Contacts of the helix formed by residues 2378 - 2385 (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 LEU2378 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2377F LEU* 1.3 81.2 - - + +
2379F ALA* 1.3 60.6 + - - +
2381F ILE* 3.4 4.8 + - + -
2382F GLU* 2.9 31.2 + - + +
2465F ASP 4.9 4.7 - - - +
2466F ASP* 4.8 12.1 - - + +
2469F GLY* 3.5 44.9 - - - +
2470F ILE* 3.8 6.3 - - + +
2473F LEU* 4.2 16.8 - - + -
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Residues in contact with ALA2379 (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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2377F LEU 3.3 3.9 - - - +
2378F LEU* 1.3 79.2 - - - +
2380F THR* 1.3 58.6 + - - +
2382F GLU* 3.3 6.1 + - - +
2383F GLU* 2.9 30.6 + - - +
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Residues in contact with THR2380 (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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2324F TRP* 6.3 0.4 - - + -
2368F ALA* 3.3 32.7 - - + +
2377F LEU* 3.5 11.3 + - - -
2378F LEU 3.3 0.4 - - - -
2379F ALA* 1.3 78.4 - - - +
2381F ILE* 1.3 59.4 + - - +
2383F GLU* 3.3 6.4 + - + +
2384F ALA* 2.9 27.9 + - + +
2423F ILE* 5.0 8.5 - - + -
2427F TYR* 4.5 17.9 - - + +
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Residues in contact with ILE2381 (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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2377F LEU* 3.2 29.7 + - + +
2378F LEU* 3.8 7.4 - - + +
2379F ALA 3.3 0.2 - - - -
2380F THR* 1.3 77.0 - - - +
2382F GLU* 1.3 62.2 + - - +
2384F ALA* 3.3 3.6 + - + -
2385F ILE* 3.3 35.3 + - + +
2423F ILE* 5.2 2.7 - - + -
2424F MET* 4.8 11.4 - - + -
2427F TYR* 3.6 46.9 - - + -
2470F ILE* 5.7 5.2 - - + -
2473F LEU* 3.7 25.6 - - + +
2495F PHE* 6.2 1.3 - - + -
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Residues in contact with GLU2382 (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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2378F LEU* 2.9 21.7 + - + +
2379F ALA* 3.8 6.1 - - - +
2381F ILE* 1.3 77.9 - - - +
2383F GLU* 1.3 59.5 + - - +
2385F ILE* 3.3 18.2 + - - +
2473F LEU* 4.7 19.7 - - + +
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Residues in contact with GLU2383 (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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2379F ALA 2.9 17.0 + - - +
2380F THR* 3.8 7.0 - - + +
2382F GLU* 1.3 75.2 - - - +
2384F ALA* 1.3 64.9 + - - +
2385F ILE 3.5 5.0 - - - +
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Residues in contact with ALA2384 (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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2380F THR* 2.9 18.5 + - + +
2381F ILE* 3.7 7.9 - - + +
2382F GLU 3.3 0.2 - - - -
2383F GLU* 1.3 79.4 - - - +
2385F ILE* 1.3 67.9 + - + +
2423F ILE* 4.4 27.8 - - + -
2424F MET* 5.1 4.3 - - + +
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Residues in contact with ILE2385 (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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2381F ILE* 3.3 29.7 + - + +
2382F GLU* 3.3 16.4 - - - +
2383F GLU 3.5 5.7 - - - +
2384F ALA* 1.3 86.3 - - + +
2424F MET* 3.8 28.7 - - + -
2473F LEU* 5.5 3.6 - - + -
2474F PRO* 5.6 6.1 - - + +
2495F PHE* 4.1 38.8 - - + +
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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