Contacts of the helix formed by residues 3979 - 4001 (chain B) 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 ARG3979 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3915B VAL* 5.0 9.5 - - + +
3919B LEU* 4.0 33.0 - - + +
3978B SER* 1.3 74.2 - - - +
3980B LEU* 1.3 62.8 + - - +
3981B TRP 3.4 2.0 - - - -
3982B ASP* 3.6 15.9 - - + +
3983B ALA* 3.1 22.0 + - - +
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Residues in contact with LEU3980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3915B VAL* 4.6 12.7 - - + +
3960B LEU* 4.9 5.4 - - + -
3975B LEU* 3.7 42.8 - - + +
3978B SER* 3.3 7.5 + - - +
3979B ARG* 1.3 78.1 - - - +
3981B TRP* 1.3 62.2 + - - +
3983B ALA* 3.2 16.2 + - - +
3984B VAL* 3.6 16.3 + - - +
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Residues in contact with TRP3981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3975B LEU* 5.0 1.2 + - - +
3976B ALA 5.9 2.9 - - - +
3978B SER 4.7 2.9 + - - +
3979B ARG* 3.4 0.4 - - - +
3980B LEU* 1.3 78.5 - - - +
3982B ASP* 1.3 58.8 + - - +
3984B VAL* 3.2 23.6 - - + +
3985B VAL* 3.4 11.4 - - - +
4038B GLN* 5.6 5.8 - - + +
4042B MET* 5.0 17.0 - - + +
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Residues in contact with ASP3982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3919B LEU* 5.2 7.9 - - + +
3979B ARG* 3.2 25.4 + - + +
3980B LEU 3.2 1.0 - - - -
3981B TRP* 1.3 77.4 - - - +
3983B ALA* 1.3 58.7 + - - +
3985B VAL* 3.3 21.4 - - + +
3986B GLY* 3.8 6.1 + - - -
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Residues in contact with ALA3983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3918B LEU* 4.7 23.3 - - + +
3919B LEU* 5.2 6.7 - - + +
3922B GLN* 5.1 6.5 - - + +
3957B PHE* 5.7 1.3 - - + -
3979B ARG 3.1 10.8 + - - +
3980B LEU* 3.2 12.0 + - - +
3982B ASP* 1.3 79.2 - - - +
3984B VAL* 1.3 61.4 + - + +
3985B VAL 3.3 0.4 - - - -
3986B GLY* 3.4 2.0 + - - -
3987B PHE* 2.9 47.5 + - + -
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Residues in contact with VAL3984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957B PHE* 4.6 23.3 - - + -
3980B LEU 3.6 12.3 + - - +
3981B TRP* 3.2 23.8 - - + +
3983B ALA* 1.3 74.3 - - + +
3985B VAL* 1.3 57.7 + - + +
3987B PHE* 4.1 6.5 - - + -
3988B LEU* 2.7 46.9 + - + +
4018B MET* 5.1 12.3 - - + +
4022B LEU* 5.7 14.4 - - + -
4042B MET* 5.8 5.6 - - + -
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Residues in contact with VAL3985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3981B TRP 3.4 13.2 - - - +
3982B ASP* 3.3 22.4 - - + +
3984B VAL* 1.3 81.2 - - + +
3986B GLY* 1.3 63.0 + - - +
3988B LEU* 4.1 5.9 - - - +
3989B HIS* 3.3 22.9 + - - +
4042B MET* 5.4 5.8 - - + +
4045B GLU* 4.8 17.9 - - + +
4046B SER* 4.3 30.1 - - - +
4049B ASN* 4.8 8.2 - - - +
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Residues in contact with GLY3986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3922B GLN* 5.8 4.5 - - - -
3982B ASP 3.8 5.2 + - - -
3983B ALA 3.4 5.9 + - - -
3984B VAL 3.2 0.4 - - - -
3985B VAL* 1.3 84.8 - - - +
3987B PHE* 1.3 66.3 + - - +
3989B HIS* 3.6 5.6 + - - +
3990B VAL* 3.5 25.1 + - - +
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Residues in contact with PHE3987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3918B LEU* 4.5 8.7 - - + -
