Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 1OQY
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 GLU 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A VAL* 3.2 40.7 + - + +
159A THR 2.7 28.0 + - - +
160A GLY 3.2 1.1 - - - +
161A SER* 1.3 76.3 - - - +
163A TYR* 1.3 89.2 + - - +
164A GLU* 4.7 1.9 - - - +
165A THR* 3.4 9.7 + - - -
166A MET* 3.4 8.3 + - - +
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Residues in contact with TYR 163 (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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158A VAL* 4.7 4.3 - - + -
161A SER 2.7 2.0 + - - -
162A GLU* 1.3 96.3 - - + +
164A GLU* 1.3 76.8 + - + +
166A MET* 3.3 8.7 + - - +
167A LEU* 2.6 68.7 + - + +
177A ARG 4.5 1.7 + - - -
178A GLU* 5.7 0.2 - - - -
181A VAL* 2.9 50.7 - - + +
184A LEU* 5.2 7.2 - - + -
189A ASN* 6.1 5.4 - - + -
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Residues in contact with GLU 164 (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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161A SER* 2.5 57.1 + - - +
162A GLU* 4.7 2.3 - - - +
163A TYR* 1.3 100.0 + - + +
165A THR* 1.3 61.2 + - - -
167A LEU* 3.2 13.4 - - + +
168A THR* 3.0 27.7 + - - -
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Residues in contact with THR 165 (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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157A LEU 4.5 2.9 - - - +
159A THR* 2.5 39.2 + - + +
161A SER* 2.8 25.7 + - - -
162A GLU 3.5 8.3 - - - -
164A GLU* 1.3 80.1 - - - +
166A MET* 1.3 60.4 + - + +
168A THR* 3.6 7.1 + - - -
169A GLU* 3.3 20.0 + - + +
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Residues in contact with MET 166 (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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157A LEU* 3.2 46.9 - - + -
158A VAL* 4.9 1.3 - - + +
162A GLU 3.4 7.2 + - - +
163A TYR* 3.3 11.2 + - - +
165A THR* 1.3 78.1 - - + +
167A LEU* 1.3 58.9 + - - +
168A THR 3.0 1.8 - - - -
169A GLU* 2.7 33.9 + - + -
170A ILE* 2.9 31.4 + - + +
184A LEU* 3.3 9.9 - - + -
189A ASN* 2.9 27.6 - - + +
190A ASN* 3.7 9.9 - - - -
191A PRO* 3.8 3.8 - - + -
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Residues in contact with LEU 167 (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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163A TYR* 2.6 60.4 + - + +
164A GLU* 3.2 15.3 - - + +
166A MET* 1.3 73.1 - - - +
168A THR* 1.3 53.3 + - - +
171A MET* 2.6 52.0 + - + +
177A ARG* 3.6 24.9 - - + +
180A VAL* 3.3 38.8 - - + -
181A VAL* 3.5 7.4 - - - +
184A LEU* 4.4 2.7 - - + +
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Residues in contact with THR 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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164A GLU 3.0 12.8 + - - -
165A THR* 3.7 10.1 - - - -
166A MET 3.0 0.2 - - - -
167A LEU* 1.3 76.3 - - - +
169A GLU* 1.3 65.0 + - - +
170A ILE 3.2 0.2 + - - -
171A MET* 4.2 18.4 - - + +
172A SER* 3.0 32.0 + - - +
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Residues in contact with GLU 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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157A LEU* 4.6 14.3 - - + +
165A THR* 3.3 10.3 + - + +
166A MET* 2.7 29.3 + - + +
168A THR* 1.3 82.2 - - - +
170A ILE* 1.3 57.7 + - - +
172A SER* 4.4 4.6 - - - -
173A MET* 3.7 12.6 - - - +
191A PRO* 4.2 19.1 - - - +
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Residues in contact with ILE 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 MET* 2.9 30.2 + - + +
169A GLU* 1.3 76.6 - - - +
171A MET* 1.3 71.3 + - - +
172A SER 3.0 1.8 - - - -
173A MET* 2.6 33.6 + - + +
175A TYR* 3.5 8.9 - - + -
180A VAL* 3.2 22.4 - - + -
184A LEU* 3.3 23.1 - - + -
190A ASN 3.5 0.9 - - - +
191A PRO* 3.3 37.2 - - + -
194A ALA* 3.4 8.7 - - + -
195A VAL* 4.6 1.6 - - + -
198A LEU* 3.4 21.5 - - + -
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Residues in contact with MET 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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167A LEU* 2.6 39.8 + - + +
168A THR* 4.2 18.2 - - + +
170A ILE* 1.3 73.9 - - - +
172A SER* 1.3 51.6 + - - +
173A MET 2.6 0.2 + - - -
174A GLY* 2.5 31.5 + - - -
175A TYR* 3.1 25.9 + - - +
176A GLU 3.1 17.5 - - - +
177A ARG* 3.2 46.0 - - - +
180A VAL* 3.9 4.0 - - + +
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Residues in contact with SER 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 THR* 3.0 27.2 + - - +
169A GLU 4.4 5.2 - - - -
170A ILE 2.8 2.9 + - - -
171A MET* 1.3 77.9 - - - +
173A MET* 1.3 65.3 + - - +
174A GLY* 3.0 2.1 + - - -
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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