Contacts of the helix formed by residues 106 - 123 (chain A) in PDB entry 3EJW
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY* 1.3 75.2 - - - +
107A PRO* 1.3 75.0 - - - +
108A GLU* 3.5 13.2 + - - +
109A GLN* 3.1 37.9 + - - +
110A LEU* 3.0 21.8 + - - +
284A VAL* 3.5 26.2 - - + +
285A GLN* 3.8 2.9 - - - +
298A LEU* 4.4 18.6 - - + -
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Residues in contact with PRO 107 (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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106A THR* 1.3 87.8 - - - +
108A GLU* 1.3 69.6 + - - +
111A GLY* 2.8 24.9 + - - -
143A ALA* 4.0 30.7 - - + +
144A TRP* 4.0 13.2 - - + -
147A ALA* 3.2 17.8 - - + +
285A GLN* 3.4 48.9 - - + +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR* 3.1 16.6 + - - +
107A PRO* 1.3 89.7 - - - +
109A GLN* 1.3 60.9 + - + +
112A GLY* 2.8 24.8 + - - -
147A ALA* 4.4 10.0 - - + +
151A LYS* 3.3 28.1 - - - +
284A VAL 4.5 4.7 - - - +
285A GLN 5.7 1.6 - - - +
286A GLY* 6.2 0.3 - - - -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 3.6 3.6 - - - -
106A THR* 3.1 44.0 + - - +
108A GLU* 1.3 76.3 - - + +
110A LEU* 1.3 61.5 + - + +
112A GLY* 3.8 0.6 - - - -
113A LEU* 2.9 27.9 + - - +
298A LEU* 5.3 3.0 - - - +
302A ARG* 3.2 34.8 + - - +
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Residues in contact with LEU 110 (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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104A GLN* 3.8 18.8 - - + -
105A GLY* 3.7 23.1 - - - +
106A THR 3.0 11.9 + - - +
109A GLN* 1.3 75.2 - - - +
111A GLY* 1.3 65.0 + - - +
112A GLY 3.1 0.2 - - - -
113A LEU* 3.2 5.5 + - + +
114A LEU* 3.1 28.4 + - - +
144A TRP* 3.3 44.6 - - + +
220A PHE* 3.7 21.5 - - + -
241A TRP* 4.2 10.3 - - + -
302A ARG* 3.6 34.1 - - + -
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Residues in contact with GLY 111 (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 PRO 2.8 21.9 + - - -
108A GLU 4.1 0.2 - - - -
110A LEU* 1.3 73.5 - - - +
112A GLY* 1.3 61.2 + - - +
114A LEU* 3.4 6.8 + - - +
115A VAL* 3.1 27.9 + - - +
144A TRP* 3.6 21.8 + - - +
147A ALA* 4.5 1.1 - - - -
148A ALA* 3.7 14.9 - - - +
151A LYS* 4.2 1.8 - - - -
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Residues in contact with GLY 112 (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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108A GLU 2.8 20.9 + - - -
109A GLN* 3.8 0.9 - - - -
111A GLY* 1.3 75.2 - - - +
113A LEU* 1.3 57.5 + - - +
115A VAL* 3.4 2.2 + - - +
116A ASP* 2.9 41.9 + - - +
151A LYS* 3.5 20.9 - - - +
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Residues in contact with LEU 113 (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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109A GLN 2.9 17.7 + - - +
110A LEU* 3.2 7.1 + - + +
112A GLY* 1.3 73.8 - - - +
114A LEU* 1.3 65.0 + - - +
116A ASP* 4.5 6.1 - - + +
117A MET* 2.9 44.3 + - + +
220A PHE* 4.0 18.8 - - + -
239A GLY* 4.5 11.7 - - - -
240A LEU 5.1 0.9 - - - +
302A ARG* 4.1 31.0 - - + -
303A THR 4.8 1.1 - - - +
304A VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 114 (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 LEU 3.1 19.2 + - - +
111A GLY* 3.6 13.7 - - - +
112A GLY 3.4 0.2 - - - -
113A LEU* 1.3 76.3 - - - +
115A VAL* 1.3 64.3 + - - +
117A MET* 3.5 6.4 + - + +
118A ALA* 3.0 23.1 + - - +
131A PHE* 5.3 0.9 - - + -
144A TRP* 4.4 10.3 - - + +
148A ALA* 4.6 9.0 - - + -
192A ILE* 3.8 23.2 - - + +
194A PRO* 3.7 29.8 - - + -
218A VAL* 3.7 7.7 - - - +
219A GLY* 3.9 23.6 - - - +
220A PHE* 3.4 32.3 - - + -
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Residues in contact with VAL 115 (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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111A GLY 3.1 17.1 + - - +
