Contacts of the helix formed by residues 3769 - 3781 (chain F) 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 GLY3769 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3695F HIS* 3.8 13.9 + - - -
3698F VAL* 3.5 20.0 - - - +
3699F LEU* 5.5 6.1 - - - +
3768F ARG* 1.3 74.4 - - - +
3770F ALA* 1.3 60.1 + - - -
3771F ALA 3.5 2.0 - - - -
3772F GLU* 3.8 15.9 + - - +
3773F MET* 3.6 16.3 + - - +
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Residues in contact with ALA3770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3698F VAL* 4.0 11.8 - - + +
3725F MET* 5.2 7.0 - - - -
3765F LEU* 3.3 42.0 - - + +
3768F ARG* 3.1 6.2 + - + -
3769F GLY* 1.3 75.3 - - - +
3771F ALA* 1.3 65.1 + - - +
3772F GLU 3.2 0.4 - - - -
3773F MET* 3.4 12.5 + - - +
3774F VAL* 3.5 19.6 + - - +
3795F LEU* 5.3 5.1 - - + +
3799F ILE* 6.1 2.0 - - + -
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Residues in contact with ALA3771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3765F LEU 4.6 3.1 + - - +
3766F HIS* 5.4 7.2 - - - +
3768F ARG 4.6 2.1 + - - +
3769F GLY* 3.5 0.6 - - - -
3770F ALA* 1.3 78.7 - - - +
3772F GLU* 1.3 65.0 + - + +
3774F VAL* 3.3 22.8 - - - +
3775F LEU* 3.5 13.5 - - - +
3799F ILE* 6.1 0.9 - - + -
3807F VAL* 3.9 28.5 - - + -
3810F LYS* 4.9 15.0 - - + -
3811F MET* 4.4 10.1 - - + +
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Residues in contact with GLU3772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3769F GLY* 3.8 16.7 + - - +
3770F ALA 3.2 0.6 - - - -
3771F ALA* 1.3 78.8 - - + +
3773F MET* 1.3 64.2 + - - +
3775F LEU* 3.5 5.7 + - - +
3776F GLN* 3.3 37.0 + - - +
3810F LYS* 3.1 39.2 - - - +
3813F ASP* 4.7 0.7 - - - +
3814F TYR* 3.2 43.2 - - - +
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Residues in contact with MET3773 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3698F VAL* 4.3 17.3 - - - +
3701F PHE* 5.4 9.6 - - + -
3702F SER* 5.7 5.4 - - - +
3718F TYR* 4.4 11.7 + - + +
3769F GLY 3.6 11.3 + - - +
3770F ALA* 3.4 11.3 + - - +
3771F ALA 3.3 0.6 - - - -
3772F GLU* 1.3 80.4 - - - +
3774F VAL* 1.3 63.3 + - + +
3776F GLN* 3.6 7.3 + - - +
3777F MET* 3.3 25.5 + - - +
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Residues in contact with VAL3774 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3718F TYR* 5.3 5.2 - - - +
3770F ALA 3.5 13.2 - - - +
3771F ALA* 3.3 22.9 - - - +
3773F MET* 1.3 78.3 - - + +
3775F LEU* 1.3 69.2 + - + +
3777F MET* 4.2 4.1 - - - +
3778F ILE* 3.2 27.0 + - - +
3792F THR* 4.7 20.1 - - + +
3795F LEU* 3.9 26.5 - - + -
3796F GLY* 4.9 12.8 - - - -
3799F ILE* 6.3 1.1 - - + -
3811F MET* 4.5 8.3 - - + -
3823F PHE* 4.8 0.2 - - - -
3882F PHE* 5.3 6.7 - - + -
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Residues in contact with LEU3775 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3771F ALA 3.5 15.9 + - - +
3772F GLU* 3.5 10.4 + - - +
3773F MET 3.2 0.4 - - - -
3774F VAL* 1.3 92.7 - - + +
3776F GLN* 1.3 63.4 + - - +
3777F MET 3.3 0.4 - - - -
3778F ILE 3.5 0.7 + - - -
3779F SER* 3.5 9.0 + - - -
