Contacts of the helix formed by residues 176 - 183 (chain C) in PDB entry 2ZJQ
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 ASN 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 2.3 40.8 + - - +
38C ARG* 3.4 7.7 + - - +
104C LEU* 5.2 0.7 - - - -
149C LEU* 6.2 0.4 - - - +
170C LEU* 4.8 1.5 - - + +
174C GLY 4.6 0.2 - - - +
175C VAL* 1.3 88.6 - - - +
177C VAL* 1.3 66.8 + - - +
178C TYR* 2.7 31.6 + - - +
179C ASP* 2.8 35.2 + - + +
180C ILE* 2.9 16.5 + - - +
626X A 2.9 16.6 + - - +
627X A 5.5 2.7 - - - -
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.9 15.3 - - + +
30C VAL* 3.8 32.3 - - + -
31C VAL* 4.9 5.2 - - + +
34C GLN* 4.1 3.5 + - - +
100C ARG* 5.3 2.2 - - - +
103C GLY* 3.7 11.7 - - - -
104C LEU* 3.0 40.0 - - + +
107C ALA* 4.2 16.4 - - + -
176C ASN* 1.3 71.8 + - - +
178C TYR* 1.3 66.6 + - - +
180C ILE* 2.7 17.2 - - - +
181C LEU* 3.2 12.9 - - + +
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 4.0 23.5 - - + +
34C GLN* 3.2 16.6 - - - +
35C LEU* 3.9 22.9 - - + -
38C ARG* 3.3 26.9 - - - +
176C ASN* 2.7 20.2 + - - +
177C VAL* 1.3 72.0 - - - +
179C ASP* 1.3 77.9 + - - -
181C LEU* 2.6 20.3 + - - -
182C ARG* 2.7 42.2 + - + -
12I SER* 5.3 8.1 - - - -
1216X G 2.7 45.3 + - - +
1217X U 4.3 5.3 + - - -
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Residues in contact with ASP 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 5.4 1.6 + - - -
149C LEU* 3.7 16.8 - - + +
168C SER* 4.6 5.4 + - - -
169C VAL 5.3 0.2 - - - +
170C LEU* 4.0 24.2 - - + +
176C ASN* 2.8 30.8 + - - +
178C TYR* 1.3 79.5 - - - +
180C ILE* 1.3 53.8 + - - +
182C ARG* 2.7 42.4 + - - +
183C HIS* 2.7 38.9 + - - +
626X A 5.0 5.7 + - - +
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Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LEU* 4.5 2.7 - - + +
107C ALA* 3.4 41.3 - - + +
108C ILE* 3.7 21.8 - - + +
111C ARG* 3.1 28.5 + - + +
149C LEU* 3.5 19.4 - - + +
175C VAL* 6.1 3.1 - - + -
176C ASN 2.9 15.7 + - - +
177C VAL* 2.7 36.8 - - - +
178C TYR 2.7 2.8 + - - -
179C ASP* 1.3 76.5 - - - +
181C LEU* 1.3 56.3 + - - +
183C HIS* 2.9 24.1 + - - +
184C ASP 4.3 0.2 - - - +
186C LEU* 4.2 11.6 - - + +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 3.8 36.8 - - + +
31C VAL* 5.3 10.1 - - + -
107C ALA* 5.0 5.2 - - + +
110C SER* 5.6 7.6 - - - -
111C ARG* 3.8 21.5 + - - +
177C VAL* 3.2 19.5 - - + +
178C TYR* 2.6 6.8 + - - +
180C ILE* 1.3 80.6 - - + +
182C ARG* 1.3 62.0 + - - +
11I GLY* 4.9 6.3 - - - -
12I SER* 3.6 38.6 + - - +
15I ASP* 5.5 7.9 - - + -
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LYS* 4.3 23.0 + - - +
168C SER* 5.1 3.8 + - - -
178C TYR* 2.7 42.8 + - + +
179C ASP* 2.7 35.2 + - - +
181C LEU* 1.3 80.9 - - - +
183C HIS* 1.3 84.2 + - + +
12I SER* 4.2 14.3 - - - +
1217X U 4.2 31.4 + - - +
1218X C 5.4 0.5 + - - -
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Residues in contact with HIS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ARG* 2.6 32.4 + - - -
147C LYS* 3.7 33.2 - - + +
148C VAL 3.9 12.3 - - - -
149C LEU* 4.3 20.5 - - + +
166C TRP 4.6 2.2 - - - -
167C VAL 5.0 0.7 - - - -
168C SER* 3.1 32.4 - - - -
179C ASP* 2.7 37.0 + - + +
180C ILE 2.9 4.1 - - - +
182C ARG* 1.3 113.0 + - + +
184C ASP* 1.3 56.3 + - - +
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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