Contacts of the helix formed by residues 4127 - 4149 (chain F) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE4127 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3999F ALA* 6.0 6.3 - - + -
4005F ILE* 4.8 21.8 - - + -
4060F PHE* 3.5 58.3 - + + -
4063F LEU* 5.4 3.8 - - + -
4123F PHE 5.2 6.7 - - - -
4124F ALA 5.2 8.3 - - - -
4126F ARG* 1.3 91.8 - - + +
4128F GLN* 1.3 63.0 + - - +
4129F GLU* 3.3 7.6 - - - -
4130F PRO* 3.4 18.0 - - + +
4131F ALA* 3.7 17.8 + - + +
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Residues in contact with GLN4128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4064F LYS* 6.1 4.3 - - + +
4125F ASN* 5.2 19.3 - - + +
4126F ARG 3.7 1.8 - - - +
4127F PHE* 1.3 76.1 - - - +
4129F GLU* 1.3 68.3 + - + +
4131F ALA* 3.8 5.7 + - - +
4132F ARG* 3.3 22.5 + - - +
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Residues in contact with GLU4129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4126F ARG* 3.9 15.3 - - - +
4128F GLN* 1.3 84.8 + - + +
4130F PRO* 1.3 75.8 - - + +
4132F ARG* 3.3 17.8 + - - +
4133F ASP* 4.0 4.3 + - - +
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Residues in contact with PRO4130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4005F ILE* 6.6 0.2 - - + -
4009F LYS* 4.8 24.5 - - + +
4012F LEU* 3.5 28.9 - - + +
4013F ASP* 5.2 5.6 - - - +
4016F LYS* 6.0 0.7 - - - +
4127F PHE* 3.4 22.2 - - + +
4129F GLU* 1.3 104.2 - - + +
4131F ALA* 1.3 59.0 + - - +
4132F ARG 3.3 0.7 + - - -
4133F ASP* 3.6 11.6 + - + +
4134F ILE* 3.4 15.4 + - - +
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Residues in contact with ALA4131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4012F LEU* 4.0 3.7 - - + +
4057F PHE* 4.9 16.0 - - + -
4060F PHE* 6.4 2.7 - - + -
4127F PHE* 3.7 19.9 + - + +
4128F GLN* 4.1 5.2 - - - +
4129F GLU 3.3 0.6 - - - -
4130F PRO* 1.3 78.7 - - - +
4132F ARG* 1.3 59.1 + - - +
4133F ASP 3.4 0.2 - - - -
4134F ILE* 3.7 10.0 - - + +
4135F GLY* 2.8 28.6 + - - -
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Residues in contact with ARG4132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4128F GLN 3.3 18.1 + - - +
4129F GLU* 3.3 9.3 + - - +
4130F PRO 3.2 0.8 - - - -
4131F ALA* 1.3 76.3 - - - +
4133F ASP* 1.3 63.9 + - - +
4135F GLY* 4.1 0.6 - - - -
4136F PHE* 3.4 21.7 + - - +
4168F TYR* 6.3 4.7 - - + -
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Residues in contact with ASP4133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4016F LYS* 3.7 38.1 + - + +
4129F GLU 4.0 3.9 + - - +
4130F PRO* 3.6 8.6 + - + +
4131F ALA 3.4 0.2 - - - -
4132F ARG* 1.3 78.1 - - - +
4134F ILE* 1.3 64.8 + - - +
4136F PHE* 3.4 6.3 + - - +
4137F ASN* 3.2 25.5 + - - +
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Residues in contact with ILE4134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4012F LEU* 3.7 19.3 - - + -
4015F GLN* 4.7 8.1 - - + +
4016F LYS* 4.5 23.3 - - + +
4019F VAL* 4.6 9.6 - - + -
4057F PHE* 3.6 37.2 - - + -
4130F PRO 3.4 18.4 - - - +
4131F ALA* 3.7 6.1 - - - -
4133F ASP* 1.3 78.2 + - - +
4135F GLY* 1.3 67.0 + - - +
4137F ASN* 3.0 22.2 + - + -
4138F VAL* 3.0 29.3 + - + +