3811F MET* 3.8 51.4 - - + +
3814F TYR* 4.5 17.5 - - + -
3815F LEU* 4.4 20.4 - - + -
3823F PHE* 3.2 47.8 - - + -
3882F PHE* 5.2 5.8 - - + -
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Residues in contact with GLN3776 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462F GLU* 4.1 17.4 + - - +
3702F SER* 4.1 22.4 - - - -
3705F ALA* 4.4 7.2 - - + +
3706F LEU* 3.4 33.3 - - + +
3772F GLU* 3.3 26.3 + - - +
3773F MET* 3.6 5.1 + - - +
3775F LEU* 1.3 76.1 - - - +
3777F MET* 1.3 60.3 + - - +
3779F SER* 3.5 6.9 + - - -
3780F ALA* 3.1 26.2 + - - +
3814F TYR* 2.9 41.0 + - + +
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Residues in contact with MET3777 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3701F PHE 5.9 0.7 - - - +
3704F THR* 5.8 2.2 - - - -
3705F ALA* 4.5 15.6 - - + +
3712F LEU* 5.8 4.3 - - + -
3718F TYR* 3.8 22.0 - - + +
3773F MET 3.3 17.8 + - - +
3774F VAL 4.6 2.9 - - - +
3775F LEU 3.3 0.4 - - - -
3776F GLN* 1.3 76.3 - - - +
3778F ILE* 1.3 64.4 + - - +
3780F ALA* 3.2 26.5 + - + -
3781F CYS* 3.4 14.9 + - + +
3788F MET* 3.7 29.6 - - + +
3789F VAL* 6.5 0.7 - - + -
3792F THR* 3.7 32.3 - - + +
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Residues in contact with ILE3778 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3774F VAL 3.2 18.8 - - - +
3775F LEU 3.5 0.6 + - - -
3776F GLN 3.3 0.4 - - - -
3777F MET* 1.3 77.4 - - + +
3779F SER* 1.3 61.3 + - - +
3781F CYS* 3.2 19.0 - - - -
3789F VAL* 4.8 11.7 - - + -
3792F THR* 4.0 19.3 - - - +
3793F LEU* 3.8 33.0 - - + -
3823F PHE* 3.8 31.6 - - + +
3826F SER* 3.1 31.6 + - - +
3827F ILE* 4.8 7.0 - - + -
3830F LEU* 5.4 7.4 - - + -
3882F PHE* 6.3 2.9 - - + -
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Residues in contact with SER3779 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3775F LEU 3.5 8.9 + - - -
3776F GLN* 3.5 9.7 + - - -
3777F MET 3.3 0.4 - - - -
3778F ILE* 1.3 78.9 - - - +
3780F ALA* 1.3 61.4 + - - +
3781F CYS 3.3 0.4 + - - -
3782F LYS* 3.6 10.9 + - - +
3821F VAL 4.6 2.6 + - - -
3822F GLY* 3.7 26.7 - - - +
3823F PHE* 3.7 24.5 + - - +
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Residues in contact with ALA3780 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3705F ALA* 3.9 25.1 - - + +
3710F SER 4.5 3.5 - - - +
3711F LYS 2.9 20.1 - - - +
3776F GLN 3.1 17.6 + - - +
3777F MET* 3.2 25.2 + - + +
3779F SER* 1.3 76.3 - - - +
3781F CYS* 1.3 61.6 + - - +
3782F LYS* 3.2 4.7 + - - +
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Residues in contact with CYS3781 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3711F LYS* 4.1 10.1 - - - +
3712F LEU* 5.2 5.1 - - + +
3777F MET* 3.4 13.2 + - + +
3778F ILE* 3.2 22.4 - - - +
3779F SER 3.3 1.2 - - - -
3780F ALA* 1.3 78.9 - - - +
3782F LYS* 1.3 64.5 + - - +
3783F GLY* 3.2 18.6 + - - -
3784F GLU* 3.4 39.6 + - + +
3789F VAL* 4.4 19.5 - - + -
3826F SER* 3.7 11.0 - - - -
3830F LEU* 5.3 5.8 - - - -
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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