Contacts of the helix formed by residues 176 - 181 (chain C) in PDB entry 1OJ7
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 ASP 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY 3.2 15.7 - - - +
16C LYS* 3.3 14.2 - - - +
17C GLY* 2.9 23.7 + - - -
18C ALA 4.1 2.6 + - - +
19C ILE 5.7 0.2 - - - +
49C GLN* 5.3 0.3 - - - +
137C LEU 4.9 1.9 + - - +
174C VAL* 3.9 7.6 + - + -
175C LEU* 1.3 71.8 - - - +
177C PRO* 1.3 66.6 - - - +
178C VAL* 3.0 23.2 + - - +
179C TYR* 3.1 56.7 + - + +
245C MET* 4.0 9.3 - - - +
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Residues in contact with PRO 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 3.7 22.0 - - + -
15C GLY* 4.0 5.2 - - - +
175C LEU 3.6 9.2 - - - +
176C ASP* 1.3 88.4 - - - +
178C VAL* 1.3 60.7 + - - +
179C TYR 3.2 0.2 - - - -
180C THR* 2.6 25.4 + - - +
181C TYR* 3.4 9.1 - - - -
238C TYR* 3.7 35.4 - - + +
241C ARG* 4.2 6.7 - - + -
242C ALA* 3.9 23.1 - - - +
245C MET* 3.7 17.0 - - + -
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS* 3.8 37.9 - - + +
176C ASP* 3.0 18.3 + - - +
177C PRO* 1.3 75.7 - - - +
179C TYR* 1.3 68.3 + - + +
181C TYR* 3.1 54.3 + - + +
182C THR* 4.8 2.1 + - - +
238C TYR* 4.1 9.2 - - + -
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.4 27.1 - - + +
46C VAL* 3.6 33.0 - - + +
49C GLN* 2.9 34.4 + - - +
50C VAL* 5.4 0.2 - - - +
136C VAL* 3.6 24.9 - - + -
137C LEU 3.7 23.1 - - - +
138C THR* 3.9 24.9 - - + +
176C ASP* 3.1 42.0 + - + +
178C VAL* 1.3 83.3 - - + +
180C THR* 1.3 60.7 + - + +
181C TYR 3.7 0.3 + - - -
182C THR* 3.7 14.5 + - - +
183C LEU* 4.9 1.2 - - - +
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Residues in contact with THR 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU 5.9 0.2 - - - +
138C THR* 4.6 7.6 - - - +
139C LEU 5.4 4.3 - - - +
140C PRO* 5.6 2.2 - - + -
176C ASP 4.4 0.9 - - - +
177C PRO 2.6 19.8 + - - +
179C TYR* 1.3 75.6 - - + +
181C TYR* 1.3 65.3 + - - +
182C THR 3.1 3.4 - - - -
183C LEU* 3.1 33.3 + - + +
241C ARG* 3.2 43.0 + - - +
245C MET* 3.4 35.0 - - + -
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO 3.4 19.7 - - - -
178C VAL* 3.1 37.9 + - + +
180C THR* 1.3 78.2 - - - +
182C THR* 1.3 63.5 + - + +
183C LEU 3.6 3.6 + - - +
235C PRO* 3.2 33.8 - - - +
236C GLU* 3.5 45.6 + - + +
238C TYR* 3.2 35.9 - - - +
241C ARG* 3.7 27.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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