Contacts of the helix formed by residues 122 - 128 (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 THR 122 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1H MET* 4.7 1.3 - - + -
120R ASP 3.8 8.1 - - - +
121R ILE* 1.3 79.4 - - - +
123R PHE* 1.3 65.0 + - - +
124R ASP* 2.7 27.8 + - - +
125R GLU* 2.9 40.7 + - - +
126R LEU* 3.0 11.8 + - - +
209R VAL* 4.3 2.7 - - - -
213R ARG* 4.3 4.5 - - - +
57S VAL* 4.7 2.9 - - + +
84S ALA* 3.7 35.7 - - + +
87S CYS* 3.8 13.5 - - + -
164S TYR* 4.9 1.8 - - - +
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Residues in contact with PHE 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R THR* 1.3 72.4 - - - +
124R ASP* 1.3 60.2 + - - +
126R LEU* 3.3 5.4 + - - +
127R TYR* 3.3 41.4 + + - -
203R HIS* 3.9 30.5 - + - -
205R LEU* 3.5 29.2 - - + +
206R ASN* 3.3 28.0 - - - -
209R VAL* 3.8 16.7 - - + +
213R ARG* 5.2 0.8 - - - +
87S CYS* 4.2 10.5 + - - -
88S TYR 4.7 0.2 - - - +
89S GLY* 3.4 20.2 - - - +
90S ASP* 3.8 12.8 - - + -
166S ILE* 3.5 30.7 - - + -
167S GLY 3.6 6.1 - - - -
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Residues in contact with ASP 124 (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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122R THR* 2.7 22.5 + - - -
123R PHE* 1.3 83.5 - - - +
125R GLU* 1.3 76.1 + - - +
127R TYR* 3.3 23.7 + - - +
128R ASN* 3.5 6.8 + - - +
57S VAL* 6.1 0.7 - - - +
87S CYS* 3.7 3.3 - - - -
111S VAL* 4.6 16.6 - - + +
132S TRP* 5.5 2.6 - - - -
134S LEU* 4.8 5.3 - - + +
164S TYR* 4.2 4.0 + - - -
166S ILE* 3.6 30.7 - - + +
225S GLY 5.2 4.0 - - - +
227S ILE* 3.8 28.4 - - + +
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Residues in contact with GLU 125 (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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114R ARG* 5.7 1.2 - - - -
116R LEU* 5.5 0.3 - - - +
118R ALA* 5.5 1.2 - - - +
121R ILE* 3.4 17.9 - - + +
122R THR* 2.9 35.7 + - - +
124R ASP* 1.3 82.8 - - - +
126R LEU* 1.3 63.7 - - - +
128R ASN* 3.3 15.9 + - - +
129R ALA* 3.6 10.6 + - - +
55S ARG* 3.0 37.9 + - - -
57S VAL* 3.8 12.5 - - - +
225S GLY 5.7 4.9 - - - +
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Residues in contact with LEU 126 (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* 4.7 1.8 - - + -
112R LEU* 5.2 6.5 - - + -
116R LEU* 4.2 24.2 - - + -
121R ILE* 4.0 10.4 - - + +
122R THR 3.0 11.0 + - - +
123R PHE 3.6 7.6 - - - +
125R GLU* 1.3 75.4 - - - +
127R TYR* 1.3 65.3 + - - +
129R ALA* 2.8 19.0 + - + +
130R ILE* 3.4 12.5 + - + +
205R LEU* 3.8 36.1 - - + +
208R ALA* 3.4 45.8 - - + +
209R VAL* 4.1 8.3 - - + +
212R ALA* 4.4 5.4 - - + -
228R ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 127 (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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123R PHE* 3.3 29.9 + + - -
124R ASP* 3.3 12.1 + - - +
126R LEU* 1.3 78.4 - - - +
128R ASN* 1.3 62.0 + - - +
129R ALA 3.2 1.2 + - - -
130R ILE* 3.4 26.0 + - + +
173R PRO* 4.6 19.3 - - + +
176R LEU 4.7 2.1 + - - -
178R LEU* 4.3 18.6 + - + +
203R HIS* 4.5 7.4 + - - -
205R LEU* 3.6 24.6 - - + +
132S TRP* 4.6 14.9 - + + +
134S LEU* 3.8 21.5 - - + -
167S GLY 3.5 19.3 - - - -
168S GLY* 3.8 11.8 - - - -
169S PRO* 3.9 3.1 - - - +
170S ALA* 3.7 35.1 + - + -
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Residues in contact with ASN 128 (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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113R ASN* 2.6 24.8 + - - -
114R ARG* 3.3 29.0 + - - +
124R ASP 3.5 5.7 + - - +
125R GLU* 3.3 12.4 + - - +
126R LEU 3.2 1.0 - - - -
127R TYR* 1.3 78.1 - - - +
129R ALA* 1.3 50.3 + - - +
130R ILE 3.5 1.2 - - - +
111S VAL* 6.0 2.5 - - + -
131S GLU* 2.9 33.5 + - - +
132S TRP* 2.7 37.0 - - + +
172S ARG* 4.9 1.4 - - - +
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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