Contacts of the helix formed by residues 4004 - 4026 (chain H) 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 GLN4004 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3937H VAL* 6.0 0.8 - - - +
3938H ILE* 3.7 37.8 + - - +
3997H LYS 3.8 5.3 + - - -
3998H LEU* 3.4 46.2 - - + +
4001H ASP* 3.6 35.2 - - + +
4002H SER 3.3 0.2 - - - -
4003H SER* 1.3 79.5 - - - +
4005H ILE* 1.3 61.1 + - - +
4006H GLU* 3.2 4.7 - - - +
4007H LEU* 3.4 14.9 + - + +
4008H LEU 3.7 6.8 + - - -
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Residues in contact with ILE4005 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3998H LEU 4.9 4.7 - - - +
3999H ALA* 5.6 5.6 - - + -
4001H ASP 4.1 3.2 + - - +
4002H SER* 3.9 19.2 + - - +
4003H SER 3.6 2.3 - - - +
4004H GLN* 1.3 75.1 - - - +
4006H GLU* 1.3 62.6 + - + +
4008H LEU* 3.2 18.4 + - + +
4009H LYS* 2.9 32.8 + - + +
4126H ARG* 5.3 8.3 - - + +
4127H PHE* 4.8 21.5 - - + -
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Residues in contact with GLU4006 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4003H SER 5.1 2.2 + - - +
4004H GLN* 3.2 3.0 - - - -
4005H ILE* 1.3 85.5 - - + +
4007H LEU* 1.3 60.5 + - - +
4009H LYS* 3.6 7.4 + - - +
4010H GLU* 3.4 20.6 + - - +
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Residues in contact with LEU4007 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3938H ILE* 5.4 6.1 - - + -
3943H LYS* 3.8 37.5 - - + +
3946H PHE* 4.0 23.3 - - + -
3947H SER* 6.0 3.1 - - - +
3994H MET* 5.8 0.9 - - + -
3998H LEU* 3.6 33.7 - - + -
4004H GLN* 3.4 15.6 + - + +
4005H ILE 3.2 0.6 - - - -
4006H GLU* 1.3 77.9 - - - +
4008H LEU* 1.3 60.2 + - - +
4010H GLU* 3.4 4.3 + - - +
4011H LEU* 2.8 49.1 + - + +
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Residues in contact with LEU4008 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995H MET* 5.8 3.6 - - - +
3998H LEU* 4.0 24.9 - - + +
3999H ALA* 5.3 2.2 - - + +
4004H GLN 3.7 4.0 + - - +
4005H ILE* 3.2 24.5 + - + +
4007H LEU* 1.3 82.0 - - - +
4009H LYS* 1.3 62.2 + - - +
4011H LEU* 3.8 7.2 - - - +
4012H LEU* 3.1 25.3 + - - +
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Residues in contact with LYS4009 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4005H ILE* 2.9 21.0 + - + +
4006H GLU* 3.8 9.2 - - - +
4007H LEU 3.2 0.2 - - - -
4008H LEU* 1.3 78.5 - - - +
4010H GLU* 1.3 59.8 + - - +
4012H LEU* 3.6 3.2 + - - +
4013H ASP* 2.9 29.8 + - - +
4130H PRO* 4.8 21.4 - - + +
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Residues in contact with GLU4010 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3947H SER* 5.9 5.6 - - - +
3950H MET* 5.2 12.8 - - + +
4006H GLU 3.4 11.7 + - - +
4007H LEU* 3.4 5.6 + - - +
4009H LYS* 1.3 78.3 - - - +
4011H LEU* 1.3 67.6 + - - +
4013H ASP* 3.4 23.9 + - - +
4014H LEU* 3.7 5.9 + - - +
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Residues in contact with LEU4011 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3946H PHE* 3.5 38.6 - - + -
3950H MET* 5.9 3.4 - - - -
3991H PHE* 4.1 19.3 - - + +
3994H MET* 3.7 27.4 - - + -
3995H MET* 5.5 7.6 - - + -
3998H LEU* 5.5 1.8 - - + -
4007H LEU* 2.8 26.8 + - + +
4008H LEU* 3.8 9.2 - - - +
4009H LYS 3.3 0.2 - - - -
4010H GLU* 1.3 77.2 - - - +
4012H LEU* 1.3 57.1 + - - +
4014H LEU* 2.9 24.4 + - + +
4015H GLN* 3.0 49.5 + - - +
