongly influenced by the hydrogen bonding capacity of the side chain and its environment. Consequently, these residues adopt a wide range of chi2 angles.

(a ) Explain the meaning of each colored regions?

    This diagram shows the (phi,psi) and protein conformation correspondence. In the white area, polypeptides have colser distances. However, due to the van der Waals radi, polypeptides are excluded in these areas, i.e., the white area. Around the region where phi = -57.8 and psi = -47.0, polypeptides can form a 3.6(13) alpha helix structure, and that area is colored as red. (Right handed alpha-helix) Another red region correspond to conformation which is beta-sheet favored. Both of these red regions have no steric clashes. Note that because glycine does not have side chain, thus the glycine is not restricted by this diagram.
 

(b) Which two groups or atoms are involved for the steric hindrance in the disallowed regions of this plot?

Disallowed regions generally involve steric hindrance between the side chain C-beta methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot. Hence it frequently occurs in turn regions of proteins where any other residue would be sterically hindered.

(c) Which amino acid can adopt phi and psi angles in all regions? Why?

Glycine. As indicated in part a, glycine lacks side chain and instead, with one H atom. This gives a relatively small van der Waals rdaius comparing with other amino acids. Thus, there is no specific region which is disallowed in the Ramachandran plot, all phi and psi angles are allowed.

(a) Why is the C-N bond length of the peptide 10% shorter than that found in usual C-N amine bonds ?

This is because thepeptide bond has some double bond character (40%) due to resonance which occurs with amides. The two canonical structures are:

(b) Why the peptide bond nearly always has the trans configuration ? Which amino acid is found in the cis configuration more frequently than other amino acids ? Why?

    As shown above, because the functional groups between each peptide bonds are closer in cis form. Thus, it gives greater steric hindrance. However,  proline has a  cyclic side chain structure. In either structure, it has equivalent energies and no specific preference toward cis or trans form. Thus proline is found in the cis configuration more frequently than other amino acids.

    The majority of alpha-helices in globular proteins are curved or distorted somewhat compared with the standard Pauling-Corey model. These distortions arise from several factors including:

1. The packing of buried helices against other secondary structure elements in the core of the protein.
2. Proline residues induce distortions of around 20 degrees in the direction of the helix axis. This is because proline cannot  form a regular alpha-helix due to steric hindrance arising from its cyclic side chain which also blocks the main chain N atom and chemically prevents it forming a hydrogen bond. Janet Thornton has shown that proline causes two H-bonds in the helix to be broken since the NH group of the following residue is also prevented from forming a good hydrogen bond. Helices containing proline are usually long perhaps because shorter helices would be destabilised by the presence of a proline residue too much. Proline occurs more commonly in extended regions of polypeptide.
3. Solvent. Exposed helices are often bent away from the solvent region. This is because the exposed C=O groups tend to point towards solvent to maximise their H-bonding capacity, ie tend to form H-bonds to solvent as well as N-H groups. This gives rise to a bend in the helix axis.
4. 3(10)-Helices. Strictly, these form a distinct class of helix but they are always short and frequently occur at the termini of regular alpha-helices. The name 3(10) arises because there are three residues per turn and ten atoms enclosed in a ring formed by each hydrogen bond (note the hydrogen atom is included in this count). There are main chain hydrogen bonds between residues separated by three residues along the chain (ie O(i) to N(i+3)). In this nomenclature the Pauling-Corey alpha-helix is a 3.6(13)-helix. The dipoles of the 3(10)-helix are not so well aligned as in the alpha-helix, ie it is a less stable structure and side chain packing is less favourable.