Contacts of the helix formed by residues 122 - 128 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C VAL* 4.8 3.6 - - + -
84C ALA* 3.8 34.3 - - + +
87C CYS* 3.8 14.6 - - + -
164C TYR* 4.9 1.8 - - - +
120E ASP 3.8 8.5 - - - +
121E ILE* 1.3 78.9 - - - +
123E PHE* 1.3 67.5 + - - +
124E ASP* 2.8 27.6 + - - +
125E GLU* 2.9 39.4 + - - +
126E LEU* 3.0 11.4 + - - +
209E VAL* 4.3 3.1 - - - -
213E ARG* 4.2 4.3 - - - +
1M MET* 4.6 0.9 - - + -
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Residues in contact with PHE 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C CYS* 4.2 11.1 + - - +
88C TYR 4.7 0.2 - - - +
89C GLY* 3.4 19.7 - - - +
90C ASP* 3.7 15.5 - - + -
166C ILE* 3.4 31.9 - - + -
167C GLY 3.5 16.4 - - - -
122E THR* 1.3 71.6 - - - +
124E ASP* 1.3 60.9 + - - +
126E LEU* 3.4 4.3 + - - +
127E TYR* 3.3 31.6 + + - -
203E HIS* 3.9 27.4 - + - -
205E LEU* 3.5 32.5 - - + +
206E ASN* 3.4 27.6 - - - -
209E VAL* 3.8 15.8 - - + +
213E ARG* 5.2 1.0 - - - +
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Residues in contact with ASP 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C VAL* 6.2 0.2 - - - +
87C CYS* 3.8 2.6 - - - -
111C VAL* 4.5 18.1 - - + +
132C TRP* 5.4 3.1 - - - -
134C LEU* 4.8 5.8 - - + +
164C TYR* 4.3 3.6 + - - -
166C ILE* 3.6 31.6 - - + +
225C GLY 5.2 4.0 - - - +
227C ILE* 3.8 30.3 - - + +
122E THR* 2.8 22.2 + - - -
123E PHE* 1.3 76.7 - - - +
125E GLU* 1.3 79.6 + - - +
127E TYR* 3.3 24.9 + - - +
128E ASN* 3.5 6.8 + - - +
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.0 39.1 + - - -
57C VAL* 3.9 11.3 - - - +
225C GLY 5.7 4.8 - - - +
114E ARG* 5.8 0.5 + - - -
116E LEU* 5.5 0.2 - - - +
118E ALA* 5.4 1.6 - - - +
121E ILE* 3.4 18.6 - - + +
122E THR* 2.9 35.9 + - - +
124E ASP* 1.3 83.7 - - - +
126E LEU* 1.3 65.6 + - - +
128E ASN* 3.4 16.4 + - - +
129E ALA* 3.6 10.0 + - - +
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LEU* 4.7 2.2 - - + -
112E LEU* 5.2 7.4 - - + -
116E LEU* 4.2 24.0 - - + -
121E ILE* 4.0 12.7 - - + +
122E THR 3.0 11.0 + - - +
123E PHE 3.7 8.3 - - - +
124E ASP 3.3 0.2 - - - -
125E GLU* 1.3 75.5 - - - +
127E TYR* 1.3 64.9 + - - +
129E ALA* 2.9 17.8 + - + +
130E ILE* 3.4 11.9 + - + +
205E LEU* 3.8 37.5 - - + +
208E ALA* 3.5 46.7 - - + +
209E VAL* 4.0 8.5 - - + +
212E ALA* 4.4 2.5 - - + -
228E ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TRP* 4.4 15.1 - + + +
134C LEU* 3.8 17.5 - - + -
167C GLY 3.5 20.6 + - - -
168C GLY* 3.7 12.5 - - - -
169C PRO* 3.8 4.2 - - - +
170C ALA* 3.6 39.9 + - + -
123E PHE* 3.3 27.1 + + - -
124E ASP* 3.3 11.1 + - - +
125E GLU 3.3 0.6 - - - -
126E LEU* 1.3 78.7 - - - +
128E ASN* 1.3 62.2 + - - +
129E ALA 3.2 1.6 + - - -
130E ILE* 3.4 26.5 + - + +
173E PRO* 4.6 17.7 - - + +
176E LEU 4.7 1.6 + - - -
178E LEU* 4.3 18.5 + - + +
203E HIS* 4.5 6.8 + - - -
205E LEU* 3.6 25.9 - - + +
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Residues in contact with ASN 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL* 6.1 2.2 - - + -
131C GLU* 2.9 33.3 + - - +
132C TRP* 2.8 37.0 - - + +
172C ARG* 4.8 1.6 - - - +
113E ASN* 3.2 19.4 + - - -
114E ARG* 3.1 33.6 + - - +
124E ASP 3.5 6.3 + - - +
125E GLU* 3.4 11.4 + - - +
126E LEU 3.2 0.8 - - - -
127E TYR* 1.3 78.3 - - - +
129E ALA* 1.3 56.5 + - - +
130E ILE 3.5 1.5 - - - +
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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