Contacts of the helix formed by residues 3822 - 3833 (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 GLY3822 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3779F SER* 3.7 21.4 - - - +
3782F LYS* 5.8 0.7 - - - -
3821F VAL* 1.3 77.7 - - - +
3823F PHE* 1.3 64.1 + - - +
3824F PHE* 3.5 1.4 - - - +
3825F GLN* 3.8 24.2 - - - +
3826F SER* 3.2 22.7 + - - -
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Residues in contact with PHE3823 (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 4.8 0.2 - - - -
3775F LEU* 3.2 55.6 - - + -
3778F ILE* 3.8 24.2 - - + +
3779F SER* 3.7 13.8 - - - +
3815F LEU* 4.7 23.6 - - + -
3820F GLU 4.6 5.4 + - - +
3821F VAL* 3.6 2.8 - - - +
3822F GLY* 1.3 76.6 - - - +
3824F PHE* 1.3 93.9 + + + +
3826F SER* 3.2 17.5 + - - -
3827F ILE* 3.3 23.5 - - + +
3882F PHE* 5.2 13.5 - + - -
3886F LEU* 6.6 0.2 - - + -
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Residues in contact with PHE3824 (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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3815F LEU* 4.1 12.1 - - + -
3821F VAL* 5.8 0.2 - - - +
3822F GLY 4.5 1.0 - - - +
3823F PHE* 1.3 101.7 - + + +
3825F GLN* 1.3 65.3 + - + +
3827F ILE* 3.3 27.5 + - + +
3828F GLN* 3.5 16.5 + - - +
3894F PHE* 6.3 1.1 - + - -
3897F TYR* 3.5 39.5 - + - -
3898F LEU* 5.0 15.5 - - + -
3901F GLN* 4.1 15.0 - - + -
3908F ILE* 3.6 47.2 - - + +
3910F ILE* 5.5 9.0 - - + -
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Residues in contact with GLN3825 (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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3821F VAL* 3.4 29.8 - - + +
3822F GLY* 3.7 26.4 + - - +
3823F PHE 3.3 0.8 - - - -
3824F PHE* 1.3 79.8 - - + +
3826F SER* 1.3 60.7 + - - +
3827F ILE 3.4 0.5 + - - -
3828F GLN* 3.4 22.0 + - - +
3829F ALA* 3.6 9.7 + - - +
3906F THR* 5.3 10.3 + - + +
3908F ILE* 5.5 7.4 - - + -
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Residues in contact with SER3826 (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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3778F ILE* 3.1 36.8 + - - +
3779F SER* 4.8 0.2 - - - -
3781F CYS* 3.7 16.8 - - - -
3782F LYS* 4.7 4.0 - - - +
3783F GLY* 3.9 15.2 - - - +
3822F GLY 3.2 13.3 + - - -
3823F PHE 3.2 10.4 + - - -
3825F GLN* 1.3 74.3 - - - +
3827F ILE* 1.3 65.0 + - - +
3829F ALA* 3.5 3.9 + - - +
3830F LEU* 3.3 26.4 + - - +
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Residues in contact with ILE3827 (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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3778F ILE* 4.8 6.5 - - + -
3823F PHE* 3.3 28.5 - - + +
3824F PHE* 3.5 35.4 - - + +
3825F GLN 3.2 0.8 - - - -
3826F SER* 1.3 78.6 - - - +
3828F GLN* 1.3 66.1 + - + +
3830F LEU* 3.2 11.0 + - + +
3831F MET* 3.0 32.7 + - + +
3879F LEU* 5.7 5.8 - - + -
3883F LEU* 4.6 21.3 - - + -
3910F ILE* 3.9 31.0 - - + -
3913F CYS* 6.2 0.2 - - - -
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Residues in contact with GLN3828 (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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3824F PHE 3.5 11.0 + - - +
3825F GLN* 3.4 13.4 + - - +
3826F SER 3.3 0.6 - - - -
3827F ILE* 1.3 79.2 - - + +
3829F ALA* 1.3 60.2 + - - +
3831F MET* 3.4 12.9 + - - +
3832F GLN* 3.4 24.5 + - - +
3908F ILE* 3.3 33.8 - - + +
3910F ILE* 6.1 0.7 - - + -
3913F CYS* 4.1 26.2 - - + -
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Residues in contact with ALA3829 (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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3783F GLY* 3.7 36.3 - - - +
3785F THR* 6.1 0.2 - - - -
3825F GLN 3.6 8.0 + - - +
3826F SER 3.5 3.5 + - - +
3827F ILE 3.2 0.8 - - - -
3828F GLN* 1.3 79.5 - - - +
3830F LEU* 1.3 62.5 + - - +
3832F GLN* 3.4 7.2 + - - +
3833F THR* 3.1 28.2 + - + +
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Residues in contact with LEU3830 (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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3778F ILE* 5.4 8.3 - - + -
3781F CYS* 5.3 4.9 - - - -
3783F GLY 5.4 0.9 - - - -
3784F GLU 4.2 16.8 - - - +
3785F THR* 3.9 20.6 - - + -
3789F VAL* 4.3 19.3 - - + -
3793F LEU* 4.9 6.7 - - + -
3826F SER* 3.3 21.5 + - - +
3827F ILE* 3.2 11.1 + - + +
3829F ALA* 1.3 77.3 - - - +
3831F MET* 1.3 61.6 + - - +
3833F THR* 3.0 14.5 + - - -
3834F CYS* 3.6 15.2 - - - -
3875F PHE* 3.9 22.4 - - + -
3879F LEU* 3.7 29.7 - - + +
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Residues in contact with MET3831 (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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3827F ILE* 3.0 30.5 + - + +
3828F GLN* 3.7 10.1 - - - +
3829F ALA 3.2 0.4 - - - -
3830F LEU* 1.3 79.7 - - - +
3832F GLN* 1.3 65.3 + - + +
3833F THR 3.6 0.2 + - - -
3834F CYS* 3.8 14.4 + - - +
3879F LEU* 3.7 26.9 - - + -
3880F PHE* 3.6 28.0 - - + -
3883F LEU* 5.3 8.5 - - + -
3910F ILE* 5.4 2.5 - - + -
3913F CYS* 3.6 36.1 - - + +
3914F THR* 3.7 22.4 - - + +
3917F TYR* 4.3 8.3 - - + -
3920F ARG* 3.3 18.0 + - - -
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Residues in contact with GLN3832 (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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3828F GLN* 3.4 15.6 + - - +
3829F ALA* 3.4 8.8 + - - +
3830F LEU 3.3 0.4 - - - -
3831F MET* 1.3 82.3 - - - +
3833F THR* 1.3 59.9 + - + +
3834F CYS 3.2 8.3 + - - +
3913F CYS* 5.4 9.5 + - - +
3916F ASP* 5.7 6.9 - - - +
3920F ARG* 3.9 30.8 + - - +
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Residues in contact with THR3833 (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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3783F GLY 6.1 0.9 - - - +
3785F THR* 3.7 28.0 - - + +
3829F ALA* 3.1 16.1 + - + +
3830F LEU* 3.0 23.1 + - - +
3831F MET 3.4 0.2 - - - -
3832F GLN* 1.3 75.9 - - + +
3834F CYS* 1.3 62.2 + - - +
3835F SER* 3.2 5.7 + - - -
3875F PHE* 4.8 6.8 - - - -
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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