Contacts of the helix formed by residues 167 - 175 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ALA* 3.8 19.9 - - - +
165A ILE 4.1 0.2 + - - -
166A LEU* 1.3 74.5 - - - +
168A ASP* 1.3 64.5 + - - +
169A SER* 3.3 12.0 + - - -
170A SER* 3.0 27.3 + - - -
171A CYS* 3.0 20.6 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA* 5.2 0.6 - - - +
166A LEU 3.5 2.7 + - - -
167A SER* 1.3 72.0 - - - +
169A SER* 1.3 58.0 + - - +
171A CYS* 3.4 6.8 + - - +
172A LYS* 2.6 69.1 + - - +
179A ILE* 4.4 10.7 - - - +
180A THR 5.2 1.4 - - - +
181A SER* 6.1 0.3 - - - -
183A MET 4.8 5.4 - - - +
184A PHE* 6.0 0.5 - - - -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER* 3.3 12.8 + - - -
168A ASP* 1.3 77.1 + - - +
170A SER* 1.3 63.1 + - - +
172A LYS* 3.5 5.8 + - - +
173A SER* 2.9 33.2 + - - -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 3.4 24.9 - - - +
167A SER* 3.0 26.1 + - - -
169A SER* 1.3 78.1 + - - +
171A CYS* 1.3 60.0 + - - +
173A SER* 3.4 8.5 + - - -
174A ALA* 3.0 28.8 + - - +
189A LEU* 5.3 14.4 - - - +
226A PRO* 5.7 0.2 - - - +
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Residues in contact with CYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 5.2 0.7 - - - +
167A SER 3.0 12.8 + - - +
168A ASP* 3.5 13.5 - - - +
170A SER* 1.3 77.0 + - - +
172A LYS* 1.3 59.1 + - - +
174A ALA* 3.1 6.4 + - - +
175A TYR* 3.0 26.0 + - - -
179A ILE* 3.6 30.3 - - + +
184A PHE* 4.1 3.8 - - - -
185A CYS* 2.1 65.3 - - + +
226A PRO* 5.5 0.9 - - - -
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 2.6 51.1 + - - +
169A SER* 4.0 5.6 - - - +
171A CYS* 1.3 74.6 - - - +
173A SER* 1.3 56.8 + - - +
175A TYR 3.1 1.7 - - - +
176A PRO* 2.9 35.3 - - + +
177A GLY 5.9 1.6 - - - +
179A ILE* 3.9 39.0 - - + +
180A THR 5.5 2.2 - - - -
181A SER* 6.3 0.6 - - - +
79C ASN 5.6 6.5 - - - +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A SER* 2.9 22.7 + - - -
170A SER* 3.6 9.4 - - - -
171A CYS 3.2 0.2 - - - -
172A LYS* 1.3 76.1 - - - +
174A ALA* 1.3 61.6 + - - +
176A PRO* 3.5 13.2 - - - +
45C TYR* 4.3 13.7 + - - -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A SER 3.0 13.2 + - - +
171A CYS 3.1 8.5 + - - +
173A SER* 1.3 77.6 - - - +
175A TYR* 1.3 59.1 + - + +
176A PRO* 3.4 3.8 - - - +
189A LEU* 5.2 4.0 - - + -
224A ASN 3.5 22.2 - - - +
225A LYS* 2.6 35.2 + - - -
226A PRO* 3.7 21.8 - - + -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A CYS 3.0 12.5 + - - +
172A LYS* 3.1 7.4 - - - +
174A ALA* 1.3 85.7 - - + +
176A PRO* 1.3 67.4 - - - +
177A GLY 3.3 0.7 + - - -
178A GLN* 3.2 30.6 + - + +
179A ILE* 3.9 19.2 + - + +
185A CYS* 4.1 2.2 - - - -
216A TRP* 3.7 21.5 - + - -
217A GLY* 3.5 1.2 - - - -
218A SER* 3.2 32.2 + - - -
225A LYS* 3.3 35.4 + - + +
226A PRO* 2.6 45.1 + - + -
228A VAL* 3.6 21.3 - - + -
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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