Contacts of the helix formed by residues 3808 - 3813 (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 GLN3808 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3800F LEU* 5.0 7.9 - - + -
3804F ASN 4.9 2.5 - - - +
3805F ALA* 3.3 21.5 + - + +
3806F ASP 3.3 0.6 - - - -
3807F VAL* 1.3 84.9 - - + +
3809F GLN* 1.3 62.7 + - - +
3811F MET* 3.2 20.6 + - - +
3812F LEU* 3.4 15.2 + - - +
3886F LEU* 4.4 17.5 - - + +
3891F ASN* 4.8 9.9 - - - +
3894F PHE* 4.8 8.8 - - + -
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Residues in contact with GLN3809 (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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3766F HIS* 5.0 4.4 + - - -
3805F ALA 3.4 9.1 + - - +
3806F ASP* 3.2 29.2 + - - +
3808F GLN* 1.3 79.3 - - - +
3810F LYS* 1.3 70.2 + - + +
3811F MET 3.4 0.7 + - - -
3812F LEU* 3.6 26.1 - - + +
3813F ASP* 3.3 16.8 - - - +
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Residues in contact with LYS3810 (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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3766F HIS* 3.5 34.3 - - + +
3771F ALA* 4.9 11.6 - - + +
3772F GLU* 3.1 31.5 + - - +
3806F ASP 3.9 2.9 - - - +
3807F VAL* 3.3 9.6 + - - +
3808F GLN 3.2 0.8 - - - -
3809F GLN* 1.3 82.9 - - + +
3811F MET* 1.3 58.4 + - - +
3813F ASP* 2.9 33.1 + - - +
3814F TYR* 4.0 2.1 - - - +
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Residues in contact with MET3811 (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* 4.4 14.1 - - + +
3774F VAL* 4.5 8.3 - - + -
3775F LEU* 3.8 41.1 - - + +
3796F GLY* 6.5 0.2 - - - -
3800F LEU* 4.2 17.0 - - + -
3807F VAL* 3.6 33.7 - - + +
3808F GLN* 3.2 11.6 + - - +
3809F GLN 3.2 0.8 - - - -
3810F LYS* 1.3 80.8 - - - +
3812F LEU* 1.3 64.2 + - - +
3813F ASP 3.5 0.7 - - - -
3814F TYR* 3.8 3.5 + - - +
3815F LEU* 3.3 29.0 + - + +
3882F PHE* 4.9 7.4 - - + -
3886F LEU* 4.4 20.9 - - - -
3894F PHE* 5.0 10.5 - - + -
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Residues in contact with LEU3812 (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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3808F GLN* 3.4 6.0 + - + +
3809F GLN* 3.6 29.2 - - + +
3811F MET* 1.3 77.8 - - - +
3813F ASP* 1.3 73.3 + - + +
3815F LEU* 3.5 11.5 + - - +
3816F LYS* 3.2 30.6 + - + +
3891F ASN* 5.9 0.9 - - - +
3893F ASP* 4.1 31.0 - - + +
3894F PHE* 4.1 28.4 - - + -
3897F TYR* 5.6 5.9 - - + -
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Residues in contact with ASP3813 (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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3772F GLU* 4.7 0.7 - - - +
3809F GLN 3.5 12.4 - - - +
3810F LYS* 2.9 41.2 + - - +
3812F LEU* 1.3 82.4 - - + +
3814F TYR* 1.3 77.9 + - - +
3816F LYS* 3.3 14.4 + - - +
3817F ASP* 3.4 15.8 + - - +
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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