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Residues in contact with GLY4135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4057F PHE* 5.0 9.6 - - - -
4131F ALA 2.8 21.9 + - - -
4132F ARG* 4.1 0.7 - - - -
4133F ASP 3.3 0.4 - - - -
4134F ILE* 1.3 79.9 - - - +
4136F PHE* 1.3 57.9 + - - +
4138F VAL* 4.0 3.8 + - - +
4139F ALA* 3.6 17.8 + - - +
4165F ILE* 4.9 10.6 - - - +
4168F TYR* 6.6 0.4 - - - -
4169F PHE* 4.6 4.4 - - - +
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Residues in contact with PHE4136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4132F ARG 3.4 17.8 + - - +
4133F ASP* 4.0 3.1 - - - +
4134F ILE 3.2 0.4 - - - -
4135F GLY* 1.3 75.5 - - - +
4137F ASN* 1.3 62.8 + - - +
4139F ALA* 3.7 7.3 - - - +
4140F VAL* 3.2 30.6 + - + +
4169F PHE* 4.5 11.4 - - + -
4172F TYR* 5.8 5.8 - - + +
4191F GLU* 5.2 14.4 - - + -
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Residues in contact with ASN4137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4016F LYS* 3.3 29.7 + - - +
4019F VAL* 4.1 14.7 - - + +
4020F VAL* 4.3 7.3 - - - +
4023F LEU* 3.3 29.5 - - - +
4133F ASP* 3.2 21.5 + - - +
4134F ILE* 3.0 19.1 + - + +
4136F PHE* 1.3 76.6 - - - +
4138F VAL* 1.3 65.1 + - - +
4140F VAL* 3.2 19.2 - - - +
4141F LEU* 3.2 17.6 - - - +
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Residues in contact with VAL4138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4019F VAL* 6.0 0.4 - - + -
4057F PHE* 5.0 9.9 - - + -
4134F ILE* 3.0 35.8 + - + +
4135F GLY* 4.5 4.5 - - - +
4137F ASN* 1.3 76.0 - - - +
4139F ALA* 1.3 62.3 + - - +
4141F LEU* 3.4 20.7 - - + +
4142F LEU* 3.1 26.7 + - + +
4162F ALA* 5.7 8.5 - - + -
4165F ILE* 5.8 8.1 - - + -
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Residues in contact with ALA4139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4135F GLY 3.6 13.8 + - - +
4136F PHE 3.5 8.3 + - - +
4137F ASN 3.2 0.8 - - - -
4138F VAL* 1.3 79.9 - - - +
4140F VAL* 1.3 62.5 + - + +
4142F LEU* 3.5 4.9 + - - +
4143F THR* 3.3 23.4 + - - +
4165F ILE* 4.5 10.5 - - - +
4166F LEU* 4.6 14.4 - - + +
4169F PHE* 3.8 24.5 - - + -
4173F LEU* 4.6 9.5 - - + +
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Residues in contact with VAL4140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4023F LEU* 4.3 15.3 - - + +
4136F PHE* 3.2 15.7 - - + +
4137F ASN* 3.2 27.8 - - - +
4139F ALA* 1.3 78.5 - - + +
4141F LEU* 1.3 60.6 + - - +
4143F THR* 3.3 18.2 - - - +
4144F ASN* 3.4 13.0 - - - +
4173F LEU* 4.2 19.1 - - + -
4189F TYR* 4.0 37.6 - - + +
4190F PHE 4.7 7.9 - - - +
4191F GLU* 5.8 2.2 - - + -
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Residues in contact with LEU4141 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4019F VAL* 4.3 27.6 - - + +
4022F LEU* 5.6 7.2 - - + -
4023F LEU* 3.7 21.8 - - + -
4137F ASN* 3.2 21.1 + - - +
4138F VAL* 3.4 26.2 - - + +
4140F VAL* 1.3 79.0 - - - +
4142F LEU* 1.3 72.4 + - + +
4144F ASN* 3.2 10.9 + - - +
4145F LEU* 3.1 25.8 + - + +
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Residues in contact with LEU4142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4138F VAL* 3.1 22.4 + - + +
4139F ALA* 4.0 5.8 - - - +
4140F VAL 3.4 0.6 - - - -
4141F LEU* 1.3 83.3 - - + +
4143F THR* 1.3 49.5 + - - +
