Contacts of the helix formed by residues 3979 - 4001 (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 ARG3979 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3915D VAL* 5.0 9.1 - - + +
3919D LEU* 4.0 32.9 - - + +
3978D SER* 1.3 74.9 - - - +
3980D LEU* 1.3 62.4 + - - +
3981D TRP 3.4 2.2 - - - -
3982D ASP* 3.2 16.2 + - + +
3983D ALA* 3.1 22.0 + - - +
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Residues in contact with LEU3980 (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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3915D VAL* 4.6 12.3 - - + +
3960D LEU* 4.9 5.4 - - + -
3975D LEU* 3.7 43.1 - - + +
3978D SER* 3.3 8.1 + - - +
3979D ARG* 1.3 77.0 - - - +
3981D TRP* 1.3 62.1 + - - +
3983D ALA* 3.2 16.1 + - - +
3984D VAL* 3.6 15.6 + - - +
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Residues in contact with TRP3981 (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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3975D LEU* 5.0 1.6 + - - +
3976D ALA 5.9 2.5 - - - +
3978D SER 4.7 2.8 + - - +
3979D ARG 3.4 0.4 - - - -
3980D LEU* 1.3 78.9 - - - +
3982D ASP* 1.3 57.9 + - - +
3984D VAL* 3.2 24.3 - - + +
3985D VAL* 3.4 11.4 - - - +
4038D GLN* 5.6 5.6 - - + +
4042D MET* 5.0 17.7 - - + +
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Residues in contact with ASP3982 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3919D LEU* 5.2 6.7 - - + +
3978D SER 5.5 0.2 + - - -
3979D ARG* 3.2 24.7 + - + +
3980D LEU 3.2 1.2 - - - -
3981D TRP* 1.3 77.0 - - - +
3983D ALA* 1.3 60.2 + - - +
3984D VAL 3.6 0.2 - - - -
3985D VAL* 3.3 20.4 - - + +
3986D GLY* 3.8 5.7 + - - -
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Residues in contact with ALA3983 (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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3918D LEU* 4.7 24.5 - - + +
3919D LEU* 5.2 6.7 - - + +
3922D GLN* 5.1 5.9 - - + +
3957D PHE* 5.7 1.3 - - + -
3979D ARG 3.1 10.6 + - - +
3980D LEU* 3.2 12.5 + - - +
3982D ASP* 1.3 79.3 - - - +
3984D VAL* 1.3 60.6 + - + +
3985D VAL 3.3 0.4 - - - -
3986D GLY* 3.4 2.3 + - - -
3987D PHE* 2.9 47.4 + - + -
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Residues in contact with VAL3984 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957D PHE* 4.6 22.7 - - + -
3980D LEU 3.6 12.1 + - - +
3981D TRP* 3.2 23.3 - - + +
3983D ALA* 1.3 76.9 - - + +
3985D VAL* 1.3 57.4 + - + +
3987D PHE* 3.6 7.4 - - + +
3988D LEU* 2.7 47.0 + - + +
4018D MET* 5.1 12.8 - - + +
4022D LEU* 5.7 13.5 - - + -
4042D MET* 5.8 5.6 - - + -
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Residues in contact with VAL3985 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3981D TRP 3.4 13.9 - - - +
3982D ASP* 3.3 22.0 - - + +
3984D VAL* 1.3 82.0 - - + +
3986D GLY* 1.3 63.1 + - - +
3988D LEU* 4.1 5.9 - - - +
3989D HIS* 3.3 22.5 + - - +
4042D MET* 5.4 4.9 - - + +
4045D GLU* 4.8 17.9 - - + +
4046D SER* 4.3 29.8 - - - +
4049D ASN* 4.8 7.8 - - - +
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Residues in contact with GLY3986 (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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3922D GLN* 5.8 5.4 - - - -
3982D ASP 3.8 5.4 + - - -
3983D ALA* 3.4 5.7 + - - -
3984D VAL 3.2 0.2 - - - -
3985D VAL* 1.3 85.8 - - - +
3987D PHE* 1.3 64.6 - - - +
3989D HIS* 3.6 6.0 + - - +
3990D VAL* 3.5 25.1 + - - +
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Residues in contact with PHE3987 (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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3918D LEU* 4.5 8.3 - - + -