3921B LEU* 4.9 7.4 - - + -
3922B GLN* 3.6 39.7 - - + -
3925B ILE* 4.3 21.5 - - + -
3953B ALA* 5.8 2.2 - - + -
3957B PHE* 3.6 38.8 - + - -
3983B ALA* 2.9 32.7 + - + +
3984B VAL* 3.1 8.9 + - + +
3986B GLY* 1.3 73.7 - - - +
3988B LEU* 1.3 62.6 + - + +
3989B HIS 3.1 2.1 + - - -
3990B VAL* 3.2 9.4 + - + +
3991B PHE* 2.9 62.6 + + + -
4014B LEU* 6.3 1.8 - - + -
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Residues in contact with LEU3988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3984B VAL* 2.7 29.8 + - + +
3985B VAL* 4.3 5.6 - - - +
3987B PHE* 1.3 74.8 - - + +
3989B HIS* 1.3 61.1 + - - +
3991B PHE* 3.8 18.1 - - + +
3992B ALA* 3.2 24.1 + - - +
4015B GLN* 4.8 10.5 - - + -
4046B SER* 5.5 5.4 - - - -
4049B ASN* 4.7 15.3 - - + +
4050B VAL* 4.9 17.9 - - + -
4053B ILE* 5.6 12.1 - - + -
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Residues in contact with HIS3989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3930B TRP* 4.1 29.9 + + - -
3985B VAL 3.3 17.6 + - - +
3986B GLY* 3.8 8.1 - - - +
3987B PHE 3.1 0.8 - - - -
3988B LEU* 1.3 79.3 - - - +
3990B VAL* 1.3 64.5 + - + +
3992B ALA* 3.7 7.4 + - - +
3993B HIS* 3.5 47.4 + + - -
4049B ASN* 3.2 25.2 + - - +
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Residues in contact with VAL3990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925B ILE* 5.5 8.5 - - + -
3926B SER* 4.5 18.4 - - - +
3929B TYR* 4.5 16.6 - - + +
3930B TRP* 4.5 17.0 - - + -
3986B GLY 3.5 15.3 - - - +
3987B PHE* 3.2 17.2 + - + +
3989B HIS* 1.3 87.4 - - + +
3991B PHE* 1.3 83.4 + - + +
3993B HIS* 3.4 7.5 + - - +
3994B MET* 3.2 33.7 + - - +
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Residues in contact with PHE3991 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925B ILE* 5.5 7.2 - - + -
3946B PHE* 5.4 4.5 - + - -
3987B PHE* 2.9 55.2 + + + +
3988B LEU* 4.1 13.0 - - + +
3989B HIS 3.4 0.2 - - - -
3990B VAL* 1.3 88.6 - - + +
3992B ALA* 1.3 61.1 + - - +
3994B MET* 3.7 22.7 - - + -
3995B MET* 3.2 28.9 + - - +
4011B LEU* 4.1 12.5 - - + +
4014B LEU* 3.7 22.7 - - + -
4015B GLN* 3.1 45.5 - - + +
4053B ILE* 5.7 2.4 - - - +
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Residues in contact with ALA3992 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988B LEU 3.2 18.6 + - - +
3989B HIS* 3.7 6.7 + - - +
3990B VAL 3.3 0.6 - - - -
3991B PHE* 1.3 77.8 - - - +
3993B HIS* 1.3 66.2 + - + +
3995B MET* 4.6 2.2 - - - +
3996B MET* 3.3 27.1 - - - +
4049B ASN* 4.5 8.1 - - + +
4052B MET* 3.8 34.9 - - + +
4053B ILE* 5.0 10.3 - - + +
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Residues in contact with HIS3993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3930B TRP* 5.7 7.0 + - - -
3933B SER* 6.0 2.2 - - - +
3989B HIS* 3.5 46.8 + + - -
3990B VAL* 3.4 8.7 + - - +
3991B PHE 3.2 0.6 - - - -
3992B ALA* 1.3 90.1 - - + +
3994B MET* 1.3 63.2 + - - +
3995B MET 3.3 1.6 - - - -
3996B MET* 3.5 8.6 + - - +
3997B LYS* 3.4 28.8 + - + +
4052B MET* 5.7 11.0 - - + +
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Residues in contact with MET3994 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925B ILE* 5.3 3.8 - - + +
3928B PHE* 5.6 6.1 - - + -
3929B TYR* 5.4 12.6 - - + -
3946B PHE* 3.5 37.0 - - + -
3990B VAL* 3.2 26.3 + - - +
