Contacts of the strand formed by residues 103 - 112 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101R GLN 4.0 0.7 - - - -
102R PRO* 1.3 77.9 - - - +
104R ILE* 1.3 59.6 + - - +
139R VAL* 3.2 4.1 - - - -
140R VAL* 2.7 52.0 + - + +
147R TRP* 3.3 64.2 - - - +
236R MET* 3.8 33.2 - - + +
237R VAL 3.3 18.4 - - - +
238R ALA* 3.7 16.4 - - - +
239R VAL* 4.0 3.8 - - - -
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Residues in contact with ILE 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R ARG* 1.3 72.5 - - - +
105R GLU* 1.3 61.0 + - - +
137R LEU* 4.2 21.5 - - + -
138R GLU 3.2 9.9 - - - +
139R VAL* 3.5 31.2 - - + -
165R VAL* 5.9 0.2 - - + -
185R MET* 3.9 12.0 - - + +
236R MET* 3.3 4.9 - - - -
237R VAL* 3.1 44.5 + - + +
239R VAL* 3.4 15.0 - - + -
245R PHE* 3.1 48.7 - - + -
257R ALA* 6.0 0.4 - - + -
259R PHE* 4.7 5.6 - - + -
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Residues in contact with GLU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104R ILE* 1.3 76.0 - - - +
106R ALA* 1.3 59.3 + - - +
107R GLU* 3.0 24.5 - - + +
137R LEU* 3.4 7.7 - - - +
138R GLU* 2.8 40.1 + - + +
140R VAL* 3.8 9.4 - - + +
185R MET* 4.5 5.6 - - - -
232R ALA* 3.5 22.7 - - + +
234R GLY 4.2 3.8 - - - +
235R PRO 5.2 0.2 - - - -
236R MET* 3.7 26.8 + - + +
1262R PO4 2.6 43.9 + - - -
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Residues in contact with ALA 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105R GLU* 1.3 73.1 - - - +
107R GLU* 1.3 62.6 + - - +
136R ALA 3.6 5.8 - - - +
137R LEU* 4.3 2.9 - - + -
183R MET* 3.8 38.2 - - + +
185R MET* 4.5 6.6 - - - +
232R ALA* 3.6 0.9 - - - -
233R LEU* 2.9 31.6 + - + +
234R GLY 5.2 1.2 + - - -
247R ALA* 3.8 23.3 - - + -
249R ILE* 4.7 2.5 - - + -
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Residues in contact with GLU 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R VAL 4.5 2.8 - - - +
105R GLU* 3.0 35.1 - - + +
106R ALA* 1.3 80.6 - - - +
108R ILE* 1.3 67.6 + - - +
136R ALA* 2.8 41.1 + - + +
138R GLU* 3.1 23.8 - - + +
229R LEU* 3.3 21.8 - - + +
230R THR 4.9 0.2 - - - +
231R GLY* 2.9 39.0 + - - +
232R ALA* 3.6 6.9 + - - +
233R LEU* 4.0 6.0 - - - +
249R ILE* 3.6 8.0 - - - +
1262R PO4 4.5 0.9 + - - -
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Residues in contact with ILE 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R GLU* 1.3 76.7 - - - +
109R ALA* 1.3 68.8 + - - +
110R LEU* 4.1 16.2 - - + -
133R VAL* 4.2 13.5 - - + -
134R LEU 3.9 4.5 - - - +
178R LEU* 4.2 8.5 - - + -
181R CYS* 3.5 31.6 - - - -
204R PRO* 3.8 23.6 - - + -
229R LEU* 4.0 0.8 - - - -
230R THR* 2.7 46.4 + - - +
231R GLY 4.4 1.6 + - - -
233R LEU* 4.2 17.3 - - + +
249R ILE* 4.5 5.8 - - + -
252R ILE* 3.8 18.6 - - + -
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Residues in contact with ALA 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R GLU 4.1 0.6 + - - -
108R ILE* 1.3 73.1 - - - +
110R LEU* 1.3 63.1 + - - +
133R VAL* 3.4 5.2 - - - +
134R LEU* 2.8 48.0 + - + +
136R ALA* 4.1 8.5 - - + -
166R ILE* 4.9 2.2 - - + -
227R ILE* 4.2 18.2 - - + -
228R ILE 3.2 5.8 - - - +
229R LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108R ILE* 4.1 10.5 - - + -
109R ALA* 1.3 83.5 - - - +
111R VAL* 1.3 65.4 + - - +
112R LEU* 5.1 4.0 - - + -
126R LEU* 4.7 0.9 - - + -
130R ILE* 4.3 21.5 - - + -
132R TRP 3.4 2.7 - - - +
133R VAL* 3.8 20.6 - - + -
178R LEU* 5.3 2.7 - - + -
204R PRO* 6.1 0.4 - - + -
205R LEU* 3.7 31.9 - - + -
208R ALA* 3.8 16.2 - - + -
226R ASP 3.7 0.7 - - - +
227R ILE* 3.3 6.9 - - - +
228R ILE* 2.8 45.2 + - + +
230R THR* 3.8 24.5 - - + -
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Residues in contact with VAL 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110R LEU* 1.3 79.2 - - - +
112R LEU* 1.3 59.1 + - - +
130R ILE* 3.6 4.3 - - - +
131R GLU* 2.6 48.7 + - - +
132R TRP* 2.9 28.3 + - + +
134R LEU* 3.9 23.3 - - + -
225R GLY* 3.8 23.3 - - - +
226R ASP 3.4 3.1 - - - +
227R ILE* 4.4 14.6 - - + -
124T ASP* 4.5 16.6 - - + +
128T ASN* 6.1 1.8 - - + -
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Residues in contact with LEU 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110R LEU* 5.1 8.1 - - + -
111R VAL* 1.3 77.6 - - - +
113R ASN* 1.4 59.1 + - - +
114R ARG 3.9 12.3 - - - +
116R LEU* 3.9 20.6 - - + -
126R LEU* 5.2 5.4 - - + -
129R ALA* 3.2 19.1 - - + +
130R ILE* 5.1 4.9 - - + -
131R GLU* 3.9 10.0 - - - +
222R LEU* 3.8 35.2 - - + -
223R ARG 3.9 15.0 - - - +
224R THR* 4.1 0.5 + - - -
225R GLY* 3.0 24.6 + - - -
226R ASP* 3.3 21.1 + - + +
228R 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