Contacts of the helix formed by residues 4004 - 4026 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3937D VAL* 6.0 0.8 - - - +
3938D ILE* 3.7 37.7 + - - +
3997D LYS 3.8 5.3 + - - -
3998D LEU* 3.4 46.2 - - + +
4001D ASP* 3.6 34.4 - - + +
4003D SER* 1.3 80.1 - - - +
4005D ILE* 1.3 61.9 + - - +
4006D GLU* 3.2 4.3 - - - +
4007D LEU* 3.4 15.1 + - + +
4008D LEU 3.7 6.4 + - - -
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Residues in contact with ILE4005 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3998D LEU 4.9 5.4 - - - +
3999D ALA* 5.6 5.6 - - + -
4001D ASP 4.1 3.2 + - - +
4002D SER* 3.9 17.9 + - - +
4003D SER 3.6 2.2 - - - +
4004D GLN* 1.3 75.9 - - - +
4006D GLU* 1.3 63.3 + - + +
4008D LEU* 3.2 17.3 + - + +
4009D LYS* 2.9 32.7 + - + +
4126D ARG 5.3 8.1 - - - +
4127D PHE* 4.8 21.1 - - + -
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Residues in contact with GLU4006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4003D SER 5.1 2.2 + - - +
4004D GLN* 3.2 2.6 - - - -
4005D ILE* 1.3 85.5 - - + +
4007D LEU* 1.3 60.0 + - - +
4009D LYS* 3.8 6.4 - - - +
4010D GLU* 3.4 20.8 + - - +
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Residues in contact with LEU4007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3938D ILE* 5.4 7.0 - - + -
3943D LYS* 3.8 38.1 - - + +
3946D PHE* 4.0 24.6 - - + -
3947D SER* 6.0 2.7 - - - +
3994D MET* 5.8 0.4 - - + -
3998D LEU* 3.6 34.3 - - + -
4004D GLN* 3.4 15.0 + - + +
4005D ILE 3.2 0.6 - - - -
4006D GLU* 1.3 76.8 - - - +
4008D LEU* 1.3 58.9 + - - +
4010D GLU* 3.4 5.1 + - - +
4011D LEU* 2.8 48.4 + - + +
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Residues in contact with LEU4008 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995D MET* 5.8 4.0 - - - +
3998D LEU* 4.0 24.7 - - + +
3999D ALA* 5.3 1.8 - - + +
4004D GLN 3.7 4.0 + - - +
4005D ILE* 3.2 24.1 + - + +
4007D LEU* 1.3 81.5 - - - +
4009D LYS* 1.3 61.4 + - - +
4011D LEU* 3.8 7.9 - - - +
4012D LEU* 3.1 25.5 + - - +
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Residues in contact with LYS4009 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4005D ILE* 2.9 21.8 + - + +
4006D GLU* 3.8 8.5 - - - +
4007D LEU 3.2 0.2 - - - -
4008D LEU* 1.3 78.5 - - - +
4010D GLU* 1.3 60.0 + - - +
4012D LEU* 3.6 3.2 + - - +
4013D ASP* 2.9 30.6 + - - +
4130D PRO* 4.8 21.7 - - + +
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Residues in contact with GLU4010 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3947D SER* 5.9 5.2 - - - +
3950D MET* 5.2 12.9 - - + +
4006D GLU 3.4 12.0 + - - +
4007D LEU* 3.4 5.4 + - - +
4009D LYS* 1.3 76.5 - - - +
4011D LEU* 1.3 67.5 + - - +
4013D ASP* 3.4 22.8 + - - +
4014D LEU* 3.7 5.5 + - - +
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Residues in contact with LEU4011 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3946D PHE* 3.5 37.0 - - + -
3950D MET* 5.9 3.6 - - - -
3991D PHE* 4.1 18.4 - - + +
3994D MET* 3.7 27.8 - - + -
3995D MET* 5.5 8.1 - - + -
3998D LEU* 5.5 2.2 - - + -
4007D LEU* 2.8 27.5 + - + +
4008D LEU* 3.8 8.5 - - - +
4009D LYS 3.3 0.2 - - - -
4010D GLU* 1.3 77.7 - - - +
4012D LEU* 1.3 58.3 + - - +
4014D LEU* 2.9 24.7 + - + +
4015D GLN* 3.0 50.9 + - - +
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Residues in contact with LEU4012 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4008D LEU 3.1 17.6 + - - +
