Contacts of the helix formed by residues 396 - 402 (chain F) in PDB entry 6IWQ
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 ARG 396 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288F ALA 3.3 18.4 + - - -
289F GLN* 4.2 3.2 + - - +
291F ALA 3.1 23.4 + - - -
292F LYS* 4.0 34.6 + - - +
294F GLY 4.0 12.8 - - - +
295F GLN 2.8 23.8 + - - +
297F LEU* 3.9 29.6 - - + -
394F ILE 3.4 2.0 + - - -
395F GLU* 1.3 73.5 - - - +
397F GLU* 1.3 66.1 + - - +
399F PHE* 3.3 2.7 + - - +
400F PHE* 3.2 51.7 + - + -
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Residues in contact with GLU 397 (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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116F LYS* 2.2 47.5 - - - +
295F GLN 4.5 0.2 + - - -
322F ARG* 3.6 9.6 - - - +
395F GLU* 3.2 18.9 + - - +
396F ARG* 1.3 81.2 - - - +
398F PHE* 1.3 64.0 + - - +
400F PHE* 3.1 10.4 + - + +
401F GLU* 2.9 27.4 + - + +
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Residues in contact with PHE 398 (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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115F PHE* 3.9 19.1 - + - -
322F ARG* 3.4 30.3 - - - +
323F THR* 3.4 49.6 - - + -
394F ILE* 3.8 22.4 - - + -
395F GLU* 3.1 19.0 + - + +
397F GLU* 1.3 75.7 - - - +
399F PHE* 1.3 62.7 + - - +
401F GLU* 3.0 25.4 + - - +
402F LEU* 3.0 47.2 + - + +
423F ILE* 4.4 10.5 - - + -
428F GLY* 4.7 7.2 - - - -
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Residues in contact with PHE 399 (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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284F ARG 5.3 0.9 - - - -
285F SER* 5.8 0.9 - - - -
297F LEU* 4.1 12.1 - - + -
299F TYR* 3.4 31.0 - + - -
392F PHE* 4.7 3.1 - + - -
394F ILE* 3.2 31.6 - - + +
395F GLU 3.0 10.2 + - - +
396F ARG* 3.7 10.3 - - - +
397F GLU 3.3 0.2 - - - -
398F PHE* 1.3 77.1 - - - +
400F PHE* 1.3 62.9 + - + +
402F LEU* 3.1 11.5 + - + -
404F LEU* 3.0 64.4 + - + -
405F TYR* 4.3 23.6 - + - -
419F ILE* 3.3 29.2 - - + -
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Residues in contact with PHE 400 (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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288F ALA* 3.7 32.8 - - + -
289F GLN* 4.1 16.4 - - + -
297F LEU* 5.2 0.7 - - + -
396F ARG* 3.2 57.5 + - + -
397F GLU* 3.1 10.5 + - + +
399F PHE* 1.3 77.0 - - + +
401F GLU* 1.3 55.7 + - - +
403F GLY* 2.6 27.2 + - - +
404F LEU* 3.6 31.0 - - + +
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Residues in contact with GLU 401 (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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114F THR 4.2 2.4 - - - +
115F PHE* 3.1 28.1 - - + +
116F LYS* 2.7 34.3 + - - +
322F ARG* 2.4 38.5 + - - -
397F GLU* 2.9 16.1 + - + +
398F PHE* 3.0 14.7 + - - +
400F PHE* 1.3 76.8 - - - +
402F LEU* 1.3 59.0 + - - +
403F GLY 3.4 0.5 + - - -
501F PHE* 3.4 18.0 - - - -
505F HIS* 4.4 5.2 - - + -
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Residues in contact with LEU 402 (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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115F PHE* 3.8 28.5 - - + -
394F ILE* 5.3 1.6 - - + -
398F PHE* 3.0 37.0 + - + +
399F PHE* 3.1 10.3 + - + +
400F PHE 3.1 0.4 - - - -
401F GLU* 1.3 75.4 - - - +
403F GLY* 1.3 58.8 + - - +
404F LEU 3.2 1.7 + - - +
419F ILE* 4.2 14.8 - - + -
422F LYS* 2.9 55.0 + - + +
423F ILE* 3.5 32.8 - - + -
426F CYS* 4.8 1.1 - - + -
501F PHE* 3.9 21.0 - - + -
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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