Contacts of the strand formed by residues 103 - 112 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C GLN 4.0 0.7 - - - -
102C PRO* 1.3 77.6 - - - +
104C ILE* 1.3 57.8 + - - +
139C VAL* 3.2 3.2 - - - -
140C VAL* 2.7 51.8 + - + +
147C TRP* 3.3 64.0 - - - +
236C MET* 3.8 32.8 - - + +
237C VAL 3.1 20.4 - - - +
238C ALA* 3.6 17.2 - - + +
239C VAL* 3.9 5.2 - - - -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 1.3 72.2 - - - +
105C GLU* 1.3 60.8 + - - +
137C LEU* 4.2 20.4 - - + -
138C GLU 3.2 9.4 - - - +
139C VAL* 3.5 31.6 - - + -
185C MET* 3.8 13.7 - - + +
236C MET* 3.3 4.5 - - - -
237C VAL* 3.0 41.6 + - + +
239C VAL* 3.5 14.1 - - + -
245C PHE* 3.0 52.9 - - + -
257C ALA* 6.0 0.7 - - + -
259C PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ILE* 1.3 75.5 - - - +
106C ALA* 1.3 59.7 + - - +
107C GLU* 3.1 22.7 - - + +
137C LEU* 3.4 7.9 - - - +
138C GLU* 2.8 46.2 + - + +
140C VAL* 3.7 8.7 - - - +
185C MET* 4.3 6.3 - - - -
232C ALA* 3.4 25.1 - - + +
234C GLY 4.2 7.2 - - - +
235C PRO 5.2 0.2 - - - -
236C MET* 3.7 23.7 + - + +
1262C PO4 2.7 40.4 + - - -
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLU* 1.3 74.0 - - - +
107C GLU* 1.3 63.1 + - - +
136C ALA 3.6 7.0 - - - +
137C LEU* 4.3 2.9 - - + -
183C MET* 3.7 41.9 - - + +
185C MET* 4.5 6.0 - - - +
232C ALA* 3.7 0.5 - - - -
233C LEU* 2.9 31.0 + - + +
234C GLY 5.1 0.6 + - - -
247C ALA* 3.7 20.9 - - + -
249C ILE* 4.6 2.5 - - + -
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL 4.5 2.0 - - - +
105C GLU* 3.1 34.4 - - + +
106C ALA* 1.3 80.8 - - - +
108C ILE* 1.3 66.9 + - - +
136C ALA* 2.8 39.8 + - + +
138C GLU* 3.1 21.6 - - + +
229C LEU* 3.3 23.1 - - + +
231C GLY* 3.0 36.8 + - - +
232C ALA* 3.5 8.2 + - - +
233C LEU* 4.0 6.0 - - - +
249C ILE* 3.6 8.5 - - - +
1262C PO4 4.1 1.9 + - - -
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C GLU* 1.3 76.7 - - - +
109C ALA* 1.3 68.5 + - - +
110C LEU* 4.1 16.6 - - + -
133C VAL* 4.2 13.0 - - + -
134C LEU 3.9 3.1 - - - +
178C LEU* 4.2 8.5 - - + -
181C CYS* 3.5 31.9 - - - -
204C PRO* 3.9 23.1 - - + -
229C LEU* 4.0 0.5 - - - -
230C THR* 2.7 45.7 + - - +
231C GLY 4.5 1.4 + - - -
233C LEU* 4.2 17.0 - - + +
249C ILE* 4.5 6.7 - - + -
252C ILE* 3.7 19.7 - - + -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C GLU 4.1 1.2 + - - -
108C ILE* 1.3 75.2 - - - +
110C LEU* 1.3 64.8 + - - +
133C VAL* 3.4 6.1 - - - +
134C LEU* 2.8 50.5 + - + +
136C ALA* 4.1 8.5 - - + -
166C ILE* 4.9 2.0 - - + -
227C ILE* 4.2 17.5 - - + -
228C ILE 3.3 5.2 - - - +
229C LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 4.1 11.9 - - + -
109C ALA* 1.3 81.1 - - - +
111C VAL* 1.3 66.0 + - - +
112C LEU* 5.1 4.9 - - + +
126C LEU* 4.7 0.9 - - + -
130C ILE* 4.4 21.1 - - + -
132C TRP 3.5 2.2 - - - +
133C VAL* 3.8 20.4 - - + -
178C LEU* 5.3 3.1 - - + -
204C PRO* 6.1 0.2 - - + -
205C LEU* 3.7 31.9 - - + -
208C ALA* 3.8 15.9 - - + -
226C ASP 3.7 0.7 - - - +
227C ILE* 3.3 7.0 - - - +
228C ILE* 2.8 44.8 + - + +
230C THR* 3.8 24.0 - - + -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU* 1.3 78.8 - - - +
112C LEU* 1.3 59.7 + - - +
130C ILE* 3.6 4.9 - - - +
131C GLU* 2.7 48.8 + - - +
132C TRP* 2.9 29.1 + - + +
134C LEU* 3.9 22.2 - - + -
225C GLY* 3.9 23.1 - - - +
226C ASP 3.4 2.7 - - - +
227C ILE* 4.4 14.6 - - + -
124E ASP* 4.5 16.8 - - + +
128E ASN* 5.9 2.2 - - + +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU* 5.1 8.3 - - + -
111C VAL* 1.3 78.1 - - - +
113C ASN* 1.4 58.9 + - - +
114C ARG 3.9 12.6 - - - +
116C LEU* 4.0 21.5 - - + -
126C LEU* 5.2 5.8 - - + -
129C ALA* 3.2 20.0 - - + +
130C ILE* 5.1 4.3 - - + -
131C GLU* 3.9 10.2 - - - +
222C LEU* 3.8 34.1 - - + -
223C ARG 3.8 15.3 - - - +
224C THR* 4.1 0.2 + - - -
225C GLY* 2.9 25.2 + - - +
226C ASP* 3.2 21.6 + - + +
228C ILE* 3.9 21.1 - - + -
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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
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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