Contacts of the helix formed by residues 106 - 120 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ASP 3.5 14.2 - - - +
105B GLN* 1.3 70.7 - - - +
107B ALA* 1.4 68.6 + - - +
108B ILE 3.1 0.9 - - - -
109B ALA* 3.2 22.8 + - - +
110B GLN 4.1 0.7 + - - -
129B GLY* 3.7 10.0 - - - -
132B MET* 3.9 27.6 - - + +
133B ILE 4.7 2.6 - - - +
134B MET* 5.2 0.5 - - - +
176B PHE* 3.7 30.5 - - + -
233B THR* 3.7 27.2 - - + +
234B LYS* 5.3 1.7 + - - +
261B LEU* 4.4 7.7 - - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.0 32.3 - - + -
105B GLN* 3.1 7.6 + - + +
106B GLU* 1.4 82.4 - - - +
108B ILE* 1.4 55.9 + - - +
109B ALA 3.1 2.5 - - - -
110B GLN* 2.8 29.1 + - + +
111B ILE* 2.9 19.0 + - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 3.8 22.2 - - + +
81B ILE* 4.0 13.2 - - + -
99B PHE* 3.6 28.5 - - + -
101B ASP* 3.7 17.7 - - + +
103B THR* 3.4 26.0 - - - +
105B GLN* 3.1 29.6 + - + +
107B ALA* 1.4 76.4 - - - +
109B ALA* 1.4 55.5 + - - +
111B ILE* 3.7 7.6 - - + +
112B LEU* 2.9 43.3 + - + +
130B SER* 3.9 6.7 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU 3.2 14.1 + - - +
107B ALA 3.1 0.6 - - - -
108B ILE* 1.4 77.4 - - - +
110B GLN* 1.4 52.1 + - - +
113B ASP* 2.8 31.2 + - - +
129B GLY 3.7 9.6 + - - +
130B SER 4.2 0.9 - - - -
132B MET 3.7 7.0 - - - +
133B ILE 5.1 0.2 - - - +
134B MET* 3.2 28.5 - - + -
143B PHE* 3.3 18.6 - - - -
145B GLN* 3.7 18.2 - - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.9 44.0 + - + -
133A ILE* 5.4 1.8 - - - +
106B GLU 4.1 0.8 + - - +
107B ALA* 2.8 21.2 + - + +
109B ALA* 1.4 69.5 - - - +
111B ILE* 1.4 65.8 + - + +
113B ASP* 3.0 13.3 + - - +
114B PHE* 2.9 25.0 + - + +
134B MET* 3.4 22.0 - - + +
135B ALA* 3.4 31.5 - - - +
136B ASP 5.0 2.5 + - - +
177B PRO* 5.7 1.2 - - - +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.2 16.8 - - + -
76B THR 3.9 15.7 - - - +
78B PRO* 3.8 33.7 - - + +
81B ILE* 3.8 24.7 - - + -
82B ILE* 4.4 11.7 - - + -
107B ALA* 2.9 22.6 + - + +
108B ILE* 3.7 11.2 - - + +
110B GLN* 1.4 71.6 - - + +
112B LEU* 1.4 51.5 + - - +
114B PHE* 3.2 8.8 + - + +
115B ILE* 2.8 53.4 + - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 4.1 9.9 - - + -
85B ILE* 3.6 30.7 - - + -
99B PHE* 3.6 39.9 - - + -
108B ILE* 2.9 28.1 + - + +
109B ALA 3.7 3.4 - - - +
111B ILE* 1.4 68.9 - - - +
113B ASP* 1.3 61.8 + - - +
115B ILE* 4.4 2.7 - - + +
116B SER* 2.9 30.7 + - - -
123B ILE* 3.6 15.9 - - + +
130B SER* 3.6 23.3 - - - -
143B PHE* 3.8 22.6 - - + -
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA 2.8 14.4 + - - +
110B GLN* 3.0 17.1 + - - +
112B LEU* 1.3 74.4 - - - +
114B PHE* 1.4 58.4 + - - +
116B SER* 3.2 2.6 + - - -
117B ALA* 2.9 30.9 + - - +
134B MET* 3.8 11.9 - - + -
136B ASP 4.7 0.5 - - - +
137B LYS* 3.2 20.0 - - - +
138B ASP* 3.1 25.2 + - - +
141B SER* 2.6 31.0 + - - -