3991B PHE* 3.7 28.0 - - + +
3993B HIS* 1.3 76.7 - - - +
3995B MET* 1.3 63.8 + - - +
3996B MET 3.2 0.4 - - - -
3997B LYS* 4.3 10.3 - - + +
3998B LEU* 2.9 44.4 + - + +
4007B LEU* 5.8 0.7 - - + -
4011B LEU* 3.7 18.6 - - + -
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Residues in contact with MET3995 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3991B PHE 3.2 18.7 + - - +
3992B ALA* 5.0 1.6 - - - -
3993B HIS 3.3 0.4 - - - -
3994B MET* 1.3 84.0 - - + +
3996B MET* 1.3 61.8 + - + +
3998B LEU* 4.3 3.8 - - - +
3999B ALA* 3.3 24.4 + - - +
4008B LEU* 5.8 3.3 - - - +
4011B LEU* 5.5 7.9 - - + -
4053B ILE* 5.6 4.5 - - + -
4056B PHE* 3.7 27.9 - - + -
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Residues in contact with MET3996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3992B ALA 3.3 24.2 - - - +
3993B HIS* 3.5 8.3 + - - +
3994B MET 3.2 0.2 - - - -
3995B MET* 1.3 78.3 - - + +
3997B LYS* 1.3 62.7 + - + +
3999B ALA* 3.7 3.2 + - - +
4000B GLN* 3.6 19.2 + - - +
4052B MET* 4.6 28.0 - - + +
4056B PHE* 3.9 33.9 - - + -
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Residues in contact with LYS3997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3932B TYR 3.4 21.1 - - - -
3933B SER* 3.8 19.9 + - - +
3935B LYS 3.2 19.7 + - - -
3936B ASP* 3.7 18.5 + - - +
3938B ILE* 4.5 14.1 - - + -
3993B HIS* 3.4 18.4 - - + +
3994B MET* 3.2 13.7 + - + +
3996B MET* 1.3 77.5 - - + +
3998B LEU* 1.3 68.9 + - + +
3999B ALA 3.4 0.3 + - - -
4000B GLN* 3.4 16.1 + - - +
4001B ASP* 4.0 2.1 + - - +
4004B GLN* 3.8 10.1 + - - -
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Residues in contact with LEU3998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3938B ILE* 4.7 15.0 - - + -
3994B MET* 2.9 36.5 + - + +
3995B MET* 4.6 2.7 - - - +
3997B LYS* 1.3 82.9 - - + +
3999B ALA* 1.3 57.3 + - - +
4000B GLN 3.4 0.2 - - - -
4001B ASP 3.3 20.1 - - - +
4004B GLN* 3.4 52.9 - - + +
4005B ILE* 4.8 2.8 + - - +
4007B LEU* 3.6 40.2 - - + -
4008B LEU* 4.0 20.9 - - + +
4011B LEU* 5.5 1.3 - - + -
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Residues in contact with ALA3999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995B MET 3.3 19.9 + - - +
3996B MET* 4.1 5.6 - - - +
3997B LYS 3.2 0.8 - - - -
3998B LEU* 1.3 76.9 - - - +
4000B GLN* 1.3 63.6 + - - +
4001B ASP 3.3 3.8 + - - +
4002B SER* 4.9 1.9 + - - -
4005B ILE* 5.6 7.9 - - + -
4008B LEU* 5.3 2.2 - - + +
4056B PHE* 4.6 13.0 - - + -
4060B PHE* 5.1 10.5 - - + -
4127B PHE* 6.0 7.1 - - + -
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Residues in contact with GLN4000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3996B MET 3.6 10.5 + - - +
3997B LYS* 3.4 11.6 + - - +
3998B LEU 3.4 1.0 - - - -
3999B ALA* 1.3 80.6 - - - +
4001B ASP* 1.3 58.3 + - + +
4002B SER* 3.8 5.4 + - - -
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Residues in contact with ASP4001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3997B LYS 4.0 1.8 + - - +
3998B LEU 3.3 16.5 + - - +
3999B ALA 3.3 2.2 - - - +
4000B GLN* 1.3 77.6 - - - +
4002B SER* 1.3 64.4 + - - +
4003B SER* 3.3 6.9 + - - +
4004B GLN* 3.5 38.6 + - + +
4005B ILE* 4.1 1.4 + - - +
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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