Contacts of the helix formed by residues 4162 - 4169 (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 ALA4162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4054F LEU* 5.1 10.1 - - + -
4058F ASP* 4.1 6.1 - - - -
4138F VAL* 5.7 9.4 - - + -
4142F LEU* 5.7 8.1 - - + -
4158F PHE 3.2 17.2 + - - +
4159F LEU* 3.4 7.2 - - - +
4160F GLU 3.2 0.8 - - - -
4161F LEU* 1.3 76.4 - - - +
4163F GLU* 1.3 60.7 + - - +
4164F SER 3.2 2.5 - - - -
4165F ILE* 3.3 20.9 + - + +
4166F LEU* 3.4 16.5 + - + +
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Residues in contact with GLU4163 (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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4159F LEU 3.2 5.4 + - - +
4160F GLU* 3.3 20.0 + - - +
4161F LEU 3.4 1.4 + - - -
4162F ALA* 1.3 77.9 - - - +
4164F SER* 1.3 60.7 + - - +
4165F ILE 3.3 0.2 - - - -
4166F LEU* 3.4 28.0 - - + +
4167F GLU* 3.4 12.6 + - - +
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Residues in contact with SER4164 (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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4058F ASP* 3.9 28.6 + - - -
4061F LEU* 3.3 19.9 - - - +
4162F ALA* 3.2 1.0 - - - +
4163F GLU* 1.3 77.7 - - - +
4165F ILE* 1.3 64.1 + - - +
4167F GLU* 3.6 6.4 + - - +
4168F TYR* 3.5 12.1 + - - +
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Residues in contact with ILE4165 (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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4057F PHE* 6.0 3.6 - - + -
4058F ASP* 3.9 13.9 + - - +
4061F LEU* 4.0 11.2 - - + -
4135F GLY* 4.9 11.9 - - - +
4138F VAL* 5.8 8.5 - - + -
4139F ALA* 4.5 6.4 - - + +
4162F ALA* 3.3 17.4 + - + +
4164F SER* 1.3 80.1 - - - +
4166F LEU* 1.3 61.8 + - - +
4168F TYR* 3.4 4.3 + - - +
4169F PHE* 3.3 22.9 + - - +
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Residues in contact with LEU4166 (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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4139F ALA* 4.6 18.4 - - + +
4142F LEU* 6.0 7.0 - - + -
4159F LEU* 4.0 17.0 - - + +
4162F ALA* 3.4 18.0 + - + +
4163F GLU* 3.4 22.2 - - + +
4165F ILE* 1.3 77.2 - - - +
4167F GLU* 1.3 69.6 + - + +
4169F PHE 3.5 1.3 + - - +
4170F ARG* 3.1 25.2 + - + +
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Residues in contact with GLU4167 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4163F GLU 3.4 17.1 + - - +
4164F SER* 3.9 7.0 - - - +
4165F ILE 3.3 0.6 - - - -
4166F LEU* 1.3 87.1 - - + +
4168F TYR* 1.3 60.3 + - - +
4170F ARG* 3.7 14.2 - - - +
4171F PRO* 4.3 3.1 - - - +
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Residues in contact with TYR4168 (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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4061F LEU* 3.6 46.9 - - + -
4064F LYS* 4.9 19.1 + - + +
4132F ARG* 6.3 4.0 - - + -
4135F GLY 6.6 0.2 - - - -
4164F SER 3.5 2.5 + - - +
4165F ILE 3.4 4.6 + - - +
4166F LEU 3.3 0.6 - - - -
4167F GLU* 1.3 79.6 - - - +
4169F PHE* 1.3 61.5 + - + +
4170F ARG 3.2 4.9 + - - -
4171F PRO* 3.6 12.5 - - - +
4172F TYR* 3.9 22.6 - + - -
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Residues in contact with PHE4169 (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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4135F GLY 4.6 3.1 - - - +
4136F PHE* 4.5 17.0 - - + -
4139F ALA* 3.8 28.7 - - + -
4165F ILE 3.3 8.8 + - - +
4166F LEU 3.5 3.3 + - - +
4167F GLU 3.5 0.2 - - - -
4168F TYR* 1.3 82.5 - - + +
4170F ARG* 1.3 61.5 + - - +
4171F PRO* 3.6 1.1 - - - -
4172F TYR* 3.9 13.7 - - + -
4173F LEU* 3.4 26.4 + - + +
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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