Contacts of the helix formed by residues 176 - 183 (chain C) 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 ASN 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C LEU* 4.9 0.8 - - - +
166C ILE* 2.8 40.1 - - + +
169C SER* 3.8 4.0 - - - -
170C ILE* 4.2 8.3 - - + -
175C PHE* 1.3 69.6 - - - +
177C MET* 1.3 54.9 + - - +
178C VAL* 2.8 8.0 + - - +
179C ALA* 2.7 38.3 + - - +
180C SER 3.3 7.4 + - - -
335C GLY 3.0 20.1 + - - +
336C ASN* 3.1 29.4 + - - +
338C TYR* 2.6 23.5 + - - -
444C LEU* 4.1 2.0 - - + +
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Residues in contact with MET 177 (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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169C SER* 3.0 18.3 + - - +
173C PHE* 3.2 40.2 - - + -
175C PHE* 3.1 13.4 + - - +
176C ASN* 1.3 72.5 - - - +
178C VAL* 1.3 60.7 + - - +
179C ALA 3.4 0.2 - - - -
180C SER* 3.7 4.7 - - - +
181C ASP* 2.9 49.0 + - - +
219C GLY* 4.1 16.6 - - - -
220C TRP 4.3 1.1 - - - +
221C SER* 3.1 38.4 - - - +
222C THR* 3.9 26.9 - - - +
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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
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158C LEU* 4.2 10.5 - - + -
162C PHE* 4.2 26.5 - - + -
165C ALA* 3.6 32.3 - - + +
166C ILE* 3.8 16.6 - - + -
169C SER* 3.8 8.7 - - - +
176C ASN* 2.8 6.7 + - - +
177C MET* 1.3 78.8 - - - +
179C ALA* 1.3 67.7 + - - +
181C ASP* 3.4 10.5 + - - +
182C MET* 3.4 21.6 + - + +
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Residues in contact with ALA 179 (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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156C LEU* 4.2 15.7 - - + +
158C LEU* 4.2 11.8 - - + +
176C ASN* 2.7 23.6 + - - +
178C VAL* 1.3 74.4 - - - +
180C SER* 1.3 71.9 + - - +
181C ASP 2.6 1.9 + - - -
182C MET* 2.6 25.3 + - - +
183C ILE* 3.4 7.8 + - - +
336C ASN 3.8 14.6 - - - +
338C TYR* 3.9 9.0 - - + -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASN 3.3 8.1 + - - -
177C MET* 4.1 6.5 - - - -
178C VAL 3.4 0.2 - - - -
179C ALA* 1.3 82.1 - - - +
181C ASP* 1.3 61.1 + - - +
183C ILE* 3.1 19.3 + - - +
221C SER* 2.7 18.4 + - - -
222C THR* 3.6 9.7 - - - +
225C ARG* 2.5 35.4 + - - +
338C TYR* 3.1 33.8 - - - -
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Residues in contact with ASP 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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177C MET* 2.9 35.6 + - - +
178C VAL* 3.7 7.6 - - - +
179C ALA 2.6 5.5 + - - -
180C SER* 1.3 74.1 - - - +
182C MET* 1.3 57.0 + - - +
183C ILE 3.4 3.5 - - - +
221C SER* 2.8 29.8 + - - -
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Residues in contact with MET 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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149C PRO* 3.3 31.0 - - + +
156C LEU* 4.1 11.2 - - + -
158C LEU* 4.0 24.0 - - + -
162C PHE* 4.1 28.7 - - + -
178C VAL* 3.4 20.2 - - + +
179C ALA* 2.6 26.0 + - - +
181C ASP* 1.3 72.1 - - + +
183C ILE* 1.3 59.9 + - - -
184C SER 4.1 0.9 + - - -
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Residues in contact with ILE 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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149C PRO* 4.7 0.2 - - - -
150C GLY* 3.8 21.3 - - - +
156C LEU* 3.6 33.2 - - + -
179C ALA 3.7 6.7 - - - +
180C SER* 3.1 10.9 + - - +
181C ASP 4.3 4.0 - - - +
182C MET* 1.3 79.5 - - - +
184C SER* 1.3 72.6 + - - +
185C LEU* 3.4 3.6 + - - +
187C ARG* 3.5 36.6 - - + +
221C SER* 5.8 0.2 - - - -
225C ARG* 3.0 18.5 + - - +
337C THR 4.6 0.2 - - - +
338C TYR* 3.5 43.3 - - + -
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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