Contacts of the strand formed by residues 103 - 112 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E GLN 4.0 0.7 - - - -
102E PRO* 1.3 78.6 - - - +
104E ILE* 1.3 58.4 + - - +
139E VAL* 3.2 4.0 - - - -
140E VAL* 2.7 53.0 + - + +
147E TRP* 3.3 64.0 - - - +
236E MET* 3.8 33.8 - - + +
237E VAL 3.2 19.5 - - - +
238E ALA* 3.7 15.9 - - + +
239E VAL* 3.9 4.3 - - - -
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Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 1.3 72.2 - - - +
105E GLU* 1.3 61.2 + - - +
137E LEU* 4.2 21.5 - - + -
138E GLU 3.2 9.4 - - - +
139E VAL* 3.5 30.7 - - + -
185E MET* 3.9 13.5 - - + +
236E MET* 3.2 4.7 - - - -
237E VAL* 3.0 41.3 + - + +
239E VAL* 3.5 15.3 - - + -
245E PHE* 3.0 48.9 - - + -
257E ALA* 6.0 0.2 - - + -
259E PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ILE* 1.3 74.7 - - - +
106E ALA* 1.3 60.0 + - - +
107E GLU* 3.0 19.2 - - - +
137E LEU* 3.4 8.1 - - - +
138E GLU* 2.8 42.5 + - + +
140E VAL* 3.7 10.6 - - - +
185E MET* 4.4 5.8 - - - -
232E ALA* 3.4 26.8 - - + +
234E GLY 4.2 6.5 - - - +
236E MET* 3.7 22.5 + - + +
1262E PO4 2.4 40.1 + - - -
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E GLU* 1.3 73.4 - - - +
107E GLU* 1.3 63.9 + - - +
136E ALA 3.6 6.3 - - - +
137E LEU* 4.3 2.9 - - + -
183E MET* 3.8 38.2 - - + +
185E MET* 4.4 6.2 - - - +
232E ALA* 3.6 0.2 - - - -
233E LEU* 2.9 31.2 + - + +
234E GLY 5.1 0.8 + - - -
247E ALA* 3.8 23.3 - - + -
249E ILE* 4.7 2.7 - - + -
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Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL 4.5 1.8 - - - +
105E GLU* 3.0 33.8 - - + +
106E ALA* 1.3 81.8 - - - +
108E ILE* 1.3 66.8 + - - +
136E ALA* 2.8 40.6 + - + +
138E GLU* 3.1 23.5 - - + +
229E LEU* 3.3 21.4 - - + +
231E GLY* 2.9 39.2 + - - +
232E ALA* 3.6 7.3 + - - +
233E LEU* 4.0 6.3 - - - +
249E ILE* 3.6 8.0 - - - +
1262E PO4 3.9 1.9 + - - -
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E GLU* 1.3 76.7 - - - +
109E ALA* 1.3 69.3 + - - +
110E LEU* 4.1 16.4 - - + -
133E VAL* 4.2 13.7 - - + -
134E LEU 3.8 4.7 - - - +
178E LEU* 4.2 8.1 - - + -
181E CYS* 3.5 32.3 - - - -
204E PRO* 3.8 23.6 - - + -
229E LEU 4.0 0.2 - - - -
230E THR* 2.7 47.3 + - - +
231E GLY 4.5 1.2 + - - -
233E LEU* 4.2 17.3 - - + +
249E ILE* 4.5 6.1 - - + -
252E ILE* 3.8 18.2 - - + -
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E GLU 4.1 1.0 - - - -
108E ILE* 1.3 74.1 - - - +
110E LEU* 1.3 64.2 + - - +
133E VAL* 3.4 6.1 - - - +
134E LEU* 2.8 50.9 + - + +
136E ALA* 4.1 8.3 - - + -
166E ILE* 4.9 2.0 - - + -
227E ILE* 4.2 17.3 - - + -
228E ILE 3.2 6.7 - - - +
229E LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ILE* 4.1 11.0 - - + -
109E ALA* 1.3 81.3 - - - +
111E VAL* 1.3 66.1 + - - +
112E LEU* 5.1 3.8 - - + -
126E LEU* 4.7 0.9 - - + -
130E ILE* 4.4 20.2 - - + -
132E TRP 3.5 3.1 - - - +
133E VAL* 3.8 21.5 - - + -
178E LEU* 5.3 3.1 - - + -
204E PRO* 6.1 0.2 - - + -
205E LEU* 3.7 31.4 - - + -
208E ALA* 3.7 15.9 - - + -
226E ASP 3.7 0.7 - - - +
227E ILE* 3.3 7.2 - - - +
228E ILE* 2.8 48.0 + - + +
230E THR* 3.7 24.5 - - + -
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Residues in contact with VAL 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASP* 4.5 15.0 - - + +
128B ASN* 6.0 2.0 - - + -
110E LEU* 1.3 78.8 - - - +
112E LEU* 1.3 59.3 + - - +
130E ILE* 3.6 4.2 - - - +
131E GLU* 2.6 49.3 + - - +
132E TRP* 2.9 27.5 + - + +
134E LEU* 3.9 23.1 - - + -
225E GLY* 3.9 22.2 - - - +
226E ASP 3.4 2.9 - - - +
227E ILE* 4.4 14.6 - - + -
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Residues in contact with LEU 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LEU* 5.1 7.2 - - + -
111E VAL* 1.3 77.8 - - - +
113E ASN* 1.4 60.4 + - - +
114E ARG 4.0 13.0 - - - +
116E LEU* 4.0 21.5 - - + -
126E LEU* 5.2 5.6 - - + -
129E ALA* 3.1 20.2 - - + +
130E ILE* 5.0 4.9 - - + -
131E GLU* 3.9 10.1 - - - +
222E LEU* 3.8 34.1 - - + -
223E ARG 3.9 15.7 - - - +
224E THR* 4.1 0.5 + - - -
225E GLY* 2.9 25.0 + - - +
226E ASP* 3.2 20.4 + - + +
228E 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