4009D LYS 3.6 4.7 + - - +
4011D LEU* 1.3 77.1 - - - +
4013D ASP* 1.3 62.1 + - - +
4014D LEU 3.1 0.9 + - - -
4015D GLN* 3.3 19.7 + - + +
4016D LYS* 3.4 19.7 + - + +
4057D PHE* 4.3 15.0 - - + -
4130D PRO* 3.5 43.1 - - + +
4131D ALA* 4.0 4.3 - - + +
4134D ILE* 3.7 33.4 - - + -
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Residues in contact with ASP4013 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954D LYS* 5.3 13.2 - - + +
4009D LYS 2.9 19.6 - - - +
4010D GLU* 3.5 16.3 - - - +
4011D LEU 3.1 1.2 - - - -
4012D LEU* 1.3 79.2 - - - +
4014D LEU* 1.3 57.8 + - - +
4016D LYS* 3.2 31.8 - - - +
4017D ASP* 2.8 30.5 - - - +
4130D PRO* 5.2 7.1 - - - +
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Residues in contact with LEU4014 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925D ILE* 5.8 3.6 - - + -
3946D PHE* 6.2 2.7 - - + -
3950D MET* 5.2 14.4 - - + +
3953D ALA* 3.4 44.9 - - + +
3954D LYS* 4.2 8.5 - - + -
3957D PHE* 3.9 19.5 - - + -
3987D PHE* 6.3 2.2 - - + -
3991D PHE* 3.7 28.9 - - + -
4010D GLU 3.7 5.1 + - - +
4011D LEU* 2.9 16.5 + - + +
4013D ASP* 1.3 78.1 - - - +
4015D GLN* 1.3 69.5 + - - +
4017D ASP* 3.3 9.1 + - + +
4018D MET* 3.3 16.8 + - + +
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Residues in contact with GLN4015 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988D LEU* 4.8 10.5 - - + -
3991D PHE* 3.1 51.2 - - + +
4011D LEU* 3.0 40.4 + - - +
4012D LEU* 3.3 28.9 + - + +
4014D LEU* 1.3 79.5 - - - +
4016D LYS* 1.3 58.2 + - - +
4018D MET* 3.2 7.0 + - - +
4019D VAL* 2.9 31.0 + - - +
4134D ILE* 4.7 8.0 - - + +
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Residues in contact with LYS4016 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954D LYS* 5.6 4.4 - - - +
4012D LEU* 3.4 7.7 + - + +
4013D ASP* 3.2 46.1 + - - +
4015D GLN* 1.3 78.7 - - - +
4017D ASP* 1.3 83.1 + - - +
4019D VAL 4.1 0.4 - - - -
4020D VAL* 3.7 11.6 + - - +
4130D PRO 6.0 0.7 - - - +
4133D ASP* 3.7 40.3 + - + +
4134D ILE* 4.5 16.3 - - + +
4137D ASN* 3.3 23.9 + - - +
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Residues in contact with ASP4017 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954D LYS* 3.5 33.6 - - + +
3957D PHE* 4.3 19.5 - - + +
3958D ASN* 4.1 18.9 - - - +
3961D THR* 5.5 1.9 - - - +
4013D ASP 2.8 18.2 - - - +
4014D LEU* 3.3 7.8 + - + +
4015D GLN 3.2 0.6 - - - -
4016D LYS* 1.3 100.9 + - - +
4018D MET* 1.3 58.3 + - - +
4020D VAL* 3.3 21.3 - - + +
4021D MET* 4.2 4.7 + - - +
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Residues in contact with MET4018 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3957D PHE* 3.7 36.5 - - + -
3984D VAL* 5.1 10.7 - - + +
4014D LEU* 3.3 11.2 + - + +
4015D GLN* 3.2 11.5 + - - +
4017D ASP* 1.3 77.4 - - - +
4019D VAL* 1.3 63.9 + - - +
4020D VAL 3.2 1.8 - - - -
4021D MET* 3.3 13.4 + - - +
4022D LEU* 3.3 14.8 - - - +
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Residues in contact with VAL4019 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4015D GLN 2.9 16.3 + - - +
4016D LYS 4.0 0.2 + - - -
4017D ASP 3.6 0.2 - - - -
4018D MET* 1.3 75.5 - - - +
4020D VAL* 1.3 62.5 + - - +
4021D MET 3.3 0.3 + - - -
4022D LEU* 3.4 22.7 + - + +
4023D LEU* 3.5 14.4 + - - +
4134D ILE* 4.6 10.8 - - + -
4137D ASN* 4.1 20.6 - - - +
4138D VAL* 6.0 0.2 - - + -
4141D LEU* 4.3 17.3 - - + +
