Contacts of the helix formed by residues 3876 - 3895 (chain A) in PDB entry 5NUG
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 LEU3876 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3822A HIS* 2.8 48.9 - - + +
3824A LEU* 4.7 0.4 - - + -
3825A TYR* 3.7 7.3 - - + -
3875A MET* 1.3 77.9 - - - +
3877A HIS* 1.3 64.2 + - - +
3878A GLN* 3.2 4.9 - - + +
3879A ASP* 3.1 27.5 + - - +
3880A HIS* 3.2 12.7 + - - +
4046A VAL* 4.0 11.7 - - + -
4130A ILE* 4.0 17.3 - - + -
4146A VAL* 3.7 24.2 - - + -
4148A GLU* 3.5 14.8 - - + -
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Residues in contact with HIS3877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3876A LEU* 1.3 72.0 - - - +
3878A GLN* 1.3 61.5 + - + +
3880A HIS* 3.3 41.1 + + - +
3881A ILE* 4.5 17.3 + - + +
4006A HIS* 5.7 3.7 + - - -
4018A MET* 6.1 0.7 - - + -
4021A MET* 5.9 6.4 - - + +
4022A GLU* 5.7 9.0 - - + -
4148A GLU* 2.7 24.8 + - + +
4151A PRO* 3.6 41.6 - - + +
4195A ARG* 5.5 4.5 - - - +
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Residues in contact with GLN3878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3876A LEU* 3.2 3.5 + - + -
3877A HIS* 1.3 78.5 - - + +
3879A ASP* 1.3 71.2 + - - +
3880A HIS 3.8 0.2 + - - -
3881A ILE* 4.8 7.7 + - - +
3882A THR* 4.8 6.6 + - - +
4002A LEU* 5.9 1.4 - - - +
4195A ARG* 5.7 7.9 - - - +
4331A LEU* 5.8 4.4 - - - +
4335A GLN* 4.2 46.2 - - + +
4338A ASP* 4.9 8.5 - - - +
4339A MET* 5.3 5.2 - - - +
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Residues in contact with ASP3879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3821A ILE* 4.0 16.2 - - + +
3822A HIS* 4.3 8.2 - - - -
3825A TYR* 2.7 29.6 + - - +
3875A MET* 3.5 5.5 - - + +
3876A LEU* 3.1 22.3 + - - +
3878A GLN* 1.3 85.7 - - - +
3880A HIS* 1.3 62.6 + - - +
3881A ILE 3.3 2.9 - - - -
3882A THR* 2.3 33.4 + - - -
3883A PHE 3.3 2.3 + - - -
4338A ASP* 6.1 0.5 - - - +
4342A LYS* 3.2 16.0 + - - +
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Residues in contact with HIS3880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3868A PHE* 3.4 30.4 - + - -
3872A ALA* 3.5 37.7 + - + +
3875A MET* 4.0 13.2 - - + +
3876A LEU 3.2 12.0 + - - +
3877A HIS* 3.3 41.5 + + - +
3878A GLN 3.4 0.6 - - - -
3879A ASP* 1.3 76.8 - - - +
3881A ILE* 1.3 62.4 + - + +
3883A PHE* 3.6 3.1 + - - +
3884A ALA 3.5 13.7 + - - -
4018A MET* 3.5 26.2 + - + +
4021A MET* 3.7 23.4 - - + +
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Residues in contact with ILE3881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3877A HIS* 4.5 19.0 + - + +
3878A GLN 4.8 4.5 + - - +
3879A ASP 3.3 0.6 - - - -
3880A HIS* 1.3 76.7 - - + +
3882A THR* 1.3 61.3 + - - +
3884A ALA* 3.2 4.7 + - + +
3885A MET* 2.9 26.5 + - + +
4002A LEU* 4.3 27.4 - - + +
4005A ALA* 4.1 19.7 - - + -
4006A HIS* 3.3 45.3 - - + +
4009A VAL* 5.5 1.8 - - + -
4018A MET* 4.0 15.3 - - + -
4335A GLN* 5.6 0.9 - - - +
4339A MET* 3.4 19.7 - - + -
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Residues in contact with THR3882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3878A GLN 4.8 2.0 - - - +
