Contacts of the helix formed by residues 3875 - 3885 (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 PHE3875 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3785F THR* 4.9 10.1 - - + -
3786F GLY 5.2 3.4 - - - -
3789F VAL* 4.4 18.8 - - + -
3790F SER* 4.3 22.7 - - - -
3793F LEU* 4.7 10.5 - - + +
3830F LEU* 3.9 42.0 - - + -
3833F THR* 4.8 8.7 - - - -
3834F CYS* 5.1 6.1 - - - -
3872F ASP* 3.3 16.7 + - + +
3874F GLU* 1.3 79.4 - - - +
3876F THR* 1.3 73.5 + - - +
3877F GLN 3.3 1.6 - - - -
3878F ASP* 3.5 4.8 + - - +
3879F LEU* 3.3 34.9 + - + +
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Residues in contact with THR3876 (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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3834F CYS* 3.7 24.2 - - + +
3835F SER 5.2 0.5 + - - -
3870F MET* 6.2 0.3 - - - +
3872F ASP* 3.1 27.3 + - - +
3875F PHE* 1.3 78.5 - - - +
3877F GLN* 1.3 65.7 + - - +
3878F ASP 3.3 0.9 + - - -
3879F LEU* 3.4 11.1 + - - -
3880F PHE* 3.7 39.2 + - + +
3917F TYR* 3.9 5.6 - - - +
3952F VAL* 3.7 29.0 - - + +
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Residues in contact with GLN3877 (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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3794F LYS* 5.6 8.5 - - - +
3797F ILE* 5.6 5.6 - - - +
3872F ASP 4.6 0.2 + - - -
3873F ASP 3.2 24.7 + - - +
3874F GLU* 4.1 15.3 + - - +
3876F THR* 1.3 79.3 - - - +
3878F ASP* 1.3 73.3 + - - +
3881F ARG* 3.2 23.6 + - - +
3952F VAL* 5.6 9.5 - - + +
3955F GLN* 5.0 16.6 - - + +
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Residues in contact with ASP3878 (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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3790F SER 6.0 0.7 - - - +
3793F LEU* 4.9 22.9 - - + +
3794F LYS* 5.5 4.3 - - + +
3797F ILE* 4.1 17.0 - - + +
3874F GLU 4.7 5.4 - - - +
3875F PHE* 3.5 6.3 + - - +
3876F THR 3.2 0.2 - - - -
3877F GLN* 1.3 97.4 - - + +
3879F LEU* 1.3 64.9 + - - +
3881F ARG* 3.8 7.5 - - - +
3882F PHE* 3.2 23.0 + - - +
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Residues in contact with LEU3879 (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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3793F LEU* 4.7 13.9 - - + +
3827F ILE* 5.5 6.3 - - + +
3830F LEU* 3.7 39.7 - - + +
3831F MET* 3.7 22.9 - - - -
3834F CYS* 4.5 10.1 - - - -
3875F PHE* 3.3 29.5 + - + +
3876F THR* 3.4 6.9 + - - +
3878F ASP* 1.3 79.3 - - - +
3880F PHE* 1.3 93.1 + - + +
3882F PHE* 3.4 10.4 + - - +
3883F LEU* 3.7 18.8 + - + +
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Residues in contact with PHE3880 (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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3831F MET* 3.6 36.1 - - + -
3834F CYS* 4.5 1.6 - - - -
3876F THR* 3.7 34.4 + - + +
3877F GLN 5.5 0.2 - - - +
3879F LEU* 1.3 87.8 - - + +
3881F ARG* 1.3 64.8 + - - +
3882F PHE 3.3 0.2 - - - -
3883F LEU* 3.5 11.9 + - + +
3884F GLN* 3.1 24.1 + - - +
3914F THR* 5.0 7.9 - - + -
3917F TYR* 3.6 43.3 - + + -
3952F VAL* 5.3 4.0 - - + -
3955F GLN* 4.6 21.0 - - + +
3956F VAL* 4.4 22.2 - - + -
3959F SER* 4.5 13.1 - - - -
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Residues in contact with ARG3881 (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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3797F ILE* 4.5 19.7 - - + +
3801F ASN* 4.8 8.9 + - - -
3877F GLN* 3.2 25.7 + - - +
3878F ASP* 3.6 8.6 + - - +
3879F LEU 3.2 0.4 - - - -
3880F PHE* 1.3 77.3 - - - +
3882F PHE* 1.3 64.2 + - - +
3884F GLN* 3.5 6.2 + - - +
3885F LEU* 3.2 63.7 + - + +
3955F GLN* 3.6 38.3 + - + +
3958F ASN* 5.3 3.8 - - - +
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Residues in contact with PHE3882 (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* 5.3 5.6 - - + -
3775F LEU* 5.2 7.6 - - + -
3778F ILE* 6.3 2.5 - - + -
3793F LEU* 4.6 24.7 - - + -
3796F GLY* 3.9 39.3 - - - -
3797F ILE* 3.8 14.3 - - + +
3800F LEU* 4.7 8.6 - - + +
3811F MET* 4.9 13.7 - - + -
3823F PHE* 5.2 13.2 - + - -
3878F ASP 3.2 18.1 + - - +
3879F LEU 3.8 4.7 - - - +
3880F PHE 3.3 0.6 - - - -
3881F ARG* 1.3 79.3 - - - +
3883F LEU* 1.3 74.9 + - + +
3885F LEU* 3.7 4.3 + - - +
3886F LEU* 3.2 47.5 + - + +
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Residues in contact with LEU3883 (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* 4.6 22.0 - - + -
3831F MET* 5.3 12.6 - - + -
3879F LEU* 3.8 17.0 - - + +
3880F PHE* 3.5 14.9 + - + +
3881F ARG 3.3 0.2 - - - -
3882F PHE* 1.3 87.6 - - + +
3884F GLN* 1.3 64.9 + - - +
3886F LEU* 3.5 35.1 + - + +
3887F CYS 4.4 0.9 + - - -
3898F LEU* 5.5 5.1 - - + +
3910F ILE* 3.8 30.5 - - + -
3914F THR* 5.6 2.5 - - + +
3959F SER* 5.8 0.4 - - - -
3963F TYR* 3.4 32.2 + - - +
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Residues in contact with GLN3884 (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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3880F PHE 3.1 17.5 + - - +
3881F ARG* 4.0 10.3 - - - +
3882F PHE 3.3 0.2 - - - -
3883F LEU* 1.3 79.7 - - - +
3885F LEU* 1.3 66.5 + - + +
3886F LEU 3.2 1.1 + - - -
3887F CYS* 3.6 7.6 + - - +
3888F GLU* 3.9 6.4 + - - -
3955F GLN 5.4 2.0 - - - +
3958F ASN* 4.3 10.3 - - + +
3959F SER* 4.1 26.2 - - - +
3962F GLU* 4.0 21.9 - - + +
3963F TYR* 5.0 1.7 - - - -
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Residues in contact with LEU3885 (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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3797F ILE* 4.5 9.6 - - + +
3800F LEU* 3.1 50.6 - - + +
3801F ASN* 3.7 24.7 - - - +
3803F GLY* 5.6 1.1 - - - -
3804F ASN 5.8 0.2 - - - +
3881F ARG* 3.2 64.4 + - + +
3882F PHE* 3.7 4.7 + - - +
3883F LEU 3.4 0.2 - - - -
3884F GLN* 1.3 81.2 - - + +
3886F LEU* 1.3 62.3 + - - +
3887F CYS 3.3 1.6 - - - -
3888F GLU* 3.6 23.6 + - + +
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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
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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