Contacts of the helix formed by residues 126 - 137 (chain E) in PDB entry 2FG8
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 ASP 126 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E ASN* 3.3 24.1 + - - +
12E TYR* 3.7 13.2 - - - -
13E SER 4.5 1.2 + - - -
16E VAL* 4.2 9.4 - - + +
76E ARG* 3.0 27.9 + - - -
121E GLY* 2.8 21.7 + - - +
124E ARG* 4.1 9.0 - - + +
125E THR* 1.3 72.3 - - - +
127E PRO* 1.3 64.1 - - - +
128E HIS* 3.2 3.5 + - - +
129E LEU* 3.3 21.2 + - + +
130E CYS* 3.3 22.1 + - - -
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Residues in contact with PRO 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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11E ASN* 3.9 10.1 - - - +
125E THR* 3.2 16.6 - - - +
126E ASP* 1.3 83.5 - - - +
128E HIS* 1.3 61.3 + - - +
130E CYS* 3.5 7.3 + - + +
131E ASP* 3.1 24.6 + - - +
115H LEU* 3.5 26.9 - - + +
118H HIS* 3.6 38.4 - - + +
134H GLU* 3.8 5.2 - - - +
138H LEU* 3.6 17.4 - - + +
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Residues in contact with HIS 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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72E MET* 3.6 32.7 - - + +
75E GLN* 5.8 0.7 - - + -
76E ARG* 3.8 23.4 + - - +
126E ASP* 3.3 2.3 + - - +
127E PRO* 1.3 77.3 - - + +
129E LEU* 1.3 62.4 + - - +
131E ASP* 3.3 4.1 + - - +
132E PHE* 2.9 40.3 + + + +
115H LEU* 6.1 2.2 - - + -
138H LEU* 3.9 18.8 - - + +
139H ASP* 3.3 38.5 + - + -
142H VAL* 3.6 31.1 - - + +
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Residues in contact with LEU 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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16E VAL* 3.7 26.2 - - + -
20E VAL* 4.5 10.1 - - + -
69E LEU* 6.3 0.2 - - + -
72E MET* 3.8 29.4 - - + -
76E ARG* 4.1 0.4 - - - +
117E LEU* 3.4 37.9 - - + +
118E HIS* 5.9 0.2 - - - -
121E GLY* 3.9 19.1 - - - -
126E ASP* 3.3 22.1 + - - +
128E HIS* 1.3 77.5 + - - +
130E CYS* 1.3 63.3 + - - +
132E PHE* 3.4 3.5 - - + +
133E LEU* 3.1 38.8 + - + +
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Residues in contact with CYS 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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118E HIS* 3.6 37.0 - - + +
121E GLY* 3.7 15.0 - - - -
122E SER* 3.6 24.7 - - - -
126E ASP 3.3 14.3 + - - +
127E PRO* 3.7 10.3 - - + +
128E HIS 3.2 0.6 - - - -
129E LEU* 1.3 77.8 - - - +
131E ASP* 1.3 63.3 + - - +
133E LEU* 3.3 2.6 + - - -
134E GLU* 2.8 31.2 + - - +
134H GLU* 5.2 3.1 - - - +
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Residues in contact with ASP 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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203D CS 4.0 2.6 - - - -
127E PRO 3.1 17.6 + - - +
128E HIS* 3.9 4.9 - - - +
130E CYS* 1.3 73.6 - - - +
132E PHE* 1.3 66.8 + - - +
134E GLU* 3.2 9.4 + - - +
135E THR* 3.0 42.4 + - - -
201E CS 3.2 26.7 - - - -
134H GLU* 3.8 39.5 + - + +
135H THR* 5.2 1.8 + - - -
138H LEU* 5.8 0.7 - - + -
139H ASP* 5.8 2.3 - - - +
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Residues in contact with PHE 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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68E ARG* 3.6 29.4 - - + -
69E LEU* 3.6 24.7 - - + -
72E MET* 3.7 37.0 - - + -
128E HIS* 2.9 29.4 + + + +
129E LEU* 3.4 9.0 - - + +
131E ASP* 1.3 78.9 - - - +
133E LEU* 1.3 73.7 + - + +
135E THR* 4.9 0.9 - - - -
136E HIS* 3.3 54.0 + + - +
137E PHE* 3.7 20.5 - + - -
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Residues in contact with LEU 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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69E LEU* 4.8 3.8 - - + -
114E LEU* 3.9 22.2 - - + +
117E LEU* 3.8 26.5 - - + -
118E HIS* 3.8 40.2 - - + +
129E LEU* 3.1 26.4 + - + +
130E CYS 3.3 5.1 + - - +
131E ASP 3.2 0.2 - - - -
132E PHE* 1.3 103.8 - - + +
134E GLU* 1.3 57.2 + - - +
137E PHE* 3.0 21.9 + - + +
138E LEU* 2.9 31.8 + - + +
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Residues in contact with GLU 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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127D PRO* 4.2 8.7 - - - +
130D CYS* 5.6 0.7 - - - +
131D ASP* 3.5 40.1 + - + +
118E HIS* 2.9 28.8 + - + +
130E CYS 2.8 19.1 - - - +
131E ASP* 3.2 8.4 + - - +
133E LEU* 1.3 77.8 - - - +
135E THR* 1.3 61.4 + - - +
136E HIS 3.5 0.4 + - - -
138E LEU* 3.8 15.4 - - + +
139E ASP* 4.3 17.7 + - - +
201E CS 3.4 26.7 - - - -
206E CS 3.3 23.6 - - - -
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Residues in contact with THR 135 (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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203D CS 3.4 26.7 - - - -
131E ASP* 3.0 26.7 + - - -
132E PHE* 4.1 0.4 - - - -
134E GLU* 1.3 78.2 - - - +
136E HIS* 1.3 86.9 + - + +
137E PHE 3.8 0.2 - - - -
139E ASP* 6.1 0.2 - - - +
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Residues in contact with HIS 136 (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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68E ARG* 3.4 43.6 + - + +
132E PHE* 3.3 49.9 + + - -
135E THR* 1.3 102.1 + - + +
137E PHE* 1.3 71.1 + - + +
140E GLU* 3.5 16.2 - - - +
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Residues in contact with PHE 137 (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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27E TYR* 3.2 42.2 - + - -
65E GLY* 3.8 16.2 - - - -
68E ARG* 4.1 11.0 - - + -
69E LEU* 3.8 26.2 - - + -
114E LEU* 3.5 24.9 - - + -
132E PHE* 3.7 31.2 - + - -
133E LEU* 3.0 25.6 + - + +
134E GLU 4.4 0.2 - - - -
135E THR 3.8 1.0 - - - -
136E HIS* 1.3 95.8 - - + +
138E LEU* 1.3 66.6 + - + +
139E ASP 3.5 1.7 - - - +
140E GLU* 3.1 12.5 + - - +
141E GLU* 2.9 27.1 + - + +
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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