Contacts of the helix formed by residues 106 - 120 (chain D) in PDB entry 5EWL
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 GLU 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D ASP 3.5 14.0 - - - +
105D GLN* 1.4 70.3 - - - +
107D ALA* 1.4 66.3 + - - +
108D ILE 3.2 0.4 - - - -
109D ALA* 3.1 26.6 + - - +
110D GLN* 3.8 1.7 + - - +
129D GLY 3.7 10.1 - - - -
132D MET* 3.5 29.5 - - + +
133D ILE 4.8 1.9 - - - +
134D MET* 5.3 1.7 - - - +
176D PHE* 3.8 29.7 - - + -
233D THR* 3.7 28.8 - - + +
234D LYS* 5.3 1.4 + - - +
235D GLU* 6.2 0.2 - - - +
261D LEU* 4.4 6.6 - - + +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 3.9 32.3 - - + -
105D GLN* 3.1 7.9 + - + +
106D GLU* 1.4 82.6 - - - +
108D ILE* 1.3 66.6 + - - +
109D ALA 3.0 2.2 - - - -
110D GLN* 2.8 22.5 + - + +
111D ILE* 2.9 17.5 + - + +
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D THR* 3.6 24.2 - - + -
81D ILE* 3.8 19.5 - - + -
99D PHE* 3.5 29.2 - - + -
101D ASP* 3.8 10.8 - - + +
103D THR* 3.4 25.8 - - - +
105D GLN* 3.0 30.1 + - + +
107D ALA* 1.3 77.0 - - - +
109D ALA* 1.4 56.4 + - - +
111D ILE* 3.2 9.9 + - - +
112D LEU* 2.9 37.9 + - + +
130D SER* 3.7 20.4 - - - +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU 3.1 16.0 + - - +
107D ALA 3.0 0.4 - - - -
108D ILE* 1.4 77.0 - - - +
110D GLN* 1.3 54.1 + - - +
112D LEU 3.3 1.9 + - - -
113D ASP* 3.0 24.4 + - - +
129D GLY 3.4 16.3 + - - +
130D SER* 3.8 2.5 - - - +
132D MET 3.7 19.1 - - - +
134D MET* 4.1 10.8 - - + -
143D PHE* 3.3 20.1 - - + -
145D GLN* 3.7 13.7 - - - +
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Residues in contact with GLN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TYR* 4.2 41.6 + - + -
133C ILE* 5.7 1.4 - - - +
106D GLU 3.8 1.0 + - - +
107D ALA* 2.8 23.5 + - + +
109D ALA* 1.3 73.7 - - - +
111D ILE* 1.4 62.7 + - + +
113D ASP* 2.9 20.3 + - - +
114D PHE* 3.0 15.6 + - - +
134D MET* 3.7 23.2 - - + +
135D ALA* 3.6 29.5 - - - +
136D ASP 5.5 0.4 + - - -
177D PRO* 5.8 0.6 - - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 4.1 13.5 - - + -
76D THR 3.9 15.7 - - - +
78D PRO* 3.8 39.5 - - + +
81D ILE* 3.9 24.2 - - + -
82D ILE* 4.1 14.6 - - + -
107D ALA* 2.9 24.1 + - + +
108D ILE* 3.7 8.3 - - + +
110D GLN* 1.4 70.4 - - + +
112D LEU* 1.4 57.2 + - - +
114D PHE* 3.5 7.5 + - + +
115D ILE* 3.0 46.7 + - + +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ILE* 4.0 11.7 - - + -
85D ILE* 3.8 29.4 - - + -
99D PHE* 3.6 33.2 - - + -
108D ILE* 2.9 23.2 + - + +
109D ALA 3.7 1.1 - - - +
110D GLN 3.2 0.2 - - - -
111D ILE* 1.4 74.2 - - - +
113D ASP* 1.3 59.5 + - - +
115D ILE* 4.6 1.6 - - - -
116D SER* 2.9 32.0 + - - -
123D ILE* 3.6 14.2 - - + +
130D SER* 3.6 31.0 - - - -
143D PHE* 3.6 27.8 - - + -
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ALA 3.0 11.5 + - - +
