Contacts of the helix formed by residues 167 - 175 (chain C) in PDB entry 4AOR
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 SER 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ALA* 3.9 21.1 - - - +
166C LEU* 1.3 74.6 - - - +
168C ASP* 1.3 63.1 + - - +
169C SER* 3.2 21.1 + - - -
170C SER* 2.6 40.8 + - - -
171C CYS* 2.9 8.8 + - - +
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Residues in contact with ASP 168 (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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166C LEU 3.6 1.6 + - - -
167C SER* 1.3 72.8 - - - +
169C SER* 1.3 58.8 + - - +
171C CYS* 3.1 7.1 + - - +
172C LYS* 2.8 63.9 + - - +
179C ILE* 4.4 7.4 - - - +
183C MET 5.4 2.1 - - - +
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Residues in contact with SER 169 (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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167C SER* 3.2 13.9 + - - -
168C ASP* 1.3 81.1 + - - +
170C SER* 1.3 59.0 + - - +
172C LYS* 3.3 7.3 + - - +
173C SER* 2.8 34.1 + - - -
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Residues in contact with SER 170 (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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166C LEU* 3.6 11.3 - - - +
167C SER* 2.6 40.2 + - - -
169C SER* 1.3 78.5 + - - +
171C CYS* 1.3 59.8 + - - +
173C SER* 3.8 7.5 - - - -
174C ALA* 3.0 28.6 + - - +
189C LEU* 4.4 26.4 - - - +
226C PRO* 5.6 0.2 - - - +
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Residues in contact with CYS 171 (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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166C LEU 5.3 0.2 - - - +
167C SER 2.9 13.7 + - - +
168C ASP* 3.1 15.2 + - - +
170C SER* 1.3 78.4 + - - +
172C LYS* 1.3 57.5 + - - +
174C ALA* 3.2 5.1 + - - +
175C TYR* 3.0 23.6 + - - +
179C ILE* 3.7 30.0 - - + +
184C PHE* 4.0 5.4 - - - -
185C CYS* 2.0 65.5 - - + +
226C PRO* 5.6 0.4 - - - -
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Residues in contact with LYS 172 (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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168C ASP* 2.8 48.1 + - - +
169C SER* 3.9 6.3 - - - +
171C CYS* 1.3 78.8 - - - +
173C SER* 1.3 55.5 + - - +
175C TYR 4.4 1.3 - - - +
176C PRO* 3.1 33.2 - - + +
177C GLY 6.1 0.7 - - - +
179C ILE* 3.6 42.1 + - + +
180C THR 4.8 4.6 + - - -
181C SER* 5.4 2.0 - - - +
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Residues in contact with SER 173 (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* 2.8 19.9 + - - -
170C SER* 3.9 7.8 - - - -
172C LYS* 1.3 77.2 - - - +
174C ALA* 1.3 61.9 + - - +
176C PRO* 3.6 14.5 - - - +
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Residues in contact with ALA 174 (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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170C SER 3.0 18.2 + - - +
171C CYS 3.4 5.8 - - - +
173C SER* 1.3 78.8 - - - +
175C TYR* 1.3 69.9 - - + +
176C PRO* 3.5 4.6 - - - +
189C LEU* 5.0 3.6 - - + -
224C ASN* 3.4 24.5 - - - +
225C LYS* 2.9 28.2 + - - -
226C PRO* 3.9 15.5 - - + -
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Residues in contact with TYR 175 (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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171C CYS 3.0 10.3 + - - -
172C LYS* 3.2 6.5 - - - +
174C ALA* 1.3 86.1 - - + +
176C PRO* 1.3 66.5 - - - +
177C GLY 3.3 0.5 + - - -
178C GLN* 3.2 28.2 + - + +
179C ILE* 3.8 23.4 + - + +
185C CYS* 4.0 3.8 - - - -
216C TRP* 3.7 26.7 - + + -
217C GLY* 3.6 1.2 - - - -
218C SER* 3.2 28.1 + - - -
225C LYS* 3.2 37.4 - - + +
226C PRO* 2.6 44.4 + - + -
228C VAL* 3.5 22.7 - - + -
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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