112A GLY* 3.9 5.2 - - - +
113A LEU 3.3 0.2 - - - -
114A LEU* 1.3 76.2 - - + +
116A ASP* 1.3 58.0 + - - +
118A ALA* 3.1 6.8 + - - +
119A ALA* 2.7 33.3 + - - +
148A ALA* 3.5 33.2 - - + +
151A LYS* 4.3 13.5 - - + -
152A ILE* 3.8 17.3 - - + -
155A GLU* 4.9 4.9 - - - +
156A HIS* 3.6 32.8 - - + +
159A TRP* 4.2 2.2 - - + -
192A ILE* 4.9 3.1 - - + -
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Residues in contact with ASP 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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112A GLY* 2.9 28.6 + - - +
113A LEU* 3.8 9.0 - - + +
115A VAL* 1.3 78.4 - - - +
117A MET* 1.3 63.3 + - + +
119A ALA* 3.3 8.5 + - - +
120A GLU* 3.1 27.9 + - + +
155A GLU* 4.4 15.4 - - - +
156A HIS* 5.6 0.3 + - - -
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Residues in contact with MET 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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113A LEU* 2.9 44.1 + - + +
114A LEU* 3.8 19.5 - - + +
116A ASP* 1.3 78.6 - - - +
118A ALA* 1.3 62.4 + - - +
120A GLU* 3.4 16.0 + - - +
121A GLY 3.9 2.4 + - - -
216A THR* 4.5 0.7 - - - +
218A VAL* 3.7 16.6 - - + +
219A GLY 3.7 31.4 - - - +
220A PHE* 4.2 1.3 - - + -
237A ARG* 3.7 25.8 + - - +
238A PHE* 3.4 32.8 - - - +
239A GLY* 3.5 6.1 - - - +
304A VAL* 4.3 9.0 - - + -
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Residues in contact with ALA 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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114A LEU 3.0 14.7 + - - +
115A VAL 3.1 6.9 + - - +
117A MET* 1.3 75.9 - - - +
119A ALA* 1.3 65.1 + - - +
121A GLY* 3.0 13.0 + - - -
122A VAL* 3.0 16.7 + - - +
159A TRP* 4.1 11.4 - - + -
190A ALA* 4.9 10.3 - - + -
192A ILE* 4.0 21.8 - - + -
216A THR* 3.8 4.5 - - - +
218A VAL* 3.9 19.2 - - + +
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Residues in contact with ALA 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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115A VAL 2.7 19.3 + - - +
116A ASP* 3.3 10.3 + - - +
118A ALA* 1.3 72.8 - - - +
120A GLU* 1.3 62.9 + - - +
121A GLY 3.2 0.5 + - - -
122A VAL 4.4 0.7 - - - +
123A LYS* 3.4 21.3 + - - +
156A HIS* 4.0 28.9 - - + +
159A TRP* 3.8 12.9 - - + -
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Residues in contact with GLU 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 ASP* 3.1 19.9 + - + +
117A MET* 3.4 11.2 - - - +
118A ALA 3.1 0.6 - - - -
119A ALA* 1.3 76.6 - - - +
121A GLY* 1.3 57.8 + - - +
123A LYS* 2.9 41.9 + - - +
237A ARG* 3.7 33.4 + - - +
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Residues in contact with GLY 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 MET 3.9 1.8 + - - -
118A ALA 3.0 6.1 + - - -
120A GLU* 1.3 81.4 - - - +
122A VAL* 1.3 64.1 + - - +
123A LYS* 3.5 6.7 - - - +
216A THR* 3.2 26.2 + - - -
236A GLN* 6.5 1.1 - - - -
237A ARG* 4.7 6.0 - - - +
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Residues in contact with VAL 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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118A ALA 3.0 21.3 + - - +
119A ALA 3.4 1.5 + - - +
121A GLY* 1.3 80.6 - - - +
123A LYS* 1.3 69.2 + - - +
124A LYS* 2.7 33.9 + - + +
127A ALA* 3.7 22.4 - - + -
129A VAL* 5.5 0.7 - - + -
159A TRP* 4.0 21.8 - - + +
189A ASP* 4.3 14.4 - - + +
190A ALA* 3.8 27.4 - - + -
216A THR* 4.3 2.9 - - - -
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Residues in contact with LYS 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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119A ALA 3.4 11.0 + - - +
120A GLU* 2.9 40.8 + - - +
121A GLY* 4.2 4.7 - - - +
122A VAL* 1.3 77.2 - - - +
124A LYS* 1.3 57.3 + - - +
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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