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Residues in contact with LEU4012 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4008H LEU 3.1 17.0 + - - +
4009H LYS 4.0 4.3 - - - +
4010H GLU 3.4 0.2 - - - -
4011H LEU* 1.3 76.7 - - - +
4013H ASP* 1.3 62.6 + - - +
4014H LEU 3.3 0.5 + - - -
4015H GLN* 3.3 19.0 + - + +
4016H LYS* 3.4 20.1 + - + +
4057H PHE* 4.3 15.7 - - + -
4130H PRO* 3.5 42.6 - - + +
4131H ALA* 4.0 4.0 - - + +
4134H ILE* 3.7 33.9 - - + -
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Residues in contact with ASP4013 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954H LYS* 5.3 12.8 - - + +
4009H LYS 2.9 19.8 - - - +
4010H GLU* 3.5 17.1 - - - +
4011H LEU 3.1 0.8 - - - -
4012H LEU* 1.3 78.0 - - - +
4014H LEU* 1.3 57.7 + - - +
4016H LYS* 3.2 32.2 - - - +
4017H ASP* 2.8 30.6 - - - +
4130H PRO* 5.2 6.9 - - - +
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Residues in contact with LEU4014 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925H ILE* 5.8 3.8 - - + -
3946H PHE* 6.2 3.1 - - + -
3950H MET* 5.2 13.9 - - + +
3953H ALA* 3.4 44.6 - - + +
3954H LYS* 4.2 9.9 - - + +
3957H PHE* 3.9 19.1 - - + -
3987H PHE* 6.3 1.3 - - + -
3991H PHE* 3.7 30.1 - - + -
4010H GLU 3.7 5.4 + - - +
4011H LEU* 2.9 16.1 + - + +
4013H ASP* 1.3 78.2 - - - +
4015H GLN* 1.3 68.6 + - - +
4017H ASP* 3.3 8.7 + - + +
4018H MET* 3.3 17.1 + - + +
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Residues in contact with GLN4015 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988H LEU* 4.8 11.0 - - + -
3991H PHE* 3.1 49.9 - - + +
4011H LEU* 3.0 40.9 + - - +
4012H LEU* 3.3 29.0 + - + +
4014H LEU* 1.3 80.6 - - - +
4016H LYS* 1.3 57.8 + - - +
4018H MET* 3.2 7.3 + - - +
4019H VAL* 2.9 31.2 + - - +
4134H ILE* 4.8 7.9 - - + -
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Residues in contact with LYS4016 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954H LYS* 5.6 4.2 - - - +
4012H LEU* 3.4 8.0 + - + +
4013H ASP* 3.2 47.2 + - - +
4015H GLN* 1.3 77.7 - - - +
4017H ASP* 1.3 82.8 + - - +
4019H VAL 4.1 0.2 - - - -
4020H VAL* 3.7 10.9 + - - +
4130H PRO 6.0 0.7 - - - +
4133H ASP* 3.7 41.6 + - + +
4134H ILE* 4.5 15.4 - - + +
4137H ASN* 3.3 24.2 + - - +
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Residues in contact with ASP4017 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954H LYS* 3.5 33.2 - - - +
3957H PHE* 4.3 19.9 - - + +
3958H ASN* 4.1 19.1 - - - +
3961H THR* 5.5 1.7 - - - +
4013H ASP 2.8 16.8 - - - +
4014H LEU* 3.3 7.6 + - + +
4015H GLN 3.2 0.6 - - - -
4016H LYS* 1.3 101.4 + - - +
4018H MET* 1.3 58.3 + - - +
4020H VAL* 3.3 21.7 - - + +
4021H MET* 4.2 4.9 + - - +
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Residues in contact with MET4018 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3957H PHE* 3.7 36.9 - - + -
3984H VAL* 5.1 10.0 - - + +
4014H LEU* 3.3 11.6 + - + +
4015H GLN* 3.2 11.1 + - - +
4017H ASP* 1.3 77.1 - - - +
4019H VAL* 1.3 63.5 + - - +
4020H VAL 3.3 1.6 - - - -
4021H MET* 3.3 13.7 + - - +
4022H LEU* 3.3 14.8 - - - +
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Residues in contact with VAL4019 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4015H GLN 2.9 16.3 + - - +
4016H LYS 4.0 0.2 + - - -
4018H MET* 1.3 76.2 - - - +
4020H VAL* 1.3 62.8 + - - +
4021H MET 3.3 0.7 + - - -
4022H LEU* 3.4 22.7 + - + +
4023H LEU* 3.5 15.2 + - - +
4134H ILE* 4.6 10.8 - - + -
4137H ASN* 4.1 20.4 - - - +
4138H VAL* 6.0 0.2 - - + -
