Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 3UXA
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 2.6 28.9 + - - -
161A ASN* 1.3 80.1 - - + +
163A GLU* 1.3 59.3 + - - +
164A GLU* 3.0 11.2 + - - +
165A ASP* 2.8 34.1 + - - +
166A LEU* 3.1 27.7 + - - +
197A LEU* 3.5 13.3 - - - +
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Residues in contact with GLU 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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162A ASP* 1.3 73.2 - - - +
164A GLU* 1.3 64.8 + - - +
166A LEU* 3.9 3.8 - - + +
167A ASP* 3.0 24.4 + - - +
196A LYS* 5.9 2.1 - - - +
197A LEU* 4.0 11.3 - - + +
200A MET* 3.9 40.0 - - + +
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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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3A ARG* 5.6 3.3 + - - -
162A ASP* 3.0 10.3 + - - +
163A GLU* 1.3 75.6 - - - +
165A ASP* 1.3 68.9 + - - +
167A ASP* 3.0 9.8 + - - +
168A ILE* 3.0 41.3 + - + +
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Residues in contact with ASP 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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134A VAL* 3.6 31.5 - - + +
135A LYS* 3.6 25.1 + - - +
159A VAL 4.4 0.9 - - - +
160A ILE* 3.5 22.6 - - + +
161A ASN* 2.7 32.1 + - - +
162A ASP* 2.8 24.9 + - - +
164A GLU* 1.3 72.5 - - - +
166A LEU* 1.3 59.4 - - - +
168A ILE* 3.1 4.0 + - - +
169A ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 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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160A ILE* 3.6 22.6 - - + +
162A ASP 3.1 14.8 + - - +
163A GLU* 3.9 5.6 - - + +
165A ASP* 1.3 79.2 - - - +
167A ASP* 1.3 57.5 + - - +
169A ALA* 3.2 1.8 + - - +
170A LEU* 2.9 47.6 + - + +
177A ILE* 4.2 8.5 - - + -
197A LEU* 3.7 36.8 - - + +
200A MET* 3.8 26.0 - - + +
201A ILE* 3.5 23.8 - - + -
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Residues in contact with ASP 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 GLU 3.0 17.4 + - - +
164A GLU* 3.0 10.8 + - - +
166A LEU* 1.3 77.2 - - - +
168A ILE* 1.3 60.9 + - - +
170A LEU* 3.3 10.1 + - - +
171A ARG* 2.7 61.0 + - - +
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Residues in contact with ILE 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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3A ARG* 5.4 7.6 - - - +
134A VAL* 3.8 20.0 - - + -
137A LEU 6.1 0.4 - - - +
139A GLU* 4.5 37.2 - - + +
142A LEU* 3.6 27.4 - - + -
164A GLU* 3.0 34.2 + - + +
165A ASP 3.6 6.1 - - - +
167A ASP* 1.3 79.3 - - - +
169A ALA* 1.3 63.0 + - - +
171A ARG* 3.5 15.5 - - - +
172A ILE* 3.3 23.7 + - + +
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Residues in contact with ALA 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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158A ILE* 3.8 23.8 - - + -
160A ILE* 4.3 3.8 - - + -
165A ASP 2.9 13.4 + - - +
166A LEU* 3.2 11.6 + - - +
168A ILE* 1.3 76.1 - - - +
170A LEU* 1.3 64.4 + - - +
172A ILE* 3.1 17.4 - - - +
174A ALA* 3.0 25.4 + - + -
177A ILE* 4.0 23.1 - - + -
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Residues in contact with LEU 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* 2.9 40.9 + - + +
167A ASP* 3.3 9.2 + - - +
168A ILE 3.3 0.2 - - - -
169A ALA* 1.3 77.9 - - - +
171A ARG* 1.3 63.8 + - - +
173A GLY* 2.9 14.2 + - - +
174A ALA 4.7 3.6 - - - +
177A ILE* 4.6 11.2 - - + -
200A MET 4.8 6.5 - - - +
202A PRO* 3.7 35.7 - - + -
205A VAL* 4.8 7.4 - - + -
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Residues in contact with ARG 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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139A GLU* 3.1 35.1 + - + +
167A ASP* 2.7 52.9 + - - +
168A ILE* 3.5 19.4 - - - +
169A ALA 3.2 0.4 - - - -
170A LEU* 1.3 78.6 - - - +
172A ILE* 1.3 60.8 + - + +
173A GLY* 3.2 2.4 + - - -
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Residues in contact with ILE 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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139A GLU* 4.8 7.4 - - + +
142A LEU* 3.8 40.8 - - + +
143A GLU* 4.3 29.4 - - + +
146A LEU* 4.0 27.6 - - + +
150A ARG* 4.7 3.8 + - - -
158A ILE* 4.0 21.8 - - + -
168A ILE* 3.4 13.7 - - + +
169A ALA* 3.1 20.2 - - - +
171A ARG* 1.3 78.6 - - + +
173A GLY* 1.3 60.6 + - - +
174A ALA* 4.2 3.8 - - + +
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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