Contacts of the helix formed by residues 173 - 179 (chain F) in PDB entry 1OUQ
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 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172F LEU* 1.3 78.4 - - - +
174F ILE* 1.3 65.8 + - - +
175F ALA 3.3 0.2 - - - -
176F GLU* 3.1 45.1 + - - +
177F ILE* 3.2 19.8 + - - +
200F THR* 4.2 5.9 + - - -
201F LYS* 3.5 41.3 - - - +
202F THR* 4.7 5.7 + - - -
288F GLY 5.8 1.3 - - - -
289F HIS* 4.5 10.4 - - + -
292F ARG* 3.2 32.1 - - - +
313F GLY 5.3 3.0 + - - -
314F GLY 5.6 2.8 + - - -
315F TRP* 4.9 2.4 - - - +
115G A3P 2.8 33.4 + - - -
124H A 4.2 11.7 - - - -
125H T 3.6 13.7 - - - +
116Y T 3.7 6.1 + - - -
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Residues in contact with ILE 174 (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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163F PHE* 4.0 25.1 - - + -
167F ALA* 6.3 0.2 - - + -
172F LEU 4.0 0.2 + - - -
173F ARG* 1.3 73.8 - - - +
175F ALA* 1.3 58.8 + - - +
177F ILE* 3.1 10.1 + - + +
178F ALA* 2.9 24.4 + - - +
258F THR* 3.7 21.7 - - + +
261F LEU* 3.6 19.0 - - + +
262F GLU* 3.6 29.8 - - + -
265F PHE* 4.5 1.8 - - + -
288F GLY* 3.9 28.2 + - - +
289F HIS* 5.9 0.2 + - - -
125H T 3.3 33.8 - - + +
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Residues in contact with ALA 175 (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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40F HIS* 6.1 2.2 - - + -
174F ILE* 1.3 74.9 - - - +
176F GLU* 1.3 70.1 + - - +
177F ILE 3.1 0.7 + - - -
178F ALA* 3.1 12.7 + - - +
179F ARG* 3.4 30.5 + - - +
255F GLN* 5.0 1.5 + - - +
258F THR* 3.5 17.3 - - + -
124H A 4.6 4.9 - - - +
125H T 2.9 30.6 + - - +
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Residues in contact with GLU 176 (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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172F LEU* 4.1 22.7 - - + +
173F ARG* 3.1 66.5 + - - +
174F ILE 3.3 0.2 - - - -
175F ALA* 1.3 80.2 - - - +
177F ILE* 1.3 61.6 + - - +
179F ARG* 3.5 25.2 + - - +
180F ILE* 3.9 9.4 + - - +
197F ILE* 4.4 11.2 - - + +
199F ARG 3.8 21.1 - - - +
200F THR* 3.7 16.5 - - + +
201F LYS* 3.4 11.6 + - - +
124H A 4.9 4.3 - - - +
125H T 4.9 1.4 + - - -
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Residues in contact with ILE 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F PHE* 4.1 32.3 - - + -
166F ILE* 4.1 22.7 - - + -
167F ALA* 4.1 13.9 - - + -
172F LEU* 3.7 33.2 - - + +
173F ARG 3.2 17.7 - - - +
174F ILE* 3.1 8.8 + - + +
175F ALA 3.0 0.8 - - - -
176F GLU* 1.3 74.3 - - - +
178F ALA* 1.3 63.0 + - - +
179F ARG 2.9 6.2 + - - -
180F ILE* 3.1 31.4 + - + +
239F PHE* 4.6 17.6 - - + +
261F LEU* 4.4 3.4 - - + -
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Residues in contact with ALA 178 (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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174F ILE 2.9 13.1 + - - +
175F ALA* 3.1 12.5 + - - +
177F ILE* 1.3 76.4 - - - +
179F ARG* 1.3 57.7 + - - +
180F ILE 3.7 2.4 + - - +
237F TYR* 4.2 8.1 - - - +
239F PHE* 5.2 9.3 + - - +
255F GLN* 3.6 30.7 - - - +
256F LEU* 3.4 29.7 + - - +
258F THR* 4.8 4.9 - - + -
261F LEU* 4.1 12.5 - - + +
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Residues in contact with ARG 179 (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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126A ASP* 5.1 11.2 - - - +
175F ALA* 3.4 26.4 + - - +
176F GLU* 3.5 23.4 + - - +
177F ILE 2.9 0.6 - - - -
178F ALA* 1.3 77.5 - - - +
180F ILE* 1.3 66.3 + - - +
181F ARG* 3.2 13.7 + - - +
184F ASP* 4.1 2.8 - - - +
197F ILE* 6.3 0.2 - - - +
199F ARG* 3.6 62.2 + - - +
200F THR* 5.1 1.6 - - - +
237F TYR* 3.8 7.9 - - + +
255F GLN* 3.7 23.6 - - - +
124H A 5.2 4.2 + - - -
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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