Contacts of the strand formed by residues 130 - 140 (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 ILE 130 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110R LEU* 4.3 19.1 - - + -
111R VAL 3.7 5.2 - - - +
112R LEU* 4.7 3.4 - - + +
113R ASN* 3.2 6.9 + - - +
126R LEU* 3.5 19.7 - - + +
127R TYR* 3.4 19.2 + - + +
128R ASN 3.5 1.1 - - - +
129R ALA* 1.3 77.3 - - - +
131R GLU* 1.3 61.4 + - - +
132R TRP 3.6 24.7 - - - +
133R VAL* 4.1 5.8 - - + -
173R PRO* 3.5 34.9 - - + +
178R LEU* 5.2 2.9 - - + -
205R LEU* 3.5 39.0 - - + -
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Residues in contact with GLU 131 (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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111R VAL* 2.6 28.5 + - - +
112R LEU 3.9 11.2 - - - +
113R ASN* 3.2 24.4 + - - +
129R ALA 3.6 0.8 + - - -
130R ILE* 1.3 74.1 - - - +
132R TRP* 1.3 70.6 + - + +
172R ARG* 3.3 39.2 + - - +
173R PRO* 3.8 6.1 - - - +
225R GLY* 5.3 2.4 - - - -
128T ASN* 2.9 34.4 + - - +
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Residues in contact with TRP 132 (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* 3.4 3.5 - - - -
111R VAL* 2.9 43.1 + - + -
130R ILE* 3.6 5.5 - - - +
131R GLU* 1.3 99.9 - - + +
133R VAL* 1.3 63.6 + - - +
134R LEU* 4.2 16.2 - - + -
170R ALA* 3.6 29.2 - - + -
171R GLN 3.4 20.6 - - - -
172R ARG* 3.3 42.6 - - + -
124T ASP 5.4 2.5 - - - -
127T TYR* 4.5 17.5 - + + -
128T ASN* 2.8 39.9 - - + +
173T PRO* 4.8 9.0 - - + -
174T ALA* 3.7 31.0 - - + -
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Residues in contact with VAL 133 (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* 4.2 10.3 - - + -
109R ALA 3.4 2.9 - - - -
110R LEU* 3.8 14.6 - - + -
130R ILE* 4.1 8.5 - - + -
132R TRP* 1.3 76.0 - - - +
134R LEU* 1.3 64.1 + - - +
171R GLN* 2.8 37.8 + - - +
173R PRO* 4.0 18.2 - - + -
176R LEU* 3.6 33.9 - - + -
178R LEU* 4.0 22.4 - - + -
252R ILE* 4.4 11.7 - - + -
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Residues in contact with LEU 134 (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* 3.8 2.3 - - - +
109R ALA* 2.8 53.0 + - + +
111R VAL* 3.9 25.8 - - + -
132R TRP* 4.2 7.6 - - + -
133R VAL* 1.3 78.6 - - - +
135R PRO* 1.3 75.2 - - + +
166R ILE* 4.0 22.0 - - + -
167R GLY 4.4 2.9 - - - +
169R PRO 4.4 4.0 - - - +
170R ALA* 3.8 15.7 - - + -
227R ILE* 5.1 1.1 - - + -
252R ILE* 4.2 4.7 - - - -
124T ASP* 4.8 8.7 - - + -
127T TYR* 3.8 32.5 - - + -
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Residues in contact with PRO 135 (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 3.9 5.6 - - - +
108R ILE* 5.0 0.7 - - - -
134R LEU* 1.3 92.3 - - + +
136R ALA* 1.3 60.2 + - - +
166R ILE* 3.8 1.9 - - - +
167R GLY 2.9 26.7 + - - -
168R GLY 3.6 33.7 - - - +
169R PRO 3.9 8.7 - - - +
249R ILE* 3.8 20.9 - - + -
252R ILE* 3.8 17.2 - - + +
253R GLY 4.0 3.4 - - - -
254R SER 3.7 16.6 - - - +
255R VAL* 3.8 9.9 - - + -
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Residues in contact with ALA 136 (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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106R ALA* 3.6 4.5 - - - +
107R GLU* 2.8 38.9 + - + +
109R ALA* 4.1 10.3 - - + -
135R PRO* 1.3 75.6 - - - +
137R LEU* 1.3 63.1 + - - +
164R TYR* 5.6 0.4 - - + -
165R VAL 3.1 12.6 - - - +
166R ILE* 4.5 4.9 - - + -
229R LEU* 3.9 28.3 - - + -
249R ILE* 4.8 0.3 - - - +
255R VAL* 3.7 11.5 - - - +
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Residues in contact with LEU 137 (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* 4.2 13.2 - - + -
105R GLU 3.4 9.6 - - - +
106R ALA* 4.3 1.3 - - - -
107R GLU* 5.3 0.2 - - - -
136R ALA* 1.3 78.0 - - - +
138R GLU* 1.3 59.9 + - - +
139R VAL 4.1 0.2 - - - -
164R TYR* 3.3 6.4 - - - +
165R VAL* 2.9 42.4 + - + +
185R MET* 3.9 19.1 - - - -
229R LEU* 5.7 0.2 - - - -
245R PHE* 4.4 11.7 - - + +
247R ALA* 3.8 28.9 - - + +
255R VAL* 3.8 17.9 - - + +
256R ALA* 4.0 6.7 - - - -
257R ALA* 3.9 36.8 - - + +
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Residues in contact with GLU 138 (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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60R LYS* 3.1 48.2 + - - +
82R LEU* 5.0 0.9 - - + +
86R MET* 5.6 0.3 - - - +
103R ARG 3.6 0.2 - - - +
104R ILE* 3.2 3.9 - - - -
105R GLU* 2.8 41.2 + - + +
107R GLU* 3.1 34.2 - - + +
136R ALA 4.2 0.2 - - - -
137R LEU* 1.3 74.4 - - - +
139R VAL* 1.3 63.6 + - - +
140R VAL* 3.5 16.5 + - - +
161R CYS* 3.7 15.9 - - - -
162R GLY 4.6 1.4 + - - -
163R VAL 3.8 10.0 - - - +
164R TYR* 4.2 1.8 - - + -
229R LEU* 3.8 18.2 - - + -
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Residues in contact with VAL 139 (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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94R ILE* 4.4 7.9 - - + -
99R VAL* 4.1 15.9 - - + -
102R PRO* 4.0 24.0 - - + -
103R ARG 3.2 11.2 - - - +
104R ILE* 3.5 19.1 - - + -
138R GLU* 1.3 68.9 - - - +
140R VAL* 1.3 59.3 + - - +
162R GLY* 3.2 8.0 + - - -
163R VAL* 2.8 52.0 + - + +
165R VAL* 4.7 8.5 - - + -
257R ALA* 5.9 0.4 - - + -
259R PHE* 3.8 25.6 - - + -
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Residues in contact with VAL 140 (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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60R LYS* 4.1 1.8 - - - +
99R VAL* 3.6 2.0 - - - +
101R GLN 4.0 0.2 - - - +
102R PRO* 3.4 4.9 - - - +
103R ARG* 2.7 54.8 + - + +
105R GLU* 3.8 11.7 - - - +
138R GLU* 3.5 19.4 + - + +
139R VAL* 1.3 76.4 - - - +
141R GLY* 1.3 59.6 + - - +
147R TRP* 3.6 22.2 - - + -
160R SER* 3.2 17.0 - - - +
162R GLY 4.2 0.9 - - - +
236R MET* 3.9 12.6 - - + -
1262R PO4 3.4 28.7 - - - +
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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