Contacts of the strand formed by residues 103 - 112 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101J GLN 3.9 0.7 - - - -
102J PRO* 1.3 78.5 - - - +
104J ILE* 1.3 59.0 + - - +
139J VAL* 3.2 3.8 - - - -
140J VAL* 2.7 52.8 + - + +
147J TRP* 3.3 62.7 - - - +
236J MET* 3.8 35.6 - - + +
237J VAL 3.2 20.0 - - - +
238J ALA* 3.7 15.4 - - - +
239J VAL* 3.9 3.6 - - - -
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Residues in contact with ILE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J ARG* 1.3 72.4 - - - +
105J GLU* 1.3 60.3 + - - +
137J LEU* 4.2 22.0 - - + -
138J GLU 3.2 8.7 - - - +
139J VAL* 3.5 31.9 - - + -
185J MET* 3.9 12.5 - - + +
236J MET* 3.3 5.4 - - - -
237J VAL* 3.1 40.1 + - + +
239J VAL* 3.5 14.8 - - + -
245J PHE* 3.0 50.5 - - + -
257J ALA* 6.0 0.4 - - + -
259J PHE* 4.7 4.9 - - + -
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Residues in contact with GLU 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J ILE* 1.3 74.1 - - - +
106J ALA* 1.3 60.0 + - - +
107J GLU* 3.0 23.2 - - + +
137J LEU* 3.4 8.1 - - - +
138J GLU* 2.8 44.0 + - + +
140J VAL* 3.8 8.4 - - - +
185J MET* 4.5 6.1 - - - -
232J ALA* 3.5 26.2 - - + +
234J GLY 4.2 6.5 - - - +
235J PRO 5.2 0.2 - - - -
236J MET* 3.7 25.5 + - + +
1263J PO4 2.9 35.3 + - - -
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Residues in contact with ALA 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J GLU* 1.3 73.8 - - - +
107J GLU* 1.3 63.4 + - - +
136J ALA 3.6 6.1 - - - +
137J LEU* 4.3 2.9 - - + -
183J MET* 3.7 40.7 - - + +
185J MET* 4.5 5.6 - - - +
232J ALA* 3.7 0.5 - - - -
233J LEU* 2.9 31.7 + - + +
234J GLY 5.1 1.0 + - - -
247J ALA* 3.8 21.3 - - + -
249J ILE* 4.7 3.1 - - + -
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Residues in contact with GLU 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J VAL 4.5 2.1 - - - +
105J GLU* 3.0 33.7 - - + +
106J ALA* 1.3 80.8 - - - +
108J ILE* 1.3 66.2 + - - +
136J ALA* 2.8 40.5 + - + +
138J GLU* 3.1 22.8 - - + +
229J LEU* 3.3 22.4 - - + +
230J THR 4.9 0.2 - - - +
231J GLY* 2.9 38.3 + - - +
232J ALA* 3.6 7.1 + - - +
233J LEU* 4.1 6.0 - - - +
249J ILE* 3.5 8.1 - - - +
1263J PO4 4.4 1.7 + - - -
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Residues in contact with ILE 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J GLU* 1.3 78.0 - - - +
109J ALA* 1.3 70.0 + - - +
110J LEU* 4.1 16.4 - - + -
133J VAL* 4.1 13.7 - - + -
134J LEU 3.8 4.0 - - - +
136J ALA* 5.1 0.2 - - - -
178J LEU* 4.2 8.7 - - + -
181J CYS* 3.5 32.1 - - - -
204J PRO* 3.9 22.9 - - + -
229J LEU* 4.0 0.5 - - - -
230J THR* 2.7 46.5 + - - +
231J GLY 4.5 1.2 + - - -
233J LEU* 4.2 18.4 - - + +
249J ILE* 4.4 5.8 - - + -
252J ILE* 3.8 18.2 - - + -
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Residues in contact with ALA 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J GLU 4.1 1.2 - - - -
108J ILE* 1.3 73.0 - - - +
110J LEU* 1.3 65.1 + - - +
133J VAL* 3.4 5.7 - - - +
134J LEU* 2.8 52.2 + - + +
136J ALA* 4.1 8.3 - - + -
166J ILE* 4.9 2.2 - - + -
227J ILE* 4.2 17.7 - - + -
228J ILE 3.3 5.2 - - - +
229J LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ILE* 4.1 11.7 - - + -
109J ALA* 1.3 83.3 - - - +
111J VAL* 1.3 64.1 + - - +
112J LEU* 5.1 4.5 - - + -
126J LEU* 4.7 1.1 - - + -
130J ILE* 4.4 22.9 - - + -
132J TRP 3.5 2.5 - - - +
133J VAL* 3.8 20.4 - - + -
178J LEU* 5.2 2.9 - - + -
204J PRO* 6.1 0.7 - - + -
205J LEU* 3.7 30.3 - - + -
208J ALA* 3.8 16.2 - - + -
226J ASP 3.7 0.3 - - - +
227J ILE* 3.2 6.5 - - - +
228J ILE* 2.8 44.4 + - + +
230J THR* 3.7 24.7 - - + -
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Residues in contact with VAL 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ASP* 4.8 14.8 - - + +
128G ASN* 6.3 1.1 - - + -
110J LEU* 1.3 78.2 - - - +
112J LEU* 1.3 58.3 + - - +
130J ILE* 3.6 4.2 - - - +
131J GLU* 2.7 50.1 + - - +
132J TRP* 3.0 27.8 + - + +
134J LEU* 3.9 23.1 - - + -
225J GLY* 3.9 22.4 - - - +
226J ASP 3.4 2.9 - - - -
227J ILE* 4.4 15.5 - - + -
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Residues in contact with LEU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J LEU* 5.1 8.1 - - + -
111J VAL* 1.3 79.3 - - - +
113J ASN* 1.4 59.9 + - - +
114J ARG 3.9 12.6 - - - +
116J LEU* 4.0 20.6 - - + -
126J LEU* 5.2 5.4 - - + -
129J ALA* 3.2 18.8 - - + +
130J ILE* 5.1 4.0 - - + -
131J GLU* 3.9 9.7 - - - +
222J LEU* 3.8 34.8 - - + -
223J ARG 3.9 14.8 - - - +
224J THR* 4.1 0.3 + - - -
225J GLY* 3.0 24.3 + - - -
226J ASP* 3.2 20.9 + - + +
228J ILE* 3.9 21.3 - - + -
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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