Contacts of the strand formed by residues 125 - 134 (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 VAL 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E VAL* 4.1 3.4 - - + +
102E ILE* 4.2 21.8 - - + -
113E ILE* 4.0 25.8 - - + +
116E ILE* 3.8 16.8 - - + -
117E ALA* 3.7 31.9 - - + +
121E GLY 3.9 8.5 - - - +
122E SER 3.1 8.1 + - - +
123E GLN 3.3 2.0 - - - +
124E ALA* 1.3 80.9 - - - +
126E VAL* 1.3 66.7 + - - +
127E VAL* 4.3 5.8 + - + -
165E ALA* 4.3 4.3 - - - -
166E GLY* 3.1 24.7 + - - +
167E GLU* 3.4 6.2 + - - +
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Residues in contact with VAL 126 (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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78E THR* 4.5 8.3 - - + +
99E LYS* 3.7 25.1 - - + -
100E VAL 3.0 13.1 + - - +
101E SER* 3.1 15.1 - - - -
102E ILE* 2.9 26.9 + - - +
125E VAL* 1.3 78.3 - - - +
127E VAL* 1.3 64.8 + - - +
167E GLU* 3.4 37.0 - - + +
169E LEU* 4.1 29.4 - - + +
199E ILE* 5.1 4.5 - - + -
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Residues in contact with VAL 127 (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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102E ILE* 3.3 16.6 - - + +
103E ASN* 5.3 0.7 - - - +
106E ALA* 4.6 9.2 - - + -
113E ILE* 4.0 20.6 - - + -
125E VAL* 4.2 2.9 - - + -
126E VAL* 1.3 75.0 - - - +
128E ALA* 1.3 69.7 + - - +
129E ILE* 3.7 8.9 + - + -
156E TRP* 4.4 5.6 - - - +
160E VAL* 3.5 45.1 - - + -
165E ALA* 3.7 14.1 - - + -
167E GLU 3.0 8.4 + - - +
168E ILE* 3.4 7.3 - - + +
169E LEU 3.0 21.4 + - - -
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Residues in contact with ALA 128 (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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101E SER* 3.6 19.1 - - - +
102E ILE 2.9 7.1 + - - +
103E ASN* 2.9 45.6 + - + +
107E VAL* 6.0 0.5 - - - +
126E VAL* 3.8 2.6 + - - +
127E VAL* 1.3 75.8 - - - +
129E ILE* 1.3 60.5 + - - +
130E ASP* 5.2 3.1 - - - +
156E TRP* 5.2 1.9 + - - -
169E LEU* 3.4 24.0 - - + +
171E THR* 6.0 0.4 - - - +
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Residues in contact with ILE 129 (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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103E ASN* 5.0 0.2 - - - -
127E VAL* 3.7 7.4 + - + -
128E ALA* 1.3 78.3 - - - +
130E ASP* 1.3 66.5 + - - +
131E ALA 3.9 0.5 + - - -
140E VAL* 4.1 12.3 - - + -
153E LEU* 3.5 24.5 - - + -
156E TRP* 3.6 35.9 - - + +
157E VAL* 3.9 27.1 - - + -
160E VAL* 4.5 10.8 - - + -
168E ILE* 4.1 20.4 - - + -
169E LEU 2.9 10.6 + - - +
170E LEU* 3.6 11.8 - - + +
171E THR 3.0 26.0 + - - +
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Residues in contact with ASP 130 (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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103E ASN* 3.4 23.8 + - - +
128E ALA* 4.1 3.0 + - - +
129E ILE* 1.3 74.6 + - - +
131E ALA* 1.3 58.6 + - - +
140E VAL* 3.8 4.1 - - - +
141E PHE* 2.9 42.1 + - - +
144E SER* 4.6 6.3 + - - -
145E GLY* 4.2 14.8 + - - -
171E THR* 3.3 29.9 + - - +
173E ILE* 4.0 20.4 - - + -
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Residues in contact with ALA 131 (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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129E ILE* 3.9 2.6 + - + -
130E ASP* 1.3 75.4 - - - +
132E LYS* 1.3 61.9 + - - +
138E PHE* 5.1 0.2 - - + -
139E MET 3.3 12.8 - - - +
141E PHE 4.8 0.2 - - - +
153E LEU* 3.8 36.6 - - + -
170E LEU* 4.8 1.3 - - + -
171E THR 3.1 7.8 + - - +
172E SER* 3.9 2.8 - - - -
173E ILE* 3.0 29.9 + - - +
186E MET* 3.9 20.8 - - + +
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Residues in contact with LYS 132 (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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131E ALA* 1.3 75.5 - - - +
133E ARG* 1.3 81.5 + - - +
134E VAL* 4.9 0.9 - - + -
138E PHE* 3.3 13.8 - - - -
139E MET 3.1 25.6 + - - -
141E PHE* 3.5 31.9 - - + -
173E ILE* 4.3 18.6 - - + -
174E ASP* 5.3 10.5 - - + +
186E MET* 4.9 2.2 - - - -
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Residues in contact with ARG 133 (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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132E LYS* 1.3 90.0 - - - +
134E VAL* 1.3 68.8 + - - +
136E GLY* 5.4 6.7 - - - +
137E GLU 3.4 9.2 - - - +
138E PHE* 3.6 26.8 - - + -
174E ASP* 4.3 18.1 - - + +
175E ARG* 5.8 2.4 - - - +
183E ASP* 3.3 37.3 + - - -
185E GLU* 2.8 35.8 + - - +
186E MET* 5.5 0.4 - - + +
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Residues in contact with VAL 134 (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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132E LYS* 5.1 0.2 - - + -
133E ARG* 1.3 80.4 - - - +
135E ASP* 1.3 85.8 + - - +
136E GLY 3.1 0.2 - - - -
137E GLU* 3.0 21.3 + - - +
139E MET* 3.6 33.0 - - + +
141E PHE* 4.2 13.2 - - + -
148E ASN* 4.2 15.3 - - - +
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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