Contacts of the helix formed by residues 108 - 114 (chain E) in PDB entry 1E81
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 SER 108 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E GLY 5.0 1.6 - - - -
79E SER* 3.5 10.1 + - - -
80E SER* 2.6 41.8 + - - -
107E VAL* 1.3 78.1 - - - +
109E SER* 1.3 67.7 + - - +
110E SER* 3.9 3.3 + - - -
111E PHE* 2.9 39.2 + - - +
112E THR* 3.3 8.6 + - - -
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Residues in contact with SER 109 (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 VAL 3.9 0.4 + - - -
108E SER* 1.3 73.6 - - - +
110E SER* 1.3 64.0 + - - +
112E THR* 3.2 9.5 + - - +
113E GLU* 2.9 37.2 + - - +
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Residues in contact with SER 110 (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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77E ASP* 5.2 1.5 + - - -
79E SER* 2.9 27.8 + - - -
108E SER* 3.1 5.2 + - - -
109E SER* 1.3 78.3 - - - +
111E PHE* 1.3 65.1 + - - +
113E GLU* 3.3 15.0 + - - +
114E ASP* 3.2 26.5 + - - +
400E M91 5.5 5.7 - - - +
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Residues in contact with PHE 111 (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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39E TRP* 3.4 38.4 - + - -
41E PHE* 3.9 11.9 - + + -
53E GLN* 2.9 12.3 + - - -
75E TYR* 3.9 13.7 - + - -
79E SER* 3.2 33.0 - - - -
80E SER 3.6 19.3 - - - -
107E VAL* 4.0 13.7 - - + -
108E SER* 2.9 27.1 + - - +
110E SER* 1.3 77.8 + - - +
112E THR* 1.3 62.2 + - - +
113E GLU 3.0 1.8 - - - -
114E ASP* 2.8 27.6 + - + +
117E ILE* 5.1 8.2 - - + +
120E LEU* 4.0 13.9 - - + -
400E M91 3.9 19.3 - - + -
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Residues in contact with THR 112 (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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41E PHE* 4.2 0.8 - - - -
48E SER 4.3 5.4 - - - +
49E GLU* 2.4 58.8 + - - +
50E VAL 4.0 0.7 - - - +
51E ASP* 3.4 33.5 - - + +
53E GLN* 3.0 17.6 + - - +
107E VAL* 3.5 6.1 + - - +
108E SER 3.3 4.1 + - - -
109E SER* 3.2 12.3 + - - -
111E PHE* 1.3 78.3 - - - +
113E GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 113 (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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109E SER* 2.9 27.3 + - - +
110E SER* 3.3 15.9 - - - +
111E PHE 3.0 0.2 - - - -
112E THR* 1.3 79.2 - - - +
114E ASP* 1.3 57.8 + - - +
115E SER* 3.3 9.2 + - - -
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Residues in contact with ASP 114 (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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7E ILE* 3.7 6.9 - - - +
53E GLN* 2.6 25.7 + - - +
110E SER* 3.2 14.1 + - - +
111E PHE* 2.8 15.2 + - + +
113E GLU* 1.3 76.2 - - - +
115E SER* 1.3 59.0 - - - +
116E THR* 3.3 17.4 + - - -
117E ILE* 3.5 20.1 - - + +
400E M91 3.1 40.7 - - - -
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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