3879A ASP* 2.3 33.6 + - - +
3881A ILE* 1.3 77.0 - - - +
3883A PHE* 1.3 54.4 + - - +
3885A MET* 3.2 14.8 + - - +
3886A LEU* 2.9 33.1 + - - +
4339A MET* 3.4 48.7 - - + +
4342A LYS* 2.4 40.1 + - + +
4343A MET* 4.1 4.6 - - - +
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Residues in contact with PHE3883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3811A ILE* 5.4 2.7 - - + -
3814A THR* 4.4 11.0 - - + -
3815A MET* 3.5 38.6 - - + -
3818A LEU* 3.6 28.9 - - + -
3867A ALA* 4.7 0.9 - - + -
3868A PHE* 3.7 20.9 - + - -
3871A VAL* 3.3 31.4 - - + -
3875A MET* 3.9 17.0 - - + -
3879A ASP 3.3 0.4 + - - -
3880A HIS 3.8 8.3 - - - +
3881A ILE 3.3 0.4 - - - -
3882A THR* 1.3 81.4 + - - +
3884A ALA* 1.3 56.6 + - - +
3886A LEU* 3.1 15.7 + - + +
3887A LEU* 2.9 56.2 + - + +
4342A LYS* 4.4 1.3 - - - +
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Residues in contact with ALA3884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3868A PHE* 3.4 31.2 - - + -
3880A HIS 3.5 4.9 + - - +
3881A ILE* 3.2 13.2 + - - +
3883A PHE* 1.3 79.7 - - - +
3885A MET* 1.3 56.3 + - - +
3887A LEU* 3.2 7.2 + - - +
3888A ALA* 2.9 28.1 + - - +
4009A VAL* 4.2 18.8 - - + -
4013A LEU* 4.1 4.0 - - - +
4017A PHE* 4.8 3.6 - - + -
4018A MET* 4.3 11.7 - - - -
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Residues in contact with MET3885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3881A ILE* 2.9 11.7 + - + +
3882A THR* 3.2 10.5 + - - +
3884A ALA* 1.3 76.1 - - - +
3886A LEU* 1.3 56.6 + - - +
3888A ALA* 3.2 5.2 + - - +
3889A ARG* 2.9 27.4 + - - +
3905A PHE* 4.9 5.6 - - + -
3908A PHE* 4.0 27.8 - - + -
3990A LEU* 5.3 2.9 - - - -
4005A ALA* 4.7 11.4 - - + -
4008A PHE* 4.4 15.0 - - + -
4009A VAL* 4.1 13.1 - - + +
4339A MET* 3.4 42.8 - - + +
4343A MET* 3.6 34.5 - - + -
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Residues in contact with LEU3886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3814A THR* 3.6 32.8 - - + -
3882A THR 2.9 21.6 + - - +
3883A PHE* 3.1 17.7 + - + +
3885A MET* 1.3 75.2 - - - +
3887A LEU* 1.3 57.3 + - + +
3889A ARG* 3.2 23.2 + - - +
3890A ILE* 2.9 34.7 + - + +
4342A LYS* 4.6 2.9 - - - -
4343A MET* 3.5 28.3 - - + -
4346A MET* 4.0 41.7 - - + -
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Residues in contact with LEU3887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3811A ILE* 2.9 40.6 - - + +
3814A THR* 5.8 0.9 - - + -
3864A PHE* 3.5 28.3 - - + +
3867A ALA* 5.6 1.6 - - + -
3868A PHE* 3.6 43.7 - - + +
3883A PHE* 2.9 38.5 + - + +
3884A ALA* 3.2 6.0 + - - +
3886A LEU* 1.3 77.6 - - + +
3888A ALA* 1.3 56.7 + - - +
3890A ILE* 3.2 8.4 + - + +
3891A LYS* 2.9 24.8 + - - +
4013A LEU* 4.6 6.3 - - + -
4017A PHE* 4.2 10.3 - - + -
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Residues in contact with ALA3888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3884A ALA 2.9 13.4 + - - +
3885A MET* 3.3 10.1 - - - +
3887A LEU* 1.3 74.9 - - - +
3889A ARG* 1.3 63.8 + - - +
3891A LYS* 3.2 9.4 + - - +
3892A LEU* 3.3 7.2 + - - +
4008A PHE* 3.7 20.9 - - + -
4009A VAL* 4.4 5.2 - - + -
