Contacts of the strand formed by residues 103 - 112 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B GLN 4.0 0.7 - - - -
102B PRO* 1.3 77.9 - - - +
104B ILE* 1.3 57.7 + - - +
139B VAL* 3.2 3.2 - - - -
140B VAL* 2.7 51.7 + - + +
147B TRP* 3.2 63.4 - - - +
236B MET* 3.8 34.2 - - + +
237B VAL 3.2 18.4 - - - +
238B ALA* 3.7 16.8 - - + +
239B VAL* 4.0 4.9 - - - -
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Residues in contact with ILE 104 (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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103B ARG* 1.3 71.2 - - - +
105B GLU* 1.3 61.6 + - - +
137B LEU* 4.2 20.4 - - + -
138B GLU 3.2 10.1 - - - +
139B VAL* 3.5 31.6 - - + -
185B MET* 3.9 13.6 - - + +
236B MET* 3.3 4.7 - - - -
237B VAL* 3.1 44.2 + - + +
239B VAL* 3.5 14.6 - - + -
245B PHE* 3.1 50.0 - - + -
257B ALA* 6.1 0.4 - - + -
259B PHE* 4.7 4.9 - - + -
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Residues in contact with GLU 105 (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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104B ILE* 1.3 75.3 - - - +
106B ALA* 1.3 60.4 + - - +
107B GLU* 3.1 20.2 - - + +
137B LEU* 3.4 8.6 - - - +
138B GLU* 2.8 42.2 + - + +
140B VAL* 3.7 9.6 - - - +
185B MET* 4.4 6.5 - - - -
232B ALA* 3.4 30.7 - - + +
234B GLY 4.2 6.5 - - - +
236B MET* 3.7 22.3 + - + +
1263B PO4 2.6 39.7 + - - -
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Residues in contact with ALA 106 (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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105B GLU* 1.3 72.9 - - - +
107B GLU* 1.3 62.7 + - - +
136B ALA 3.6 7.0 - - - +
137B LEU* 4.3 2.9 - - + -
183B MET* 3.8 38.0 - - + +
185B MET* 4.5 6.2 - - - +
232B ALA* 3.6 0.7 - - - -
233B LEU* 2.9 31.9 + - + +
234B GLY 5.1 1.2 + - - -
247B ALA* 3.8 22.9 - - + -
249B ILE* 4.7 2.9 - - + -
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Residues in contact with GLU 107 (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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61B VAL 4.4 1.6 - - - +
105B GLU* 3.1 26.3 - - + +
106B ALA* 1.3 81.9 - - - +
108B ILE* 1.3 66.6 + - - +
136B ALA* 2.8 39.1 + - + +
138B GLU* 3.0 31.0 - - + +
229B LEU* 3.3 22.1 - - + +
231B GLY* 2.9 38.9 + - - +
232B ALA* 3.6 7.8 + - - +
233B LEU* 4.1 6.0 - - - +
249B ILE* 3.6 8.0 - - - +
1263B PO4 4.2 1.9 + - - -
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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
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107B GLU* 1.3 76.9 - - - +
109B ALA* 1.3 69.2 + - - +
110B LEU* 4.1 16.2 - - + -
133B VAL* 4.2 14.1 - - + -
134B LEU 3.8 4.3 - - - +
136B ALA* 5.0 0.2 - - - -
178B LEU* 4.2 9.2 - - + -
181B CYS* 3.5 32.8 - - - -
204B PRO* 3.8 23.1 - - + -
229B LEU* 4.0 0.5 - - - -
230B THR* 2.7 47.1 + - - +
231B GLY 4.4 1.6 + - - -
233B LEU* 4.2 17.3 - - + +
249B ILE* 4.6 5.6 - - + -
252B ILE* 3.8 17.5 - - + -
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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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107B GLU 4.1 1.2 + - - -
108B ILE* 1.3 75.0 - - - +
110B LEU* 1.3 63.8 + - - +
133B VAL* 3.3 5.5 - - - +
134B LEU* 2.8 50.5 + - + +
136B ALA* 4.1 7.9 - - + -
166B ILE* 4.9 2.5 - - + -
227B ILE* 4.2 17.5 - - + -
228B ILE 3.3 6.1 - - - +
229B LEU* 3.7 23.6 - - + -
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Residues in contact with LEU 110 (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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108B ILE* 4.1 10.8 - - + -
109B ALA* 1.3 83.1 - - - +
111B VAL* 1.3 64.5 + - - +
112B LEU* 5.1 4.3 - - + -
126B LEU* 4.7 1.1 - - + -
130B ILE* 4.4 22.7 - - + -
132B TRP 3.5 2.7 - - - +
133B VAL* 3.8 20.4 - - + -
178B LEU* 5.3 3.1 - - + -
204B PRO* 6.1 0.2 - - + -
205B LEU* 3.7 32.3 - - + -
208B ALA* 3.7 15.7 - - + -
226B ASP 3.7 0.5 - - - +
227B ILE* 3.3 7.2 - - - +
228B ILE* 2.8 44.6 + - + +
230B THR* 3.7 24.0 - - + -
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Residues in contact with VAL 111 (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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124A ASP* 4.4 22.0 - - + +
128A ASN* 6.0 2.2 - - + -
110B LEU* 1.3 77.8 - - - +
112B LEU* 1.3 59.7 + - - +
130B ILE* 3.6 4.5 - - - +
131B GLU* 2.6 49.2 + - - +
132B TRP* 2.9 28.1 + - + +
134B LEU* 3.9 23.1 - - + -
225B GLY* 3.9 22.2 - - - +
226B ASP 3.5 2.7 - - - -
227B ILE* 4.4 7.4 - - + -
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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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110B LEU* 5.1 7.2 - - + -
111B VAL* 1.3 78.4 - - - +
113B ASN* 1.4 59.4 + - - +
114B ARG 3.9 12.6 - - - +
116B LEU* 3.9 21.5 - - + -
126B LEU* 5.2 5.6 - - + -
129B ALA* 3.2 19.7 - - + +
130B ILE* 5.0 4.9 - - + -
131B GLU* 3.8 10.8 - - - +
222B LEU* 3.8 34.3 - - + -
223B ARG 3.9 15.5 - - - +
224B THR* 4.1 0.5 + - - -
225B GLY* 3.0 24.3 + - - -
226B ASP* 3.3 20.9 + - + +
228B ILE* 3.9 20.6 - - + -
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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