4141H LEU* 4.3 17.8 - - + +
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Residues in contact with VAL4020 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3961H THR* 5.0 11.4 - - + +
4016H LYS 3.7 11.8 + - - +
4017H ASP* 3.3 24.0 - - + +
4019H VAL* 1.3 76.5 - - - +
4021H MET* 1.3 66.2 + - - +
4022H LEU 3.3 0.2 - - - -
4023H LEU* 3.2 32.3 + - + +
4024H SER* 3.2 16.0 + - - +
4137H ASN* 4.3 6.0 - - - +
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Residues in contact with MET4021 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3957H PHE* 5.3 9.4 - - + +
3960H LEU* 5.9 4.7 - - + -
3961H THR* 4.7 17.2 - - - +
3964H ILE* 6.0 0.5 - - - +
4017H ASP 4.6 5.4 - - - +
4018H MET* 3.3 16.3 + - - +
4019H VAL 3.2 0.8 - - - -
4020H VAL* 1.3 83.1 - - - +
4022H LEU* 1.3 57.8 + - + +
4024H SER* 3.2 10.0 + - - -
4025H LEU* 3.1 26.5 + - - +
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Residues in contact with LEU4022 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3984H VAL* 5.7 14.8 - - + -
4018H MET 3.3 21.3 - - - +
4019H VAL* 3.4 17.7 - - + +
4021H MET* 1.3 75.8 - - + +
4023H LEU* 1.3 68.4 + - + +
4025H LEU* 3.3 21.9 + - + +
4026H LEU* 3.4 15.8 + - - +
4039H MET* 4.0 30.9 - - + +
4042H MET* 6.5 1.6 - - + -
4141H LEU* 5.6 6.7 - - + -
4144H ASN* 5.9 0.3 + - - -
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Residues in contact with LEU4023 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4019H VAL 3.5 12.8 - - - +
4020H VAL* 3.2 24.4 + - + +
4022H LEU* 1.3 79.0 - - + +
4024H SER* 1.3 61.3 + - - +
4025H LEU 3.3 0.9 + - - -
4026H LEU* 3.4 11.7 + - - +
4027H GLU* 3.4 12.3 + - - +
4137H ASN* 3.3 25.6 - - - +
4140H VAL* 4.3 13.2 - - + +
4141H LEU* 3.7 36.3 - - + +
4144H ASN* 5.7 8.1 - - + +
4189H TYR 5.9 2.5 - - - +
5002H THR* 5.7 0.2 - - - -
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Residues in contact with SER4024 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3961H THR* 3.5 22.2 + - - -
3964H ILE* 3.2 28.2 + - - +
3965H GLN* 4.5 12.0 - - - +
3966H GLY 5.4 0.5 - - - +
3972H GLN* 5.3 2.3 - - - +
4020H VAL* 3.2 11.4 + - - -
4021H MET* 3.2 13.5 + - - -
4023H LEU* 1.3 76.1 - - - +
4025H LEU* 1.3 61.3 + - - +
4026H LEU 3.3 0.4 + - - -
4027H GLU* 3.8 14.2 + - - +
5002H THR* 4.4 18.8 - - - -
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Residues in contact with LEU4025 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3964H ILE* 5.1 10.1 - - + -
3972H GLN* 4.0 32.8 + - + +
3975H LEU* 3.7 30.5 - - + -
3976H ALA* 6.0 3.4 - - + +
4021H MET 3.1 17.8 + - - +
4022H LEU* 3.5 13.9 - - + +
4023H LEU 3.1 0.8 - - - -
4024H SER* 1.3 80.0 - - - +
4026H LEU* 1.3 63.5 + - + +
4027H GLU 3.5 1.1 + - - -
4035H ILE* 4.2 19.3 - - + +
4039H MET* 3.7 39.5 - - + -
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Residues in contact with LEU4026 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4022H LEU 3.4 12.0 + - - +
4023H LEU* 3.6 5.5 - - - +
4024H SER 3.3 0.2 - - - -
4025H LEU* 1.3 84.0 - - + +
4027H GLU* 1.3 66.4 + - - +
4028H GLY 3.6 1.1 - - - -
4029H ASN* 3.7 30.4 + - + +
4030H VAL 5.0 1.1 - - - +
4035H ILE* 4.9 6.3 - - + -
4036H ALA* 4.1 27.1 - - + +
4039H MET* 3.7 24.0 - - + -
4144H ASN* 4.1 18.0 + - - +
4145H LEU* 5.5 6.1 - - + -
4148H HIS* 3.5 38.2 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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