3921D LEU* 4.9 7.2 - - + -
3922D GLN* 3.6 39.9 - - + -
3925D ILE* 4.3 22.2 - - + -
3953D ALA* 5.8 2.0 - - + -
3957D PHE* 3.6 39.3 - + - -
3983D ALA* 2.9 32.2 + - + +
3984D VAL* 3.1 8.7 + - + +
3986D GLY* 1.3 73.9 - - - +
3988D LEU* 1.3 61.6 + - + +
3989D HIS 3.1 2.1 + - - -
3990D VAL* 3.2 9.6 + - + +
3991D PHE* 2.9 62.0 + + + -
4014D LEU* 6.3 1.3 - - + -
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Residues in contact with LEU3988 (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* 2.7 31.3 + - + +
3985D VAL* 4.3 5.6 - - - +
3987D PHE* 1.3 74.4 - - + +
3989D HIS* 1.3 60.8 + - - +
3991D PHE* 3.8 18.1 - - + +
3992D ALA* 3.2 24.8 + - - +
4015D GLN* 4.8 10.3 - - + -
4046D SER* 5.5 5.6 - - - -
4049D ASN* 4.7 14.8 - - + +
4050D VAL* 4.9 17.5 - - + -
4053D ILE* 5.6 12.1 - - + -
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Residues in contact with HIS3989 (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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3930D TRP* 4.1 30.8 + + - -
3985D VAL 3.3 18.0 + - - +
3986D GLY* 3.8 7.6 - - - +
3987D PHE 3.1 1.2 - - - -
3988D LEU* 1.3 80.1 - - - +
3990D VAL* 1.3 64.9 - - + +
3992D ALA* 3.7 7.0 + - - +
3993D HIS* 3.5 46.9 + + - -
4049D ASN* 3.2 25.4 + - - +
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Residues in contact with VAL3990 (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* 5.5 9.0 - - + -
3926D SER* 4.5 18.8 - - - -
3929D TYR* 4.5 17.0 - - + +
3930D TRP* 4.5 16.8 - - + -
3986D GLY 3.5 14.1 - - - +
3987D PHE* 3.2 17.2 + - + +
3989D HIS* 1.3 86.9 - - + +
3991D PHE* 1.3 83.2 + - + +
3992D ALA 3.3 0.2 - - - -
3993D HIS* 3.4 8.6 + - - +
3994D MET* 3.2 31.9 + - - +
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Residues in contact with PHE3991 (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* 5.5 7.2 - - + -
3946D PHE* 5.4 4.0 - + - -
3987D PHE* 2.9 55.6 + + + +
3988D LEU* 4.1 13.0 - - + +
3990D VAL* 1.3 87.5 - - + +
3992D ALA* 1.3 61.0 + - - +
3993D HIS 3.2 0.2 - - - -
3994D MET* 3.7 22.3 - - + +
3995D MET* 3.2 28.8 + - - +
4011D LEU* 4.1 12.3 - - + -
4014D LEU* 3.7 24.0 - - + -
4015D GLN* 3.1 46.7 - - + +
4053D ILE* 5.7 2.5 - - - +
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Residues in contact with ALA3992 (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 3.2 18.9 + - - +
3989D HIS* 4.0 5.8 - - - +
3990D VAL 3.3 0.6 - - - -
3991D PHE* 1.3 76.9 - - - +
3993D HIS* 1.3 66.7 + - + +
3995D MET* 5.0 2.2 - - - +
3996D MET* 3.3 27.6 - - - +
4049D ASN* 4.5 7.2 - - - +
4052D MET* 3.8 35.0 - - + +
4053D ILE* 5.0 10.1 - - + +
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Residues in contact with HIS3993 (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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3930D TRP* 5.7 6.8 + - - -
3933D SER* 6.0 2.2 - - - +
3989D HIS* 3.5 44.9 + + - -
3990D VAL* 3.4 8.8 + - - +
3991D PHE 3.2 0.4 - - - -
3992D ALA* 1.3 89.9 - - + +
3994D MET* 1.3 64.4 + - - +
3995D MET 3.3 1.6 - - - -
3996D MET* 3.5 9.4 + - - +
3997D LYS* 3.4 28.0 + - + +
4052D MET* 5.7 10.9 - - + +
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Residues in contact with MET3994 (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* 5.3 3.6 - - + +
3928D PHE* 5.6 6.1 - - + -
3929D TYR* 5.4 12.3 - - + -
3946D PHE* 3.5 38.4 - - + -
3990D VAL* 3.2 27.2 + - - +
3991D PHE* 3.7 27.4 - - + -
3993D HIS* 1.3 75.7 - - - +
3995D MET* 1.3 63.7 + - - +
3996D MET 3.2 0.7 - - - -
