Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 1UN0
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 THR 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLY* 1.3 75.4 - - - -
163A SER* 1.3 68.2 + - - +
164A ALA* 3.6 7.5 + - - +
165A GLN* 2.8 50.9 + - - +
166A THR* 2.9 12.4 + - - -
48D MET* 4.0 33.4 + - + +
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Residues in contact with SER 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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161A GLY 4.1 0.4 + - - -
162A THR* 1.3 73.1 - - - +
164A ALA* 1.3 57.4 + - - +
166A THR* 3.6 5.1 + - - -
167A LYS* 3.1 26.0 + - - +
203A ASP* 2.9 36.9 + - - +
207A TYR* 5.0 0.3 - - - -
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Residues in contact with ALA 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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162A THR* 2.9 8.9 + - - +
163A SER* 1.3 75.3 - - - +
165A GLN* 1.3 62.2 + - + +
167A LYS* 3.5 11.4 - - - +
168A VAL* 3.2 29.2 + - - +
48D MET 5.5 3.8 - - - +
49D ALA 5.2 2.9 - - - +
50D PHE 4.2 8.3 - - - +
51D LYS* 3.9 30.0 - - + +
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Residues in contact with GLN 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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123A ILE* 3.5 31.6 - - + +
124A ASP* 3.5 21.4 - - - +
127A ILE* 3.8 23.1 - - + -
158A ILE* 3.1 35.4 - - - +
161A GLY* 3.5 7.4 - - - -
162A THR* 2.8 40.6 + - - +
164A ALA* 1.3 76.5 - - + +
166A THR* 1.3 62.2 + - - +
167A LYS 3.4 0.2 - - - -
168A VAL* 3.8 5.1 + - - +
169A VAL* 3.7 5.7 + - - +
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Residues in contact with THR 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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158A ILE 4.1 0.2 + - - -
159A ALA* 2.7 32.9 + - - +
161A GLY 4.4 2.1 + - - -
162A THR 2.9 15.0 + - - -
163A SER* 3.6 12.0 - - - -
165A GLN* 1.3 73.0 - - - +
167A LYS* 1.3 67.2 + - - +
168A VAL 3.1 0.2 - - - -
169A VAL* 3.0 15.6 + - - +
170A VAL* 3.1 11.9 + - + +
199A ASN 4.4 4.1 + - - +
200A VAL* 4.0 33.4 - - + -
203A ASP* 4.5 5.8 + - + +
207A TYR* 4.2 15.5 - - + -
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Residues in contact with LYS 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 SER 3.1 14.7 + - - +
164A ALA* 3.5 11.4 - - - +
165A GLN 3.4 0.2 - - - -
166A THR* 1.3 80.7 - - - +
168A VAL* 1.3 63.9 + - + +
170A VAL* 3.2 1.7 + - - +
171A ASP* 2.8 53.4 + - - +
207A TYR* 3.3 26.9 + - - +
51D LYS 4.9 14.1 - - - +
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Residues in contact with VAL 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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127A ILE* 3.7 39.7 - - + -
132A VAL* 4.2 23.8 - - + -
164A ALA 3.2 17.0 + - - +
165A GLN 3.9 7.0 - - - +
166A THR 3.1 1.2 - - - -
167A LYS* 1.3 80.5 - - + +
169A VAL* 1.3 61.6 + - + +
171A ASP* 3.2 6.7 + - - +
172A ALA* 3.1 21.5 + - - +
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Residues in contact with VAL 169 (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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132A VAL* 4.5 4.5 - - + -
155A LEU* 3.9 27.8 - - + +
158A ILE* 3.4 33.2 - - + -
159A ALA* 4.1 15.5 - - + +
165A GLN 3.7 2.9 - - - +
166A THR 3.0 8.0 + - - +
168A VAL* 1.3 78.1 - - + +
170A VAL* 1.3 60.9 + - + +
172A ALA* 3.4 12.5 + - - +
174A ALA* 3.3 35.6 + - + +
175A VAL* 6.2 0.9 - - + -
178A PHE* 4.0 15.7 - - + -
200A VAL* 5.3 6.1 - - + -
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Residues in contact with VAL 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 THR* 3.1 15.9 + - + +
167A LYS 3.8 6.3 - - - +
169A VAL* 1.3 76.5 - - - +
171A ASP* 1.3 62.5 - - - +
173A ASP* 3.1 20.4 + - - -
174A ALA 4.2 2.2 + - - +
175A VAL* 4.5 8.2 + - + -
200A VAL* 3.7 37.5 - - + -
207A TYR* 4.0 33.4 - - + +
210A TYR* 4.1 27.4 + - + -
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Residues in contact with ASP 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 LYS* 2.8 58.1 + - - +
168A VAL* 3.2 6.9 + - - +
170A VAL* 1.3 77.6 - - - +
172A ALA* 1.3 56.8 + - - +
173A ASP* 3.1 9.9 + - - +
207A TYR* 4.8 1.6 + - - -
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Residues in contact with ALA 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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132A VAL* 3.6 31.2 - - + -
133A PRO* 4.8 12.1 - - + +
136A VAL* 3.4 25.1 - - + +
168A VAL 3.1 7.0 + - - +
169A VAL 3.6 8.5 - - - +
170A VAL 3.1 1.0 - - - -
171A ASP* 1.3 75.3 - - - +
173A ASP* 1.3 68.8 + - - +
174A ALA 3.4 0.4 - - - -
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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