110D GLN* 2.9 14.4 + - - +
112D LEU* 1.3 77.0 - - - +
114D PHE* 1.3 57.4 + - - +
116D SER* 3.2 3.1 + - - -
117D ALA* 2.9 30.4 + - - +
134D MET* 3.9 14.7 - - + +
136D ASP 4.7 0.7 - - - +
137D LYS* 3.2 23.1 - - - +
138D ASP* 3.1 26.9 + - - +
141D SER* 2.6 28.0 + - - -
143D PHE* 3.6 16.2 - - + +
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Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ALA* 3.5 42.8 - - + -
72C ILE* 3.9 22.0 - - + -
75C ALA* 4.3 4.5 - - + -
105C THR* 5.9 2.5 - - + -
106C PRO* 3.9 20.4 - - + -
109C TYR* 4.9 19.5 - + + -
82D ILE* 4.2 20.2 - - + -
110D GLN* 3.0 14.8 + - - +
111D ILE* 3.6 10.8 - - + +
113D ASP* 1.3 77.8 + - - +
115D ILE* 1.4 72.9 + - + +
117D ALA* 3.3 3.3 + - - +
118D GLN* 3.0 38.4 + - + +
138D ASP* 6.3 0.4 - - - -
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 5.2 4.0 - - + -
81D ILE* 3.8 14.6 - - + -
82D ILE* 3.7 45.5 - - + -
85D ILE* 3.8 35.0 - - + -
86D CYS* 5.5 2.5 - - - -
89D MET* 4.3 4.9 - - + -
111D ILE* 3.0 32.5 + - + +
112D LEU* 4.0 3.6 - - + +
113D ASP 3.4 0.2 - - - -
114D PHE* 1.4 77.8 - - + +
116D SER* 1.4 58.1 + - - +
118D GLN* 3.9 2.9 - - - +
119D THR* 2.8 45.5 + - + +
123D ILE* 4.0 9.9 - - + -
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU 2.9 19.3 + - - -
113D ASP 3.3 4.9 - - - -
115D ILE* 1.4 75.0 - - - +
117D ALA* 1.3 52.5 + - - +
119D THR* 4.3 0.9 - - - -
120D LEU* 2.8 34.5 + - - -
121D THR 3.1 20.8 + - - -
123D ILE* 3.7 10.8 - - - +
140D SER 4.6 0.5 - - - +
141D SER* 4.6 0.2 - - - -
142D MET* 3.0 34.2 + - - +
143D PHE* 4.0 13.7 - - - -
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ASP 2.9 16.8 + - - +
114D PHE* 4.0 3.8 - - - +
116D SER* 1.3 70.6 - - - +
118D GLN* 1.3 69.3 + - - +
120D LEU* 3.5 21.5 + - - +
138D ASP* 3.6 41.1 - - + +
140D SER* 3.4 23.0 - - - +
141D SER* 3.9 2.4 - - - +
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Residues in contact with GLN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASN* 5.3 4.4 - - - +
71C ALA* 3.3 32.6 - - - +
72C ILE* 3.5 24.2 - - + +
114D PHE* 3.0 46.6 + - + +
115D ILE 3.9 0.4 - - - +
117D ALA* 1.3 79.3 - - - +
119D THR* 1.4 60.7 + - - +
120D LEU* 3.8 4.2 + - - +
138D ASP* 5.7 1.7 - - - +
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 3.6 24.2 - - + -
86D CYS* 5.1 1.8 - - - -
89D MET* 3.6 30.8 - - + +
115D ILE* 2.8 24.3 + - + +
118D GLN* 1.4 74.9 - - - +
120D LEU* 1.3 69.1 + - - +
121D THR* 2.8 30.2 + - - -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D SER 2.8 14.5 + - - -
117D ALA 3.5 9.9 - - - +
118D GLN 3.4 3.3 - - - +
119D THR* 1.3 80.6 - - - +
121D THR* 1.3 56.6 + - - +
122D PRO* 4.4 1.7 - - - +
140D SER* 3.4 36.3 - - - +
142D MET* 3.6 25.7 - - + +
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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