Contacts of the helix formed by residues 118 - 130 (chain E) in PDB entry 7CR3
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 THR 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362D TYR* 3.4 29.2 - - + +
365D ARG* 5.0 3.4 + - - +
111E THR* 3.5 4.4 - - - +
117E LEU* 1.3 78.0 - - - +
119E ASP* 1.3 64.4 + - - +
120E GLU* 3.6 13.3 + - - +
121E GLU* 2.5 35.5 + - - +
122E VAL* 3.2 24.9 + - - +
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Residues in contact with ASP 119 (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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107E ARG* 6.4 0.4 - - + -
111E THR* 5.1 0.9 - - - -
118E THR* 1.3 77.1 - - - +
120E GLU* 1.3 100.2 + - - +
121E GLU 3.2 0.2 - - - -
122E VAL* 3.2 8.7 - - + +
123E ASP* 2.9 44.3 + - - +
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Residues in contact with GLU 120 (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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358D SER* 4.3 17.5 - - - +
365D ARG* 5.1 11.9 + - - +
118E THR* 3.9 13.4 + - - +
119E ASP* 1.3 111.7 + - - +
121E GLU* 1.3 58.4 + - + +
123E ASP* 3.8 6.3 - - - +
124E GLU* 2.9 33.5 + - - +
127E ARG* 4.5 5.4 + - - +
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Residues in contact with GLU 121 (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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344D TRP* 3.6 3.4 + - - +
358D SER* 4.3 5.8 - - - +
359D THR* 3.0 40.2 + - - +
362D TYR* 3.3 31.6 - - - +
365D ARG* 5.7 0.2 - - - +
117E LEU* 3.2 36.4 - - + +
118E THR* 2.5 41.7 + - - +
119E ASP 3.2 0.6 - - - -
120E GLU* 1.3 74.8 - - + +
122E VAL* 1.3 59.8 + - - +
124E GLU* 3.1 11.1 + - - +
125E MET* 2.9 29.5 + - - +
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Residues in contact with VAL 122 (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 LEU* 4.1 8.7 - - + +
107E ARG* 3.7 44.6 - - + +
110E MET* 4.1 13.2 - - + -
111E THR* 3.7 15.3 - - + -
117E LEU* 5.2 1.1 - - + +
118E THR 3.2 16.0 + - - +
119E ASP* 3.2 21.1 - - - +
121E GLU* 1.3 77.2 - - - +
123E ASP* 1.3 57.3 + - - +
125E MET* 3.1 21.1 + - + +
126E ILE* 3.0 35.0 + - + +
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Residues in contact with ASP 123 (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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107E ARG* 3.0 37.2 + - - +
119E ASP* 2.9 35.3 + - - +
120E GLU* 3.8 2.9 - - - +
122E VAL* 1.3 74.0 - - - +
124E GLU* 1.3 59.6 + - - +
126E ILE* 3.2 9.4 + - + +
127E ARG* 2.9 63.4 + - - +
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Residues in contact with GLU 124 (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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344D TRP* 3.5 21.7 - - + +
355D ASP* 5.7 0.7 - - - +
356D LEU* 5.5 6.4 - - - +
358D SER* 3.8 22.8 + - - +
120E GLU 2.9 18.4 + - - +
121E GLU* 3.1 10.5 + - - +
123E ASP* 1.3 75.2 - - - +
125E MET* 1.3 64.9 + - - +
127E ARG* 3.0 29.9 + - - +
128E GLU* 3.0 27.9 + - - +
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Residues in contact with MET 125 (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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340D ILE* 4.7 3.1 - - - +
341D GLN* 4.6 4.3 - - - +
344D TRP* 3.5 55.4 - - + -
106E LEU* 6.1 0.2 - - - -
110E MET* 3.7 45.3 - - + -
117E LEU* 3.7 21.8 - - + -
121E GLU 2.9 14.9 + - - +
122E VAL* 3.2 17.3 - - + +
124E GLU* 1.3 76.8 - - - +
126E ILE* 1.3 57.8 + - + +
128E GLU* 3.3 0.9 + - - +
129E ALA* 2.8 34.9 + - + +
142E PHE* 4.7 4.6 - - + -
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Residues in contact with ILE 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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103E ALA* 4.0 20.0 - - + +
106E LEU* 3.8 24.7 - - + -
107E ARG* 3.3 46.0 - - + +
122E VAL* 3.0 19.4 + - + +
123E ASP* 3.2 16.1 + - - +
125E MET* 1.3 77.8 - - + +
127E ARG* 1.3 60.3 + - + +
129E ALA* 4.6 2.2 - - - -
130E ASP* 2.8 48.2 + - + +
135E GLY* 4.7 4.9 - - - -
137E VAL* 4.7 0.9 - - + -
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Residues in contact with ARG 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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120E GLU* 4.5 6.3 + - - +
123E ASP* 2.9 49.4 + - - +
124E GLU* 3.0 38.1 + - - +
126E ILE* 1.3 77.8 - - + +
128E GLU* 1.3 60.9 + - - +
130E ASP 3.7 12.1 - - - +
131E ILE* 4.9 5.5 - - - +
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Residues in contact with GLU 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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344D TRP* 3.5 24.4 - - + -
347D TYR* 3.3 9.3 + - + -
353D ARG* 2.5 50.3 + - - -
124E GLU* 3.0 18.7 + - - +
125E MET 3.9 0.4 - - - +
127E ARG* 1.3 80.4 - - - +
129E ALA* 1.3 58.3 + - - +
131E ILE* 3.3 9.0 - - - +
142E PHE* 3.3 17.1 - - + -
145E MET* 3.2 37.7 - - - +
146E MET* 3.9 4.9 - - - -
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Residues in contact with ALA 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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90E PHE* 5.9 2.2 - - + -
106E LEU* 6.2 0.9 - - + -
125E MET* 2.8 18.4 + - + +
126E ILE* 4.2 2.2 - - - +
128E GLU* 1.3 75.1 - - - +
130E ASP* 1.3 60.7 + - - +
131E ILE* 3.0 10.4 + - - +
137E VAL* 3.5 20.9 - - + +
141E GLU* 2.9 24.8 - - - +
142E PHE* 3.4 34.1 - - + +
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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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126E ILE* 2.8 28.9 + - + +
127E ARG* 3.7 9.0 - - - +
129E ALA* 1.3 70.2 - - - +
131E ILE* 1.3 65.8 + - - +
132E ASP* 2.8 24.6 - - - +
133E GLY* 3.1 8.4 + - - -
134E ASP* 2.4 25.0 + - - +
135E GLY* 2.4 33.1 + - - -
136E GLN 3.8 7.0 - - - +
137E VAL* 3.5 21.2 - - + +
141E GLU* 3.8 4.7 - - - +
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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