Contacts of the helix formed by residues 122 - 128 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ASP 3.9 7.9 - - - +
121B ILE* 1.3 80.0 - - - +
123B PHE* 1.3 67.0 + - - +
124B ASP* 2.8 27.0 + - - +
125B GLU* 3.0 40.6 + - - +
126B LEU* 3.0 11.3 + - - +
209B VAL* 4.3 3.1 - - - -
213B ARG* 4.2 3.8 - - - +
57E VAL* 4.7 3.4 - - + -
84E ALA* 3.8 34.3 - - + +
87E CYS* 3.8 13.9 - - + -
164E TYR* 4.9 1.3 - - - +
1F MET* 4.4 0.9 - - + -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B THR* 1.3 73.6 - - - +
124B ASP* 1.3 61.5 + - - +
126B LEU* 3.4 4.3 + - - +
127B TYR* 3.3 31.4 + + - -
203B HIS* 3.9 29.4 - + - -
205B LEU* 3.5 30.7 - - + +
206B ASN* 3.4 27.4 - - - -
209B VAL* 3.8 15.5 - - + +
213B ARG* 5.2 0.6 - - - +
87E CYS* 4.3 9.9 + - - -
88E TYR 4.7 0.7 - - - +
89E GLY* 3.4 19.1 - - - +
90E ASP* 3.7 15.9 - - + -
166E ILE* 3.5 31.2 - - + -
167E GLY 3.6 16.2 - - - -
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Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B THR* 2.8 22.1 + - - -
123B PHE* 1.3 77.4 - - - +
125B GLU* 1.3 80.2 + - - +
127B TYR* 3.3 26.6 + - - +
128B ASN* 3.6 6.6 + - - +
87E CYS* 3.7 2.8 - - - -
111E VAL* 4.5 17.5 - - + +
132E TRP* 5.5 2.8 - - - -
134E LEU* 4.8 5.4 - - + -
164E TYR* 4.3 3.8 + - - -
166E ILE* 3.6 31.5 - - + +
225E GLY 5.2 4.0 - - - +
227E ILE* 3.8 29.4 - - + +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ARG* 5.8 0.5 + - - -
116B LEU* 5.6 0.2 - - - +
118B ALA* 5.4 1.6 - - - +
121B ILE* 3.4 17.9 - - + +
122B THR* 3.0 34.7 + - - +
124B ASP* 1.3 83.9 - - - +
126B LEU* 1.3 65.9 + - - +
128B ASN* 3.3 15.8 + - - +
129B ALA* 3.6 9.9 + - - +
55E ARG* 3.0 37.6 + - - -
57E VAL* 3.8 11.6 - - - +
225E GLY 5.6 6.1 - - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 4.7 2.2 - - + -
112B LEU* 5.2 6.5 - - + -
116B LEU* 4.2 23.1 - - + -
121B ILE* 4.1 10.6 - - + +
122B THR 3.0 11.0 + - - +
123B PHE 3.6 8.1 - - - +
124B ASP 3.3 0.2 - - - -
125B GLU* 1.3 75.4 - - - +
127B TYR* 1.3 60.0 + - - +
129B ALA* 2.8 23.5 + - + +
130B ILE* 3.4 13.4 + - + +
205B LEU* 3.8 36.6 - - + +
208B ALA* 3.5 45.5 - - + +
209B VAL* 4.1 8.5 - - + +
212B ALA* 4.4 5.4 - - + -
228B ILE* 5.6 1.6 - - + -
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PHE* 3.3 27.1 + + - -
124B ASP* 3.3 13.1 + - - +
126B LEU* 1.3 80.3 - - - +
128B ASN* 1.3 59.4 - - - +
129B ALA 3.2 1.2 + - - -
130B ILE* 3.4 26.6 + - + +
173B PRO* 4.6 17.4 - - + +
176B LEU 4.8 2.4 + - - -
178B LEU* 4.3 18.7 + - + +
203B HIS* 4.5 7.1 + - - -
205B LEU* 3.6 23.6 - - + +
132E TRP* 4.5 14.7 - + + +
134E LEU* 3.8 17.3 - - + -
167E GLY 3.5 20.1 + - - -
168E GLY* 3.7 17.3 - - - -
169E PRO* 3.9 3.6 - - - +
170E ALA* 3.7 35.1 + - + -
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ASN* 3.3 18.4 + - - -
114B ARG* 3.1 34.4 + - - +
124B ASP 3.6 5.1 + - - +
125B GLU* 3.3 12.4 + - - +
126B LEU 3.2 0.8 - - - -
127B TYR* 1.3 77.9 - - - +
129B ALA* 1.3 57.8 + - - +
130B ILE 3.5 1.1 - - - -
111E VAL* 6.0 1.8 - - + -
131E GLU* 2.9 33.8 + - - +
132E TRP* 2.7 39.2 - - + +
172E ARG* 4.8 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