143B PHE* 3.7 15.7 - - + +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 3.5 45.3 - - + -
72A ILE* 3.8 22.9 - - + -
75A ALA* 4.3 7.4 - - + -
105A THR* 6.0 2.9 - - + -
106A PRO* 4.0 15.5 - - + -
109A TYR* 4.9 20.9 - + + -
82B ILE* 4.2 19.7 - - + -
110B GLN* 2.9 15.0 + - + +
111B ILE* 3.4 13.0 - - - +
113B ASP* 1.4 77.4 + - - +
115B ILE* 1.4 71.9 + - + +
117B ALA* 3.3 3.7 + - - +
118B GLN* 3.0 36.8 + - + +
138B ASP* 6.4 0.2 - - - -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 5.2 4.0 - - + -
81B ILE* 3.7 18.4 - - + -
82B ILE* 3.8 33.9 - - + -
85B ILE* 3.8 34.3 - - + -
86B CYS* 5.5 4.7 - - - -
89B MET* 4.6 0.2 - - + -
111B ILE* 2.8 43.1 + - + +
112B LEU* 4.0 4.7 - - + +
114B PHE* 1.4 76.1 - - + +
116B SER* 1.4 57.6 + - - +
118B GLN* 3.9 3.0 - - - +
119B THR* 2.9 48.0 + - + +
123B ILE* 4.0 9.6 - - + -
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU 2.9 20.2 + - - -
113B ASP 3.3 5.6 - - - -
115B ILE* 1.4 76.1 - - - +
117B ALA* 1.4 52.8 + - - +
119B THR* 4.3 0.9 - - - -
120B LEU* 2.8 34.7 + - - -
121B THR 3.1 19.2 + - - -
123B ILE* 3.7 9.6 - - - +
142B MET* 3.0 33.9 + - - +
143B PHE* 4.0 12.6 - - - -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ASP 2.9 16.1 + - - +
114B PHE* 4.1 3.6 - - - +
116B SER* 1.4 70.2 + - - +
118B GLN* 1.3 68.0 + - - +
120B LEU* 3.4 16.1 - - - +
138B ASP* 3.6 40.8 - - + +
140B SER* 3.5 20.1 - - - +
141B SER* 3.9 2.4 - - - +
328B ARG* 3.2 15.4 + - - -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASN* 5.2 0.6 - - - +
71A ALA* 3.4 32.4 - - - +
72A ILE* 3.5 23.6 - - + +
114B PHE* 3.0 46.1 + - + +
115B ILE 3.9 0.7 - - - +
117B ALA* 1.3 78.9 - - - +
119B THR* 1.3 59.6 + - - +
120B LEU* 4.9 0.7 - - - +
138B ASP* 5.8 1.4 - - - +
324B THR* 3.4 15.9 + - + +
328B ARG* 2.7 47.7 + - - +
331B GLN* 4.9 2.6 + - - -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 3.7 23.8 - - + -
89B MET* 3.4 19.6 - - + +
115B ILE* 2.9 25.2 + - + +
118B GLN* 1.3 75.6 - - - +
120B LEU* 1.3 67.6 + - - +
121B THR* 2.8 24.4 + - - -
318B LYS* 3.0 28.8 - - - +
320B SER 5.2 0.7 - - - +
321B CYS* 3.8 20.6 - - - -
324B THR* 4.3 9.2 - - + -
331B GLN* 3.7 4.4 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B SER 2.8 14.1 + - - -
117B ALA 3.4 10.1 - - - +
118B GLN 3.4 0.4 - - - -
119B THR* 1.3 76.3 - - - +
121B THR* 1.3 54.6 + - - +
122B PRO* 4.4 1.0 - - - +
140B SER* 3.4 33.9 - - - +
142B MET* 3.6 15.5 - - - +
315B PRO* 5.9 1.9 - - - +
318B LYS* 3.2 15.4 + - - +
328B ARG* 4.3 22.4 - - + +
331B GLN* 3.6 37.0 - - + +
332B SER* 3.8 33.4 - - - +
333B ASN* 3.9 10.1 - - + +
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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
------------------------------------------------------------
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