4145F LEU* 3.3 16.6 - - - +
4146F SER* 2.5 28.1 + - - -
4159F LEU* 5.5 13.8 - - + +
4162F ALA* 5.7 8.3 - - + -
4166F LEU* 6.0 8.1 - - + -
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Residues in contact with THR4143 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4139F ALA 3.3 18.3 + - - +
4140F VAL* 3.3 16.4 - - - +
4142F LEU* 1.3 78.0 - - - +
4144F ASN* 1.3 61.3 + - - +
4146F SER* 3.5 7.4 - - - -
4147F GLU* 3.4 31.9 + - - +
4173F LEU* 4.4 16.4 - - + -
4189F TYR* 5.2 6.3 - - + -
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Residues in contact with ASN4144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4022F LEU 5.9 0.2 + - - -
4023F LEU* 5.7 8.1 - - + +
4026F LEU* 4.1 22.1 + - - +
4140F VAL 3.4 17.1 + - - +
4141F LEU* 3.2 9.9 + - - +
4143F THR* 1.3 79.4 - - + +
4145F LEU* 1.3 65.0 + - - +
4147F GLU* 3.7 1.5 + - - -
4148F HIS* 3.1 62.9 + - - -
4187F ARG* 4.8 11.4 - - - +
4189F TYR* 5.6 5.9 + - + +
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Residues in contact with LEU4145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4026F LEU* 5.5 5.8 - - + -
4036F ALA 5.8 1.6 - - - +
4039F MET* 4.2 24.2 - - + +
4040F VAL* 4.2 22.9 - - + -
4043F LEU* 4.3 27.1 - - + -
4141F LEU* 3.1 29.3 + - + +
4142F LEU* 3.3 23.1 - - - +
4144F ASN* 1.3 82.3 - - - +
4146F SER* 1.3 69.2 + - - +
4148F HIS* 3.7 5.3 + - - +
4149F VAL* 3.2 28.5 + - - +
4155F LEU* 5.5 6.7 - - + -
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Residues in contact with SER4146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4142F LEU 2.5 25.9 + - - -
4143F THR* 3.5 8.5 - - - -
4145F LEU* 1.3 83.1 - - - +
4147F GLU* 1.3 62.0 + - - +
4149F VAL* 3.3 24.6 - - - +
4155F LEU* 4.4 22.4 - - - -
4159F LEU* 5.5 6.6 - - - +
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Residues in contact with GLU4147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031F VAL* 5.3 0.9 - - - +
4143F THR* 3.4 25.5 + - - +
4144F ASN* 4.2 3.0 - - - +
4145F LEU 3.4 0.4 - - - -
4146F SER* 1.3 78.8 + - - +
4148F HIS* 1.3 73.4 + - + +
4149F VAL 3.7 4.7 - - - +
4187F ARG* 2.6 48.1 + - - -
5026F PHE* 4.7 6.9 - - - -
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Residues in contact with HIS4148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4026F LEU* 3.5 35.1 - - + +
4027F GLU 5.9 0.9 - - - -
4029F ASN 5.9 3.1 - - - -
4030F VAL 5.6 0.4 + - - -
4031F VAL* 3.0 59.4 - - + +
4032F ASN* 5.3 0.2 - - - +
4036F ALA* 5.2 4.6 - - + +
4144F ASN* 3.1 49.8 + - - +
4145F LEU* 4.1 5.4 - - - +
4146F SER 3.4 0.6 - - - -
4147F GLU* 1.3 87.4 - - + +
4149F VAL* 1.3 64.7 + - + +
4150F PRO* 3.6 3.1 - - - +
4186F GLU* 6.1 2.4 - - + +
4187F ARG* 5.8 7.7 + - - +
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Residues in contact with VAL4149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031F VAL 4.3 5.2 - - - +
4036F ALA* 5.0 8.3 - - + +
4037F ARG* 5.4 8.7 - - + -
4040F VAL* 3.8 25.8 - - + -
4145F LEU 3.2 20.2 - - - +
4146F SER* 3.3 22.9 - - - +
4147F GLU 3.7 4.5 - - - +
4148F HIS* 1.3 79.9 - - + +
4150F PRO* 1.3 73.6 - - + +
4151F HIS 4.6 0.9 - - - +
4152F ASP* 4.1 28.5 - - + +
4155F LEU* 4.6 4.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il