Contacts of the helix formed by residues 115 - 127 (chain A) in PDB entry 2EE4
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.3 3.0 - - + +
114A PRO* 1.3 84.4 - - + +
116A LYS* 1.3 68.6 - - - +
117A THR* 3.2 2.7 - - - +
118A GLU* 2.7 44.3 + - + +
119A ARG 2.8 12.1 + - - -
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE 5.3 0.4 - - - -
114A PRO 3.0 9.7 + - - +
115A ASP* 1.3 69.7 - - - +
117A THR* 1.3 67.4 + - - +
119A ARG* 3.1 30.6 + - - +
120A LEU* 3.1 30.0 + - + +
192A GLU* 5.6 2.0 + - - -
193A THR* 5.0 3.8 + - - +
196A GLN* 4.8 6.9 + - - -
197A GLN* 3.6 25.7 + - - +
207A ILE* 3.6 34.1 - - + -
208A VAL 4.0 6.3 + - - -
209A GLU* 5.4 2.9 - - - +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.2 2.1 - - - -
116A LYS* 1.3 78.2 - - - +
118A GLU* 1.3 70.2 + - - +
120A LEU* 2.9 14.2 + - - +
121A HIS* 2.9 45.8 + - + +
200A PHE* 5.9 0.2 - - + -
207A ILE* 4.3 16.1 - - + +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.4 18.7 - - + +
115A ASP* 2.7 38.8 + - + +
117A THR* 1.3 78.7 - - - +
119A ARG* 1.3 53.8 + - - +
120A LEU 3.1 0.3 + - - -
121A HIS* 3.9 5.9 - - - +
122A ALA* 2.8 36.7 + - - +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA 2.7 27.8 - - - +
111A ALA* 2.8 30.6 + - - +
112A LYS 5.7 0.2 - - - -
113A ILE* 3.1 28.8 + - + +
114A PRO* 5.4 2.4 + - - +
115A ASP 2.8 10.7 + - - +
116A LYS* 3.4 31.7 - - - +
118A GLU* 1.3 72.8 - - - +
120A LEU* 1.3 59.4 + - + +
123A LEU* 3.0 34.7 + - + +
189A SER* 5.2 9.3 - - - -
192A GLU* 5.5 2.2 + - - -
193A THR* 3.6 30.3 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS* 3.1 22.9 + - + +
117A THR* 2.9 7.6 + - - +
119A ARG* 1.3 73.6 - - + +
121A HIS* 1.3 67.4 + - - +
122A ALA 3.1 1.1 - - - -
123A LEU* 2.9 18.1 + - - +
124A LYS* 3.0 12.0 + - - +
193A THR* 3.3 33.9 - - + -
197A GLN* 3.4 21.5 - - + +
200A PHE* 3.7 21.5 - - + -
201A PHE* 3.9 8.3 - - + -
207A ILE* 3.3 51.8 - - + -
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Residues in contact with HIS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 2.9 44.0 + - + +
118A GLU* 3.9 7.0 - - - +
120A LEU* 1.3 72.7 - - - +
122A ALA* 1.3 62.9 + - - +
124A LYS* 3.2 32.2 + - - +
125A GLU* 3.1 22.0 + - + +
200A PHE* 3.6 27.2 - + - -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.5 13.9 - - + -
113A ILE* 3.4 24.9 - - + -
118A GLU 2.8 22.1 + - - +
119A ARG 3.8 0.9 - - - +
121A HIS* 1.3 73.1 - - - +
123A LEU* 1.3 58.1 + - - +
125A GLU* 2.8 38.0 + - - +
126A ILE* 3.5 8.1 + - - +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.8 34.5 - - + +
110A ALA* 3.8 9.6 - - + +
111A ALA* 4.3 8.5 - - + +
119A ARG* 3.0 29.6 - - + +
120A LEU 2.9 5.0 + - - +
122A ALA* 1.3 78.5 - - - +
124A LYS* 1.3 52.5 + - - +
126A ILE* 2.8 10.8 + - - +
127A VAL* 2.7 33.9 + - - +
190A VAL* 4.7 3.8 - - + +
193A THR* 4.1 21.3 - - + -
194A PHE* 3.8 23.5 - - + -
201A PHE* 3.6 30.3 - - + -
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU 3.0 6.6 + - - +
121A HIS* 3.2 31.7 + - - +
123A LEU* 1.3 75.9 - - - +
125A GLU* 1.3 57.5 + - - +
127A VAL* 3.4 13.2 - - + +
128A LYS* 2.9 29.7 - - - +
200A PHE* 3.3 47.8 - - + +
201A PHE* 3.4 31.9 - - + +
204A ASN* 6.3 1.3 - - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A HIS* 3.1 18.5 - - - +
122A ALA* 2.8 20.0 + - - +
124A LYS* 1.3 80.9 - - + +
126A ILE* 1.3 61.3 + - + +
128A LYS* 4.0 16.0 - - - +
129A LYS* 3.4 22.2 + - - +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.7 31.9 - - + -
106A GLU* 2.7 52.7 - - + +
107A LEU* 3.6 25.8 - - + +
110A ALA* 3.9 16.8 - - + -
122A ALA* 4.1 7.2 - - + +
123A LEU* 2.8 5.4 + - - +
125A GLU* 1.3 81.8 - - + +
127A VAL* 1.3 57.6 + - - +
128A LYS 2.9 5.6 - - - -
129A LYS* 2.8 34.6 + - - +
130A PHE* 3.2 7.1 - - - -
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 5.2 0.2 - - - +
123A LEU 2.7 15.6 + - - +
124A LYS* 3.4 27.4 - - + +
126A ILE* 1.3 71.5 - - - +
128A LYS* 1.3 62.6 + - + +
130A PHE* 3.4 18.9 - - + +
135A TYR* 2.6 57.5 - - + +
138A PHE* 4.4 13.7 - - + -
194A PHE* 4.0 26.0 - - + -
201A PHE* 5.3 2.0 - - + +
202A PHE* 4.4 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