Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 2WJW
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 LEU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A TYR* 3.3 35.4 - - + +
153A ASP 5.3 1.1 - - - +
154A SER* 5.5 6.5 - - - +
156A ARG 4.6 3.1 - - - +
157A GLY* 1.3 83.1 - - - +
159A SER* 1.3 67.6 + - - +
160A THR 3.1 3.4 - - - +
161A LEU* 3.4 21.9 - - + +
162A GLN* 3.1 39.3 + - - +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO 5.7 5.6 - - - -
118A THR* 6.6 0.2 - - - -
119A ASP* 3.6 12.2 + - - -
133A LYS* 3.3 34.9 + - - +
157A GLY* 4.7 0.2 - - - -
158A LEU* 1.3 79.3 - - - +
160A THR* 1.3 57.4 + - - +
162A GLN* 3.6 13.4 + - - +
163A ALA* 3.1 20.8 + - - +
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Residues in contact with THR 160 (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 LEU* 6.1 2.6 - - + +
133A LYS* 3.8 26.1 - - + +
136A LEU* 3.6 29.6 - - + -
150A TYR* 3.4 18.4 - - + +
157A GLY 6.2 0.9 - - - -
158A LEU* 3.1 1.2 - - - +
159A SER* 1.3 77.4 - - - +
161A LEU* 1.3 66.0 + - - +
163A ALA* 3.2 2.5 + - + +
164A VAL* 2.9 24.5 + - + +
210A ASP* 3.5 11.8 + - - +
238A ALA* 5.6 1.3 - - + -
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Residues in contact with LEU 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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150A TYR* 3.4 35.2 + - + -
152A TYR* 3.9 19.7 - - + +
158A LEU* 3.4 40.6 + - + +
160A THR* 1.3 76.7 - - - +
162A GLN* 1.3 57.1 + - + +
164A VAL* 3.0 5.0 + - + +
165A LEU* 2.8 65.5 + - + +
177A ALA* 4.2 13.2 - - + -
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Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 3.1 34.5 + - - +
159A SER* 3.7 12.6 - - - +
161A LEU* 1.3 85.2 - - + +
163A ALA* 1.3 57.9 + - - +
165A LEU* 3.8 5.7 - - + -
166A ASP* 2.8 46.8 + - - +
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Residues in contact with ALA 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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133A LYS* 3.7 28.0 - - + -
137A LEU* 4.4 13.5 - - + -
159A SER 3.1 15.9 + - - +
160A THR* 3.6 4.7 - - + +
161A LEU 3.2 0.2 - - - -
162A GLN* 1.3 79.0 - - - +
164A VAL* 1.3 59.4 + - + +
166A ASP* 3.8 6.8 - - - +
167A SER* 2.9 34.3 + - - -
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Residues in contact with VAL 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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136A LEU* 4.3 15.0 - - + -
137A LEU* 4.2 18.4 - - + -
140A ILE* 4.7 5.8 - - + -
148A PHE* 4.1 30.3 - - + -
150A TYR* 4.2 26.2 - - + -
160A THR* 2.9 19.9 + - + +
161A LEU* 3.0 5.6 + - - +
163A ALA* 1.3 78.6 - - + +
165A LEU* 1.3 58.7 + - + +
167A SER* 3.3 2.3 + - - -
168A ALA* 2.9 27.7 + - - +
173A TRP* 4.2 2.9 - - + -
175A VAL* 4.2 15.0 - - + -
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Residues in contact with LEU 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 LEU* 2.8 48.8 + - + +
162A GLN* 3.9 6.5 - - + +
164A VAL* 1.3 74.0 - - + +
166A ASP* 1.3 65.7 + - - +
168A ALA* 3.3 6.8 + - + +
169A ALA* 3.3 20.3 + - - +
175A VAL* 4.7 17.9 - - + +
177A ALA* 4.4 20.4 - - + -
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Residues in contact with ASP 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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162A GLN* 2.8 37.3 + - - +
163A ALA* 3.8 5.7 - - - +
165A LEU* 1.3 80.8 - - - +
167A SER* 1.3 60.6 + - - +
169A ALA* 3.4 14.6 + - - +
170A GLU* 3.4 12.1 + - - +
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Residues in contact with SER 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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137A LEU* 3.4 24.9 - - - +
141A GLU* 5.5 1.1 + - - -
163A ALA 2.9 19.5 + - - -
164A VAL 3.8 0.7 - - - -
166A ASP* 1.3 74.1 - - - +
168A ALA* 1.3 57.3 + - - +
170A GLU* 3.1 6.0 + - - +
171A LYS* 2.7 43.7 + - - +
173A TRP* 3.6 25.1 - - - -
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Residues in contact with ALA 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 VAL 2.9 16.4 + - - +
165A LEU* 3.5 10.1 - - + +
166A ASP 3.3 0.4 - - - -
167A SER* 1.3 76.7 - - - +
169A ALA* 1.3 56.4 + - - +
172A LYS* 2.8 26.3 + - - -
173A TRP* 3.0 32.3 + - + +
175A VAL* 3.8 27.4 - - + +
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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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165A LEU 3.3 8.8 + - - +
166A ASP* 3.7 11.7 - - - +
167A SER 3.2 0.4 - - - -
168A ALA* 1.3 78.2 - - - +
170A GLU* 1.3 57.9 + - - +
172A LYS* 3.0 27.4 + - - +
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP 3.4 9.7 + - - +
167A SER* 3.1 9.5 + - - +
169A ALA* 1.3 80.9 - - - +
171A LYS* 1.3 67.1 + - + +
172A LYS* 3.3 25.0 + - - +
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Residues in contact with LYS 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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141A GLU* 3.6 30.2 + - + +
146A ASP* 6.0 0.2 - - - +
167A SER* 2.7 27.2 + - - +
170A GLU* 1.3 81.5 - - + +
172A LYS* 1.3 75.6 + - - +
173A TRP* 3.4 39.2 - - + +
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Residues in contact with LYS 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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146A ASP* 4.2 8.3 - - - +
168A ALA 2.8 11.7 + - - -
169A ALA 3.0 20.7 + - - +
170A GLU* 3.3 20.4 + - - +
171A LYS* 1.3 83.3 - - - +
173A TRP* 1.3 62.9 + - - +
174A GLN* 4.0 2.9 + - - +
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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