Contacts of the helix formed by residues 6471 - 6476 (chain F) in PDB entry 2H7C
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 GLU6471 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6220F GLU* 3.7 13.7 - - - +
6246F GLU* 2.8 40.7 - - - +
6247F SER* 4.6 3.7 + - - -
6351F ASN* 3.0 24.1 + - - +
6447F TYR* 4.1 13.9 - - + +
6449F PHE* 3.7 39.8 - - + -
6469F GLY* 3.3 10.7 + - - -
6470F ASP* 1.3 71.4 - - - +
6472F LEU* 1.3 66.9 + - - +
6473F PHE 3.2 0.4 - - - -
6474F SER* 3.0 5.7 + - - -
6475F VAL* 2.9 35.2 + - + +
6496F VAL* 6.1 0.7 - - + -
6500F TRP* 5.4 1.8 - - + -
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Residues in contact with LEU6472 (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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6101F PHE* 3.7 50.3 - - + +
6103F ASN* 6.0 0.9 - - - -
6138F TRP* 3.4 37.2 - - + -
6152F TYR* 4.1 10.1 - - + -
6220F GLU* 3.4 20.0 - - + -
6246F GLU* 4.1 2.7 - - - +
6469F GLY* 3.1 22.0 + - - +
6471F GLU* 1.3 88.8 - - - +
6473F PHE* 1.3 60.2 + - + +
6475F VAL* 4.4 3.4 - - + -
6476F PHE* 2.8 41.4 + - + +
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Residues in contact with PHE6473 (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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6100F LEU 3.3 25.1 - - - -
6101F PHE* 4.3 11.2 - + - -
6102F THR 3.5 23.1 - - - -
6103F ASN* 4.9 2.7 - - + -
6453F PRO* 3.8 22.9 - - + -
6455F PHE* 3.6 47.3 - + + -
6456F SER* 5.1 2.9 - - - -
6469F GLY 4.2 11.9 - - - -
6470F ASP* 3.6 20.2 - - - +
6471F GLU 3.2 0.6 - - - -
6472F LEU* 1.3 77.7 - - + +
6474F SER* 1.3 60.7 + - - +
6476F PHE* 5.4 0.9 - - - -
6477F GLY 3.4 1.4 + - - -
6478F ALA* 2.8 49.3 + - + +
6479F PRO* 3.4 5.6 - - + +
6482F LYS* 4.9 2.5 - - + -
6489F GLU* 5.4 0.4 - - - +
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Residues in contact with SER6474 (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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6449F PHE* 3.8 11.1 - - - -
6451F TYR* 5.4 0.7 - - - -
6470F ASP 4.4 0.9 + - - -
6471F GLU 3.0 10.4 + - - -
6473F PHE* 1.3 77.6 - - - +
6475F VAL* 1.3 66.6 + - - +
6477F GLY 3.2 2.6 + - - -
6479F PRO* 5.1 0.7 - - - -
6489F GLU* 5.3 3.1 + - - +
6492F LEU* 3.6 25.1 - - - +
6493F SER* 3.0 32.8 + - - +
6496F VAL* 3.9 26.5 - - - -
6497F MET* 3.5 8.0 - - - +
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Residues in contact with VAL6475 (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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6157F LEU* 3.9 15.1 - - + +
6218F PHE* 3.9 18.8 - - + -
6246F GLU* 4.0 16.4 - - - +
6471F GLU* 2.9 23.2 + - + +
6472F LEU* 3.9 5.2 - - - +
6474F SER* 1.3 76.4 - - - +
6476F PHE* 1.3 69.6 + - + +
6496F VAL* 3.6 23.3 - - + -
6497F MET* 3.4 19.0 - - - +
6500F TRP* 3.7 41.7 - - + +
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Residues in contact with PHE6476 (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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6103F ASN* 3.1 30.5 + - + +
6138F TRP* 3.5 61.2 - + + -
6152F TYR* 4.0 26.9 - + + -
6153F ASP 3.8 19.5 - - - +
6154F GLY* 4.5 4.5 - - - -
6156F ALA* 3.9 10.1 - - - +
6157F LEU* 4.6 10.2 + - + -
6165F VAL* 4.6 19.3 - - + -
6167F THR* 4.9 1.6 - - + -
6218F PHE* 4.1 9.9 - + - -
6472F LEU* 2.8 24.3 + - + +
6475F VAL* 1.3 86.6 - - + +
6477F GLY* 1.3 64.4 + - - +
6478F ALA 3.4 1.6 - - - -
6497F MET* 4.4 2.9 - - - -
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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