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Residues in contact with VAL4020 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3961D THR* 4.9 11.4 + - + +
4016D LYS 3.7 10.9 + - - +
4017D ASP* 3.3 24.2 - - - +
4019D VAL* 1.3 76.1 - - - +
4021D MET* 1.3 66.6 + - - +
4022D LEU 3.3 0.2 - - - -
4023D LEU* 3.2 32.5 + - + -
4024D SER* 3.2 15.2 + - - -
4137D ASN* 4.3 5.6 - - - +
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Residues in contact with MET4021 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3957D PHE* 5.3 10.5 - - + +
3960D LEU* 5.9 4.5 - - + -
3961D THR* 4.7 16.8 - - - +
3964D ILE* 6.0 0.7 - - - +
4017D ASP 4.6 4.7 - - - +
4018D MET* 3.3 17.1 + - - +
4019D VAL 3.2 1.0 - - - -
4020D VAL* 1.3 84.1 - - - +
4022D LEU* 1.3 58.1 + - + +
4024D SER* 3.2 9.5 + - - -
4025D LEU* 3.1 26.9 + - - +
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Residues in contact with LEU4022 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3984D VAL* 5.7 14.6 - - + -
4018D MET 3.3 21.1 - - - +
4019D VAL* 3.4 17.7 - - + +
4020D VAL 3.3 0.2 - - - -
4021D MET* 1.3 75.1 - - + +
4023D LEU* 1.3 68.6 + - + +
4025D LEU* 3.3 20.3 + - + +
4026D LEU* 3.4 15.6 + - - +
4039D MET* 4.0 29.4 - - + +
4042D MET* 6.5 1.3 - - + -
4141D LEU* 5.6 6.1 - - + -
4144D ASN* 5.9 0.2 + - - -
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Residues in contact with LEU4023 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4019D VAL 3.5 12.1 - - - +
4020D VAL* 3.2 24.8 + - + +
4022D LEU* 1.3 79.6 - - + +
4024D SER* 1.3 60.8 + - - +
4025D LEU 3.3 0.7 + - - -
4026D LEU* 3.4 12.5 + - - +
4027D GLU* 3.4 11.8 + - - +
4137D ASN* 3.3 25.8 - - - +
4140D VAL* 4.3 12.3 - - + +
4141D LEU* 3.7 37.0 - - + +
4144D ASN* 5.7 7.9 - - + +
4189D TYR 5.9 2.5 - - - +
5002D THR* 5.7 0.2 - - - -
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Residues in contact with SER4024 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3961D THR* 3.5 22.5 + - - -
3964D ILE* 3.2 28.7 + - - +
3965D GLN* 4.5 11.8 - - - +
3966D GLY 5.4 0.3 - - - +
3972D GLN* 5.3 2.4 - - - +
4020D VAL* 3.2 11.2 + - - -
4021D MET* 3.2 13.0 + - - -
4023D LEU* 1.3 77.4 - - - +
4025D LEU* 1.3 61.1 + - - +
4026D LEU 3.3 0.4 - - - -
4027D GLU* 3.8 15.2 + - - +
5002D THR* 4.4 18.4 - - - -
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Residues in contact with LEU4025 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3964D ILE* 5.1 10.1 - - + -
3972D GLN* 4.0 32.5 + - + +
3975D LEU* 3.7 31.6 - - + -
3976D ALA* 6.0 3.6 - - + +
4021D MET 3.1 19.1 + - - +
4022D LEU* 3.5 13.7 - - + +
4023D LEU 3.1 0.8 - - - -
4024D SER* 1.3 80.3 - - - +
4026D LEU* 1.3 62.6 + - + +
4027D GLU 3.5 1.1 + - - -
4035D ILE* 4.2 18.9 - - + +
4039D MET* 3.7 38.4 - - + -
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Residues in contact with LEU4026 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4022D LEU 3.4 11.9 + - - +
4023D LEU 3.6 5.3 - - - +
4024D SER 3.3 0.2 - - - -
4025D LEU* 1.3 85.4 - - + +
4027D GLU* 1.3 64.1 + - - +
4028D GLY 3.6 1.5 - - - -
4029D ASN* 3.7 30.0 + - + +
4030D VAL 5.0 1.3 - - - +
4035D ILE* 4.9 6.3 - - + -
4036D ALA* 4.1 27.4 - - + +
4039D MET* 3.7 24.2 - - + -
4144D ASN* 4.1 17.3 + - - +
4145D LEU* 5.5 6.5 - - + -
4148D HIS* 3.5 37.7 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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