Contacts of the helix formed by residues 153 - 164 (chain E) in PDB entry 2WJZ
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 153 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E ILE* 3.5 32.3 - - + -
131E ALA* 3.8 17.5 - - + -
138E PHE* 2.9 45.4 + - + +
139E MET 4.7 0.2 - - - +
140E VAL* 3.6 13.9 - - + -
151E ILE 3.6 1.4 + - - -
152E LEU* 1.3 69.2 - - - +
154E ARG* 1.3 67.0 + - - +
157E VAL* 3.0 39.7 + - + +
170E LEU* 4.2 6.5 - - + -
186E MET* 4.2 10.3 - - + -
189E PHE* 4.3 5.4 - - + -
190E VAL* 3.9 24.5 - - + -
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Residues in contact with ARG 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E LEU* 3.3 11.6 - - + +
153E LEU* 1.3 79.6 - - - +
155E ASP* 1.3 73.4 + - - +
157E VAL* 4.3 0.2 - - - +
158E VAL* 3.4 24.9 + - + +
189E PHE* 4.1 18.0 - - + -
193E LEU* 3.5 31.2 - - + +
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Residues in contact with ASP 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 4.8 6.1 - - + -
152E LEU* 3.2 35.3 + - - +
153E LEU 3.1 0.6 - - - -
154E ARG* 1.3 90.3 - - - +
156E TRP* 1.3 60.5 + - - +
157E VAL 3.2 1.3 - - - -
158E VAL* 3.2 6.8 + - - +
159E GLU* 2.9 28.9 + - - +
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Residues in contact with TRP 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ALA* 3.6 26.2 - - + -
107E VAL* 3.5 39.4 - - + +
110E PRO* 4.0 18.6 - - + -
113E ILE* 4.3 5.6 - - + -
127E VAL* 4.4 5.1 - - + +
128E ALA 5.2 1.6 + - - -
129E ILE* 3.6 30.5 - - + +
140E VAL* 3.8 28.9 - - + +
151E ILE* 3.7 30.9 - - + +
152E LEU 3.1 6.9 + - - +
153E LEU 4.0 0.9 - - - +
155E ASP* 1.3 78.7 - - - +
157E VAL* 1.3 57.2 + - - +
159E GLU* 3.7 25.8 - - + -
160E VAL* 3.0 55.3 + - + +
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Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ILE* 3.9 15.7 - - + -
153E LEU* 3.0 40.7 + - + +
154E ARG 4.3 2.9 - - - +
156E TRP* 1.3 75.1 - - - +
158E VAL* 1.3 64.0 + - - +
160E VAL* 3.8 3.9 + - - +
161E GLU* 3.4 20.6 + - - +
168E ILE* 4.3 11.9 - - + +
170E LEU* 5.6 0.7 - - + -
190E VAL* 4.1 18.8 - - + -
193E LEU* 4.0 17.3 - - + -
194E THR* 3.6 33.7 - - + -
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Residues in contact with VAL 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ARG* 4.9 13.9 - - + +
154E ARG* 3.4 17.2 + - + +
155E ASP* 3.2 8.1 + - - +
157E VAL* 1.3 74.8 - - - +
159E GLU* 1.3 66.1 + - - +
161E GLU* 3.4 8.9 + - + +
162E LYS* 3.0 23.7 + - + +
193E LEU* 3.8 30.3 - - + +
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Residues in contact with GLU 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PRO* 5.1 1.8 - - + -
155E ASP 2.9 16.6 + - - +
156E TRP* 3.7 30.5 - - + +
158E VAL* 1.3 75.0 - - - +
160E VAL* 1.3 54.8 + - - +
162E LYS* 3.0 12.6 + - - +
163E ARG* 2.7 74.7 + - + +
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ILE* 4.1 10.5 - - + -
127E VAL* 3.5 26.2 - - + -
129E ILE* 4.5 3.1 - - + -
156E TRP* 3.0 62.5 + - + +
157E VAL* 3.9 6.3 - - - +
159E GLU* 1.3 75.1 - - - +
161E GLU* 1.3 63.0 + - - +
163E ARG* 3.4 2.4 + - - +
164E GLY 3.4 4.0 + - - -
165E ALA* 3.1 40.5 + - + +
168E ILE* 4.2 16.8 - - + -
196E LEU* 4.6 0.2 - - + -
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Residues in contact with GLU 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E VAL 3.4 10.0 + - - +
158E VAL* 3.4 11.8 + - - +
159E GLU 3.2 0.6 - - - -
160E VAL* 1.3 74.0 - - - +
162E LYS* 1.3 70.9 + - - +
164E GLY* 2.9 16.3 + - - -
165E ALA 4.0 2.8 + - - +
193E LEU 4.3 3.3 - - - +
194E THR* 3.1 31.3 + - - +
195E THR* 3.0 21.3 + - - -
196E LEU* 3.9 30.0 - - + +
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Residues in contact with LYS 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E VAL* 3.0 16.6 + - + +
159E GLU* 3.0 17.4 + - - +
161E GLU* 1.3 78.3 - - - +
163E ARG* 1.3 63.2 + - - +
164E GLY* 3.1 2.4 + - - -
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Residues in contact with ARG 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PRO* 3.4 31.4 - - + +
111E SER* 3.6 28.3 + - - +
113E ILE* 3.6 29.6 - - + -
114E THR* 2.8 44.7 + - - +
159E GLU* 2.7 49.8 + - + +
160E VAL 3.5 8.1 - - - +
161E GLU 3.1 0.2 - - - -
162E LYS* 1.3 72.6 - - - +
164E GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ILE* 3.8 4.5 - - - -
114E THR* 5.7 0.2 - - - -
117E ALA* 3.5 14.3 - - - +
122E SER* 2.7 30.2 + - - -
125E VAL* 4.7 0.3 - - - +
161E GLU 2.9 11.8 + - - -
162E LYS 3.1 2.6 + - - -
163E ARG* 1.3 80.1 - - - +
165E ALA* 1.3 66.3 + - - +
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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