In protein molecules each residue has a different ability to form contacts. In this paper
we calculated the number of contacts per residue and investigated the distribution of residue-residue contacts from 495 globular protein molecules using Contacts of Structural Units (CSU) software. It was found that the probability P(n) of amino acid residues having n pairs of contacts in all contacts fits Gaussian distribution very well. The distribution function of residue-residue contacts can be expressed as: P(n) = P0 + aexp[-b(n - nc)2]. In our calculation
P0 = -0.06
a = 11.4
b = -0.04 and nc = 9.0. According to distribution function
we found that those hydrophobic (H) residues including Leu
Val
Ile
Met
Phe
Tyr
Cys
and Trp residues have large values of the most probable number of contact nc
and hydrophilic (P) residues including Ala
Gly
Thr
His
Glu
Gln
Asp
Asn
Lys
Ser
Arg
and Pro residues have the small ones. We also compare with Fauchere-Pliska hydrophobicity scale (FPH) and the most probable number of contact nc for 20 amino acid residues
and find that there exists a linear relationship between Fauchere-Pliska hydrophobicity scale (FPH) and the most probable number of contact nc
and it is expressed as: nc = a + b × FPH
here a=8.87
and b=1.15. It is important to further explain protein folding and its stability from residue-residue contacts.
Abstract
In protein molecules each residue has a different ability to form contacts. In this paper
we calculated the number of contacts per residue and investigated the distribution of residue-residue contacts from 495 globular protein molecules using Contacts of Structural Units (CSU) software. It was found that the probability P(n) of amino acid residues having n pairs of contacts in all contacts fits Gaussian distribution very well. The distribution function of residue-residue contacts can be expressed as: P(n) = P0 + aexp[-b(n - nc)2]. In our calculation
P0 = -0.06
a = 11.4
b = -0.04 and nc = 9.0. According to distribution function
we found that those hydrophobic (H) residues including Leu
Val
Ile
Met
Phe
Tyr
Cys
and Trp residues have large values of the most probable number of contact nc
and hydrophilic (P) residues including Ala
Gly
Thr
His
Glu
Gln
Asp
Asn
Lys
Ser
Arg
and Pro residues have the small ones. We also compare with Fauchere-Pliska hydrophobicity scale (FPH) and the most probable number of contact nc for 20 amino acid residues
and find that there exists a linear relationship between Fauchere-Pliska hydrophobicity scale (FPH) and the most probable number of contact nc
and it is expressed as: nc = a + b × FPH
here a=8.87
and b=1.15. It is important to further explain protein folding and its stability from residue-residue contacts.
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