Contacts of the helix formed by residues 4726 - 4735 (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 HIS4726 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4679F LEU 4.9 4.3 - - - -
4680F GLU 4.3 10.6 + - - -
4681F PHE* 4.1 24.0 + - - -
4682F ASP* 4.6 3.6 + - - -
4686F ILE* 4.1 33.3 - - + +
4687F THR* 4.3 15.0 - - + +
4688F GLU* 6.4 0.2 - - + -
4722F VAL* 3.1 15.4 + - + +
4725F LYS* 1.3 91.5 + - + +
4727F GLY* 1.3 60.3 + - - +
4728F ASP 3.5 2.2 - - - -
4729F ILE* 3.7 26.2 + - + +
4730F TYR* 4.5 3.6 + - - +
4735F ILE* 3.8 7.9 - - - +
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Residues in contact with GLY4727 (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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4722F VAL 3.5 4.8 + - - -
4723F LEU 3.3 20.9 + - - -
4724F ASP 4.3 0.2 - - - -
4725F LYS 3.4 2.8 - - - -
4726F HIS* 1.3 76.1 - - - +
4728F ASP* 1.3 59.4 + - - +
4729F ILE 3.2 2.7 - - - -
4731F GLY 3.1 34.9 + - - +
4732F ARG* 3.7 2.2 + - - -
4735F ILE* 3.7 19.5 - - - -
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Residues in contact with ASP4728 (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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4723F LEU 4.6 1.0 + - - -
4724F ASP 5.0 5.4 + - - +
4725F LYS 4.6 4.4 + - - +
4726F HIS* 3.5 0.6 - - - +
4727F GLY* 1.3 74.5 - - - +
4729F ILE* 1.3 70.0 + - + +
4731F GLY* 4.0 5.5 + - - +
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Residues in contact with ILE4729 (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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4687F THR* 3.7 28.7 - - + +
4725F LYS 4.1 7.6 - - - +
4726F HIS* 3.7 34.1 - - + +
4727F GLY 3.2 0.8 - - - -
4728F ASP* 1.3 84.6 - - + +
4730F TYR* 1.3 76.0 + - + +
4731F GLY 3.3 0.8 + - - -
4071H ALA* 5.8 4.2 - - - +
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Residues in contact with TYR4730 (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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4686F ILE* 4.7 4.5 - - + -
4687F THR* 3.6 46.2 + - + -
4726F HIS 4.5 3.5 + - - +
4727F GLY 3.9 2.2 + - - -
4729F ILE* 1.3 94.2 - - + +
4731F GLY* 1.3 63.6 + - - +
4734F ARG* 3.3 71.9 + - + +
4735F ILE* 5.0 6.3 - - + +
4070H GLU* 4.7 13.9 - - + -
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Residues in contact with GLY4731 (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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4727F GLY 3.1 19.1 + - - +
4728F ASP* 4.0 5.2 + - - -
4729F ILE 3.3 4.4 + - - -
4730F TYR* 1.3 82.5 - - - +
4732F ARG* 1.3 62.3 + - - -
4733F GLU* 3.1 7.4 + - - -
4735F ILE* 3.3 16.1 + - - +
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Residues in contact with ARG4732 (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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4723F LEU* 6.0 3.4 - - + +
4727F GLY* 3.7 3.5 + - - -
4731F GLY* 1.3 71.6 - - - -
4733F GLU* 1.3 57.6 + - - +
4735F ILE* 4.0 10.9 - - - +
4736F ALA* 3.5 20.6 + - - +
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Residues in contact with GLU4733 (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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4731F GLY* 3.1 1.4 - - - -
4732F ARG* 1.3 78.8 - - - +
4734F ARG* 1.3 70.1 + - + +
4735F ILE 3.4 0.4 - - - -
4736F ALA* 3.5 4.5 + - - +
4737F GLU* 3.4 20.1 + - - +
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Residues in contact with ARG4734 (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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4730F TYR* 3.3 67.3 + - + +
4731F GLY 3.8 1.4 + - - -
4733F GLU* 1.3 79.7 - - + +
4735F ILE* 1.3 62.4 + - - +
4736F ALA 3.4 0.3 + - - -
4737F GLU* 3.4 19.2 + - - +
4070H GLU* 4.1 19.0 - - - +
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Residues in contact with ILE4735 (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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4686F ILE* 4.1 17.9 - - + -
4722F VAL* 3.5 40.8 - - + +
4723F LEU* 3.7 28.6 - - + +
4726F HIS 3.8 8.5 - - - +
4727F GLY* 3.7 20.6 - - - -
4730F TYR* 5.0 6.0 - - + +
4731F GLY 3.3 19.8 + - - +
4732F ARG* 4.0 11.9 - - - +
4734F ARG* 1.3 76.3 - - - +
4736F ALA* 1.3 67.5 + - - +
4737F GLU 4.4 2.6 - - - -
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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