Contacts of the helix formed by residues 179 - 190 (chain A) in PDB entry 2UVQ
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ASP 5.0 3.4 + - - -
175A ARG 5.8 1.6 + - - -
180A LEU* 1.3 72.4 + - - +
181A GLU* 2.9 21.5 + - - +
182A GLN* 3.1 50.1 + - - +
183A ILE* 3.3 24.7 + - - +
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Residues in contact with LEU 180 (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 VAL* 4.2 24.7 - - + -
179A ASP* 1.3 75.7 + - - +
181A GLU* 1.3 56.8 + - + +
183A ILE* 3.0 13.3 + - + +
184A LEU* 2.8 71.4 + - + +
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Residues in contact with GLU 181 (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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179A ASP* 2.9 16.2 + - - +
180A LEU* 1.3 78.5 - - + +
182A GLN* 1.3 59.2 + - + +
184A LEU* 4.4 4.6 - - - +
185A THR* 2.5 39.8 + - - +
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Residues in contact with GLN 182 (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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80A LEU 6.2 0.2 - - - +
82A GLY* 5.9 8.4 - - - -
179A ASP* 3.1 41.9 + - - +
181A GLU* 1.3 75.8 - - + +
183A ILE* 1.3 67.6 + - + +
185A THR* 3.4 3.2 + - - -
186A GLN* 2.9 27.8 + - - +
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Residues in contact with ILE 183 (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* 5.9 1.1 - - + -
169A ARG* 5.0 13.2 - - + +
170A VAL* 4.8 22.4 - - + +
173A ASP* 3.1 50.7 - - + +
179A ASP 3.3 25.1 + - - +
180A LEU* 3.0 12.7 + - + +
182A GLN* 1.3 79.1 - - + +
184A LEU* 1.3 64.1 + - + +
186A GLN* 3.4 6.0 + - - +
187A TYR* 3.1 22.6 + - + +
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Residues in contact with LEU 184 (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* 4.3 20.4 - - + -
170A VAL* 4.1 25.8 - - + -
180A LEU* 2.8 46.4 + - + +
181A GLU* 4.4 4.3 - - - +
183A ILE* 1.3 72.2 - - + +
185A THR* 1.3 66.0 + - - +
187A TYR* 3.1 14.6 + - + +
188A THR* 3.2 17.8 + - + +
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Residues in contact with THR 185 (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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181A GLU* 2.5 32.0 + - - +
182A GLN* 4.1 2.7 - - - -
184A LEU* 1.3 76.3 - - - +
186A GLN* 1.3 62.5 + - - +
188A THR* 3.3 7.5 + - - +
189A THR* 3.1 40.7 + - + +
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Residues in contact with GLN 186 (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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82A GLY* 3.1 29.1 + - - +
84A TYR 3.1 26.7 + - - -
85A ASN* 4.6 0.8 - - - +
86A PHE* 5.0 9.2 - - - +
87A ASP* 5.2 0.9 + - - +
169A ARG* 5.7 1.2 + - - -
182A GLN 2.9 21.2 + - - +
183A ILE* 3.6 7.2 - - - +
184A LEU 3.2 0.2 - - - -
185A THR* 1.3 77.3 - - - +
187A TYR* 1.3 62.1 + - - +
189A THR* 4.3 4.0 - - - -
190A PHE* 3.2 51.6 + - - +
191A VAL* 3.3 19.0 + - - +
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A SER* 4.0 27.7 + - - -
165A ARG* 4.8 10.3 + - - +
166A LEU* 3.8 46.5 - - + +
169A ARG* 4.0 16.8 - - - -
183A ILE* 3.1 14.3 + - + +
184A LEU* 3.1 13.2 + - + +
186A GLN* 1.3 75.4 - - - +
188A THR* 1.3 71.5 + - + +
191A VAL* 2.9 40.5 + - + -
192A LYS* 2.7 59.3 + - + +
195A PHE* 6.1 1.9 - - + +
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Residues in contact with THR 188 (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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184A LEU* 3.2 11.1 + - + +
185A THR* 3.3 15.2 + - - +
187A TYR* 1.3 94.3 - - + +
189A THR* 1.3 68.8 + - - +
192A LYS* 4.1 13.9 - - + +
193A PRO* 3.6 13.2 - - - +
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Residues in contact with THR 189 (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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185A THR* 3.1 33.2 + - + +
186A GLN* 4.3 0.3 - - - -
188A THR* 1.3 84.5 - - - +
190A PHE* 1.3 85.4 + - - +
193A PRO* 3.2 16.9 - - - +
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Residues in contact with PHE 190 (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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82A GLY 3.9 4.3 - - - -
83A GLN* 3.7 39.7 - - - -
85A ASN* 3.6 39.1 + - + +
186A GLN* 3.2 35.4 + - + +
189A THR* 1.3 103.3 + - - +
191A VAL* 1.3 63.9 + - + +
193A PRO* 3.5 4.0 - - - +
194A ALA* 3.2 25.5 + - - +
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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