Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 2WOE
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 HIS 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.7 15.6 + + - -
120A SER 3.4 21.1 - - - -
121A GLU* 3.5 20.6 + - - +
123A ASP 3.4 20.2 - - - +
124A ALA* 3.9 14.9 - - + +
158A HIS 3.9 2.0 - - - -
159A ASN* 1.3 78.6 + - - +
161A PRO* 1.3 73.0 - - + +
162A LEU* 3.1 51.6 + - + +
163A SER* 3.1 5.6 + - - -
164A ASP* 2.9 32.3 + - - -
401A AR6 4.3 3.8 + - - -
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Residues in contact with PRO 161 (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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119A TYR* 3.9 18.4 - - + +
159A ASN* 5.6 0.9 - - - +
160A HIS* 1.3 96.6 - - + +
162A LEU* 1.3 57.5 + - + +
164A ASP* 3.7 12.0 - - + +
165A ALA* 3.0 29.6 + - - +
197A HIS* 4.0 19.3 + - + +
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Residues in contact with LEU 162 (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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124A ALA* 4.7 0.2 - - + -
160A HIS* 3.1 25.5 + - + +
161A PRO* 1.3 74.5 - - + +
163A SER* 1.3 61.1 + - - +
165A ALA* 3.5 0.7 + - - +
166A ALA* 3.0 28.9 + - - +
197A HIS* 3.7 29.8 - - + +
199A ASP* 4.2 17.9 - - - +
200A PHE* 3.5 26.3 - - + -
212A TYR* 3.6 28.7 - - + +
213A ILE* 3.8 15.3 - - + -
214A VAL* 3.8 11.0 - - + -
401A AR6 5.9 0.4 - - - +
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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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123A ASP 3.9 20.0 - - - -
124A ALA* 4.9 1.3 - - - +
125A GLY 4.2 10.4 + - - -
128A ALA* 3.8 13.9 - - - +
129A ALA* 4.9 1.6 + - - +
154A ALA* 5.2 0.9 - - - +
158A HIS* 3.5 22.8 + - - +
160A HIS* 3.1 11.2 + - - -
162A LEU* 1.3 76.5 - - - +
164A ASP* 1.3 68.1 + - - +
166A ALA* 3.1 3.1 + - - +
167A CYS* 3.0 29.7 + - - -
213A ILE* 4.1 12.4 - - - +
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Residues in contact with ASP 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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151A LEU* 3.7 23.2 - - + +
154A ALA* 5.4 3.1 - - - +
155A ARG* 3.1 46.0 + - - +
158A HIS 4.1 5.0 - - - +
159A ASN* 4.2 2.1 - - - +
160A HIS 2.9 35.4 + - - +
161A PRO* 3.7 10.6 - - + +
163A SER* 1.3 72.9 + - - +
165A ALA* 1.3 63.3 + - - +
167A CYS* 3.4 3.9 + - - +
168A LEU* 3.1 25.1 + - - +
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Residues in contact with ALA 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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161A PRO 3.0 20.1 + - - +
162A LEU 3.8 4.3 - - - +
164A ASP* 1.3 77.4 - - - +
166A ALA* 1.3 57.1 + - - +
168A LEU* 3.5 5.6 + - - +
169A THR* 2.8 34.7 + - - -
193A LEU* 3.6 21.0 - - + +
196A GLN* 3.7 10.6 + - - +
197A HIS* 3.6 19.7 - - + +
200A PHE* 4.5 1.1 - - + -
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Residues in contact with ALA 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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129A ALA* 4.5 2.2 - - + -
162A LEU 3.0 10.9 + - - +
163A SER 3.1 3.1 + - - +
165A ALA* 1.3 74.3 - - - +
167A CYS* 1.3 64.2 + - - +
169A THR* 3.3 3.4 + - - -
170A LEU* 2.9 31.1 + - - +
193A LEU* 4.4 3.9 - - - +
200A PHE* 4.4 3.1 - - + -
213A ILE* 3.4 39.9 - - + -
217A MET* 3.8 23.1 - - + +
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Residues in contact with CYS 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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128A ALA* 3.8 6.7 - - - -
129A ALA* 3.5 26.7 - - - -
132A CYS* 3.4 32.0 - - - -
150A VAL* 3.6 19.8 - - + +
151A LEU* 4.5 5.2 - - + -
154A ALA* 3.9 16.6 - - - -
163A SER* 3.0 21.7 + - - +
164A ASP 3.7 4.9 - - - +
166A ALA* 1.3 75.3 - - - +
168A LEU* 1.3 58.0 + - - +
170A LEU* 3.5 3.0 + - - +
171A GLY* 3.0 24.4 + - - -
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Residues in contact with LEU 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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146A LEU* 4.7 7.0 - - + -
147A GLU* 3.8 46.9 - - + +
150A VAL* 4.6 6.3 - - + -
151A LEU* 4.9 8.3 - - + -
164A ASP 3.1 15.0 + - - +
165A ALA* 3.9 6.3 - - - +
167A CYS* 1.3 76.7 - - - +
169A THR* 1.3 61.1 + - - +
171A GLY* 3.4 1.5 + - - -
172A ARG* 2.9 81.6 + - + +
196A GLN* 6.0 3.6 - - - +
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Residues in contact with THR 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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165A ALA 2.8 21.9 + - - -
166A ALA 3.6 4.3 - - - -
168A LEU* 1.3 75.4 - - - +
170A LEU* 1.3 57.4 + - - +
172A ARG* 3.2 7.7 + - - +
173A MET* 2.9 56.1 + - + +
189A GLU* 4.1 14.5 + - + +
190A ALA* 4.9 0.2 - - - -
193A LEU* 3.5 43.0 - - + +
196A GLN* 4.8 2.4 + - - -
217A MET* 4.3 5.6 - - + -
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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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129A ALA* 3.9 26.9 - - + +
132A CYS* 5.3 5.4 - - + -
166A ALA 2.9 20.5 + - - +
167A CYS* 3.8 3.8 - - - +
169A THR* 1.3 74.9 - - - +
171A GLY* 1.3 58.0 + - - +
173A MET* 3.3 9.1 + - - +
174A VAL* 2.9 34.6 + - - +
217A MET* 3.8 32.5 - - + -
220A VAL* 5.0 5.2 - - + -
221A LEU* 5.4 0.4 - - + -
250A LEU* 4.0 21.8 - - + -
253A MET* 3.8 22.7 - - + -
254A LEU* 4.1 21.9 - - + +
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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