4012A ASN* 2.7 36.0 + - + +
4013A LEU* 3.8 19.2 - - + +
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Residues in contact with ARG3889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3885A MET 2.9 13.1 + - - +
3886A LEU* 3.4 23.9 + - - +
3888A ALA* 1.3 79.2 - - - +
3890A ILE* 1.3 66.8 + - - +
3891A LYS 3.4 0.2 + - - -
3892A LEU* 3.5 23.1 - - + +
3893A LYS* 3.8 5.2 + - - +
3900A THR* 5.7 4.1 - - + +
3905A PHE* 3.2 46.2 - - + -
3909A LEU* 4.3 10.1 - - - +
4008A PHE* 4.9 1.2 - - - -
4343A MET* 4.7 8.2 + - + +
4346A MET* 5.6 2.8 + - - +
4347A GLN* 2.7 44.0 + - - +
4350A GLU* 5.1 10.3 - - - +
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Residues in contact with ILE3890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3807A ALA* 4.0 18.1 - - + +
3810A SER* 3.7 35.7 - - - +
3811A ILE* 4.1 12.1 - - + -
3814A THR* 3.0 34.1 - - + +
3864A PHE* 4.1 13.5 - - + -
3886A LEU* 2.9 22.6 + - + +
3887A LEU* 3.2 8.3 + - + +
3889A ARG* 1.3 84.4 - - + +
3891A LYS* 1.3 62.8 + - - +
3893A LYS* 3.2 27.5 + - + +
3894A GLY 3.8 2.1 + - - -
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Residues in contact with LYS3891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3807A ALA* 6.3 0.4 - - - -
3860A THR* 6.3 3.6 - - + -
3864A PHE* 3.7 22.0 - - + -
3887A LEU 2.9 13.4 + - - +
3888A ALA 3.2 9.6 + - - +
3890A ILE* 1.3 75.7 - - - +
3892A LEU* 1.3 57.2 + - - +
3894A GLY* 2.9 20.8 + - - -
3895A THR* 3.3 26.9 + - - +
3983A ILE* 5.9 3.6 - - - +
4012A ASN* 3.8 31.3 + - - +
4013A LEU* 3.9 20.4 - - + +
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Residues in contact with LEU3892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3888A ALA 3.4 10.3 - - - +
3889A ARG* 3.5 14.8 - - + +
3891A LYS* 1.3 78.1 - - + +
3893A LYS* 1.3 58.6 + - - +
3895A THR* 2.9 32.9 + - - +
3898A GLU* 4.5 10.2 - - + +
3900A THR* 3.8 39.4 + - + +
3905A PHE* 5.2 4.5 - - + -
3983A ILE* 3.9 33.4 - - + -
3987A ILE* 4.6 9.4 - - + -
4008A PHE* 5.2 6.5 - - + -
4012A ASN* 3.1 37.7 - - - +
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Residues in contact with LYS3893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3806A THR* 5.0 13.4 - - + +
3807A ALA* 6.6 0.2 - - - -
3810A SER* 4.2 22.1 + - - +
3889A ARG 3.8 4.1 + - - +
3890A ILE* 3.2 20.7 + - + +
3892A LEU* 1.3 79.1 - - - +
3894A GLY* 1.3 61.2 + - - +
3895A THR 4.0 3.5 - - - +
3900A THR* 4.6 4.2 + - - -
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Residues in contact with GLY3894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3803A PRO* 4.7 27.2 - - - +
3807A ALA* 5.7 6.0 - - - +
3890A ILE 3.8 2.4 + - - -
3891A LYS 2.9 9.7 + - - -
3893A LYS* 1.3 78.7 - - - +
3895A THR* 1.3 61.5 + - - +
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Residues in contact with THR3895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3891A LYS* 3.3 34.9 + - - +
3892A LEU* 2.9 24.8 + - - +
3893A LYS 4.0 4.0 - - - +
3894A GLY* 1.3 79.1 - - - +
3897A GLY* 3.3 35.7 - - - +
3898A GLU* 3.4 37.3 + - + +
3983A ILE* 6.0 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