Display Sequence:
Display sequence helps to understand the primary sequence of a protein i.e. which amino acid is present at which position. Amino acid sequence of a protein can be displayed in two formats. These format are: One letter code amino acid (such as: G=Glycine, P=Proline) and three letter code amino acids (Lys=Lysine, Glu=Glutamate) (Table 1). These two types of format are used in several places to represent the primary sequence of a protein. In a protein PDB file each amino acid are represented by three letter code. In Pymol viewer the amino acids are shown in one letter code by default but user can also highlight a residue there in three letter code. In most of the protein sequence and sequence alignment web server, protein sequences are represented usually by one letter code (Figure 1).
Amino acids One letter code Three letter code
Glycine G Gly
Alanine A Ala
Valine V Val
Leucine L Leu
Isoleucine I Ile
Proline P Pro
Methionine M Met
Cysteine C Cys
Serine S Ser
Threonine T Thr
Histidine H His
Tyrosine Y Tyr
Tryptophan W Trp
Phenylalanine F Phe
Lysine K Lys
Arginine R Arg
Glutamate E Glu
Glutamine Q Gln
Aspartate D Asp
Asparagine N Asn
Figure 1. Display of amino acid sequence of a protein in several aspects. Protein primary sequence retrieved from web server (A), Three letter code amino acids in PDB format of a protein (B), One letter code amino acid sequence in Pymol viewer (C), Three letter code amino acid sequence in Pymol viewer (D), One letter code amino acids in a sequence alignment file (E).
Calculation of Biochemical properties:
This method uses both the sequence and structural information of a protein to determine the molecular weight, pKA value and the number of amino acids with different chemical properties. During the analysis of pKA value of a particular residue in a protein, the pI and residual charge at a given pH are also been determined. Isoelectric point calculator implemented in this method provides detailed analysis of isoelectric point according different scales for individual proteins with the average value considering the statistical standard deviation.
Amino acids Number Percentage (%) Amino acids Number Percentage (%)
Ala 30 10.6 Leu 26 9.2
Arg 13 4.6 Lys 13 4.6
Asn 12 4.3 Met 10 3.5
Asp 11 3.9 Phe 9 3.2
Cys 3 1.1 Pro 12 4.3
Gln 9 3.2 Ser 20 7.1
Glu 24 8.5 Thr 10 3.5
Gly 21 7.4 Trp 1 0.4
His 11 3.9 Tyr 4 1.4
Ile 19 6.7 Val 24 8.5
Detection of active site:
Active site is defined by the specific region in a protein where the main catalytic reaction takes place between the protein and its substrate. Active site constructed with a definite organization of several residues and in some cases catalytic water molecules or metal ions with proper coordination. Computational methods are increasingly gaining importance as an aid in identifying active sites. This analysis required adequate and high resolution structural information of a protein. Modern active site prediction provides information based on structural and electrostatic conformity of each residue (Figure 2).
Figure 2. Active site of a protein bound to its substrate (above). Electrostatic representation of another protein’s active site where water (cyan colour sphere) plays a catalytic role (below).
Temperature Factors (B-factor):
The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors also known as thermal factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. B-factor of an individual residue is depends upon the dihedral angles: phi (ϕ) and psi (ψ) of its C-Cα and Cα-N bond respectively. Cumulative contribution of residual B-factor regulates the overall protein stability (Figure 3).
Figure 3. Different Thermal factor (B-factor) for different residues in protein highlighted in primary sequence and 3D structure by colour legend.
Calculate bounding box: min and max coordinates:
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Blast:
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Ramachandran Plot:
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Occupancy:
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Non-standard naming convention:
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Metals:
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