Contacts of the strand formed by residues 103 - 112 (chain S) in PDB entry 2WQT
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 ARG 103 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101S GLN 3.9 0.7 - - - -
102S PRO* 1.3 78.5 - - - +
104S ILE* 1.3 58.3 + - - +
139S VAL* 3.3 3.7 - - - -
140S VAL* 2.7 51.8 + - + +
147S TRP* 3.3 64.7 - - - +
236S MET* 3.8 34.2 - - + +
237S VAL 3.2 18.6 - - - +
238S ALA* 3.7 16.1 - - - +
239S VAL* 3.9 3.8 - - - -
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Residues in contact with ILE 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S ARG* 1.3 71.8 - - - +
105S GLU* 1.3 61.0 + - - +
137S LEU* 4.2 21.1 - - + -
138S GLU 3.2 9.0 - - - +
139S VAL* 3.5 31.9 - - + -
185S MET* 3.9 13.0 - - + +
236S MET* 3.3 4.9 - - - -
237S VAL* 3.0 43.6 + - + +
239S VAL* 3.4 14.4 - - + -
245S PHE* 3.1 50.3 - - + -
257S ALA* 6.0 0.7 - - + -
259S PHE* 4.7 5.4 - - + -
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Residues in contact with GLU 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S ILE* 1.3 75.4 - - - +
106S ALA* 1.3 60.0 + - - +
107S GLU* 3.0 23.5 - - - +
137S LEU* 3.4 8.3 - - - +
138S GLU* 2.8 43.2 + - + +
140S VAL* 3.8 10.7 - - - +
185S MET* 4.5 6.1 - - - -
232S ALA* 3.4 27.3 - - + +
234S GLY 4.2 6.3 - - - +
235S PRO 5.2 0.4 - - - -
236S MET* 3.7 22.6 + - + +
1262S PO4 2.4 36.0 + - - -
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Residues in contact with ALA 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105S GLU* 1.3 74.0 - - - +
107S GLU* 1.3 62.8 + - - +
136S ALA 3.6 7.0 - - - +
137S LEU* 4.3 2.5 - - + -
183S MET* 3.8 38.5 - - + +
185S MET* 4.5 6.0 - - - +
232S ALA* 3.6 0.7 - - - -
233S LEU* 2.9 32.1 + - + +
234S GLY 5.1 1.0 + - - -
247S ALA* 3.8 22.7 - - + -
249S ILE* 4.7 2.9 - - + -
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Residues in contact with GLU 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S VAL 4.5 2.1 - - - +
105S GLU* 3.0 34.1 - - + +
106S ALA* 1.3 81.1 - - - +
108S ILE* 1.3 67.2 + - - +
136S ALA* 2.8 40.4 + - + +
138S GLU* 3.1 22.7 - - + +
229S LEU* 3.3 22.2 - - + +
231S GLY* 3.0 38.8 + - - +
232S ALA* 3.5 7.4 + - - +
233S LEU* 4.0 5.8 - - - -
249S ILE* 3.6 8.7 - - - +
1262S PO4 4.3 1.4 + - - -
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Residues in contact with ILE 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107S GLU* 1.3 76.9 - - - +
109S ALA* 1.3 69.5 + - - +
110S LEU* 4.1 16.6 - - + -
133S VAL* 4.2 13.2 - - + -
134S LEU 3.8 4.0 - - - +
178S LEU* 4.2 8.5 - - + -
181S CYS* 3.5 32.5 - - - -
204S PRO* 3.9 23.1 - - + -
229S LEU* 4.0 0.6 - - - -
230S THR* 2.7 46.2 + - - +
231S GLY 4.4 1.4 + - - -
233S LEU* 4.2 17.3 - - + +
249S ILE* 4.6 5.8 - - + -
252S ILE* 3.7 18.4 - - + -
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Residues in contact with ALA 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107S GLU 4.1 0.8 - - - -
108S ILE* 1.3 73.5 - - - +
110S LEU* 1.3 63.1 + - - +
133S VAL* 3.4 4.9 - - - +
134S LEU* 2.8 49.1 + - + +
136S ALA* 4.1 8.7 - - + -
166S ILE* 4.9 2.2 - - + -
227S ILE* 4.2 18.2 - - + -
228S ILE 3.3 6.3 - - - +
229S LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108S ILE* 4.1 11.0 - - + -
109S ALA* 1.3 82.0 - - - +
111S VAL* 1.3 66.2 + - - +
112S LEU* 5.1 4.3 - - + -
126S LEU* 4.7 1.3 - - + -
130S ILE* 4.4 22.0 - - + -
132S TRP 3.5 3.6 - - - +
133S VAL* 3.8 20.2 - - + -
178S LEU* 5.2 3.4 - - + -
204S PRO* 6.1 0.2 - - + -
205S LEU* 3.7 31.0 - - + -
208S ALA* 3.8 15.7 - - + -
226S ASP 3.7 0.9 - - - +
227S ILE* 3.3 6.5 - - - +
228S ILE* 2.8 49.0 + - + +
230S THR* 3.7 24.2 - - + -
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Residues in contact with VAL 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R ASP* 4.6 17.3 - - + +
128R ASN* 6.0 2.5 - - + -
110S LEU* 1.3 77.9 - - - +
112S LEU* 1.3 58.8 + - - +
130S ILE* 3.6 4.3 - - - +
131S GLU* 2.7 48.9 + - - +
132S TRP* 3.0 27.3 + - + +
134S LEU* 3.9 23.1 - - + -
225S GLY* 3.8 22.9 - - - +
226S ASP 3.4 3.1 - - - -
227S ILE* 4.4 14.8 - - + -
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Residues in contact with LEU 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S LEU* 5.1 7.2 - - + -
111S VAL* 1.3 78.7 - - - +
113S ASN* 1.4 59.5 + - - +
114S ARG 3.9 12.8 - - - +
116S LEU* 4.0 21.3 - - + -
126S LEU* 5.2 5.4 - - + -
129S ALA* 3.2 18.4 - - + +
130S ILE* 5.1 4.7 - - + -
131S GLU* 3.9 10.4 - - - +
222S LEU* 3.8 34.3 - - + -
223S ARG 3.9 15.7 - - - +
224S THR* 4.1 0.3 + - - -
225S GLY* 2.9 24.6 + - - -
226S ASP* 3.2 21.5 + - + +
228S ILE* 3.9 20.9 - - + -
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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