3997D LYS* 4.3 11.2 - - + +
3998D LEU* 2.9 46.2 + - + +
4007D LEU* 5.8 0.4 - - + -
4011D LEU* 3.7 18.2 - - + -
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Residues in contact with MET3995 (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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3991D PHE 3.2 18.1 + - - +
3992D ALA* 5.0 1.3 - - - -
3993D HIS 3.3 0.6 - - - -
3994D MET* 1.3 83.4 - - + +
3996D MET* 1.3 61.6 + - + +
3998D LEU* 4.6 3.9 - - - +
3999D ALA* 3.3 24.4 + - - +
4008D LEU* 5.8 3.7 - - - +
4011D LEU* 5.5 8.1 - - + -
4053D ILE* 5.6 4.7 - - + -
4056D PHE* 3.7 27.4 - - + -
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Residues in contact with MET3996 (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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3992D ALA 3.3 23.8 - - - +
3993D HIS* 3.5 7.6 + - - +
3994D MET 3.2 0.2 - - - -
3995D MET* 1.3 77.9 - - + +
3997D LYS* 1.3 63.7 + - + +
3999D ALA* 3.7 3.1 + - - +
4000D GLN* 3.6 19.4 + - - +
4052D MET* 4.6 27.8 - - + +
4056D PHE* 3.9 32.5 - - + -
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Residues in contact with LYS3997 (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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3932D TYR 3.4 20.6 - - - -
3933D SER* 3.8 20.7 + - - +
3935D LYS 3.2 20.3 + - - -
3936D ASP* 3.7 19.5 + - - +
3938D ILE* 4.5 13.5 - - + -
3993D HIS* 3.4 19.5 + - + +
3994D MET* 3.2 12.4 + - + +
3996D MET* 1.3 78.9 - - + +
3998D LEU* 1.3 70.1 + - + +
3999D ALA 3.4 0.7 + - - -
4000D GLN* 3.4 16.6 + - - +
4001D ASP* 4.0 1.9 + - - +
4004D GLN* 3.8 10.0 + - - -
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Residues in contact with LEU3998 (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* 4.7 15.5 - - + -
3994D MET* 2.9 35.9 + - + +
3995D MET* 4.6 2.2 - - - +
3997D LYS* 1.3 83.4 - - + +
3999D ALA* 1.3 57.4 + - - +
4000D GLN 3.4 0.2 - - - -
4001D ASP 3.3 20.2 - - - +
4004D GLN* 3.4 52.6 - - + +
4005D ILE* 4.8 2.8 + - - +
4007D LEU* 3.6 40.4 - - + -
4008D LEU* 4.0 20.4 - - + +
4011D LEU* 5.5 2.0 - - + -
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Residues in contact with ALA3999 (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 3.3 19.5 + - - +
3996D MET* 4.1 5.2 - - - +
3997D LYS 3.2 1.0 - - - -
3998D LEU* 1.3 77.1 - - - +
4000D GLN* 1.3 64.3 + - - +
4001D ASP 3.3 4.0 - - - +
4002D SER* 5.4 2.1 + - - -
4005D ILE* 5.6 8.3 - - + -
4008D LEU* 5.6 2.0 - - + -
4056D PHE* 4.6 13.5 - - + -
4060D PHE* 5.1 9.6 - - + -
4127D PHE* 6.0 6.9 - - + -
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Residues in contact with GLN4000 (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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3996D MET 3.6 10.5 + - - +
3997D LYS* 3.4 11.4 + - - +
3998D LEU 3.4 0.6 - - - -
3999D ALA* 1.3 80.4 - - - +
4001D ASP* 1.3 57.6 + - + +
4002D SER* 3.8 5.2 + - - -
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Residues in contact with ASP4001 (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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3997D LYS 4.0 2.1 + - - +
3998D LEU 3.3 16.8 + - - +
3999D ALA 3.3 3.1 - - - +
4000D GLN* 1.3 77.3 - - - +
4002D SER* 1.3 64.0 + - - +
4003D SER* 3.3 7.2 + - - +
4004D GLN* 3.5 37.9 + - + +
4005D ILE* 4.1 1.6 + - - +
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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
------------------------------------------------------------
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