Contacts of the helix formed by residues 122 - 128 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H ASP 3.8 8.1 - - - +
121H ILE* 1.3 78.9 - - - +
123H PHE* 1.3 65.5 - - - +
124H ASP* 2.8 25.4 + - - +
125H GLU* 2.9 40.8 + - - +
126H LEU* 3.0 12.0 + - - +
209H VAL* 4.3 2.9 - - - -
213H ARG* 4.2 4.5 - - - +
57I VAL* 4.7 3.1 - - + -
84I ALA* 3.6 37.0 - - + +
87I CYS* 3.9 12.6 - - + -
164I TYR* 4.9 1.6 - - - +
1R MET* 4.7 1.3 - - + -
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Residues in contact with PHE 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H THR* 1.3 71.8 - - - +
124H ASP* 1.3 61.1 + - - +
126H LEU* 3.4 5.2 + - - +
127H TYR* 3.3 42.0 + + - -
203H HIS* 3.8 22.0 - + - -
205H LEU* 3.5 38.1 - - + +
206H ASN* 3.3 20.0 - - - -
209H VAL* 3.8 15.6 - - + +
213H ARG* 5.2 0.6 - - - +
87I CYS* 4.3 11.5 + - - +
88I TYR 4.6 0.2 - - - +
89I GLY* 3.3 26.9 - - - +
90I ASP* 3.7 16.4 - - + -
166I ILE* 3.5 31.6 - - + -
167I GLY 3.7 5.2 - - - -
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Residues in contact with ASP 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H THR* 2.8 22.2 + - - -
123H PHE* 1.3 82.2 - - - +
125H GLU* 1.3 76.8 + - - +
127H TYR* 3.3 22.0 + - - +
128H ASN* 3.6 6.4 + - - +
57I VAL* 6.1 0.5 - - - +
87I CYS* 3.6 3.3 - - - -
111I VAL* 4.7 14.1 - - + +
132I TRP* 5.6 2.3 - - - -
134I LEU* 4.8 7.7 - - + +
164I TYR* 4.2 4.2 + - - -
166I ILE* 3.6 32.8 - - + +
225I GLY 5.3 3.8 - - - +
227I ILE* 3.9 28.2 - - + +
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H ARG* 5.8 0.5 + - - -
116H LEU* 5.5 0.3 - - - +
118H ALA* 5.4 1.2 - - - +
121H ILE* 3.4 17.0 - - + +
122H THR* 2.9 36.5 + - - +
124H ASP* 1.3 82.3 - - - +
126H LEU* 1.3 65.2 + - - +
128H ASN* 3.3 16.6 + - - +
129H ALA* 3.6 9.9 + - - +
55I ARG* 3.0 39.0 + - - -
57I VAL* 3.8 12.0 - - - +
225I GLY 5.7 4.3 - - - +
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Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LEU* 4.7 2.0 - - + -
112H LEU* 5.2 6.7 - - + -
116H LEU* 4.2 24.2 - - + -
121H ILE* 4.1 10.0 - - + +
122H THR 3.0 10.8 + - - +
123H PHE 3.6 8.1 - - - +
124H ASP 3.3 0.2 - - - -
125H GLU* 1.3 74.9 - - - +
127H TYR* 1.3 64.9 + - - +
129H ALA* 2.9 18.8 + - + +
130H ILE* 3.4 12.3 + - + +
205H LEU* 3.8 36.6 - - + +
208H ALA* 3.5 45.5 - - + +
209H VAL* 4.1 8.3 - - + +
212H ALA* 4.4 5.6 - - + -
228H ILE* 5.6 1.3 - - + -
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Residues in contact with TYR 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H PHE* 3.3 30.1 + + - -
124H ASP* 3.3 11.7 - - - +
125H GLU 3.3 0.2 - - - -
126H LEU* 1.3 78.7 - - - +
128H ASN* 1.3 61.6 + - - +
129H ALA 3.1 1.2 + - - -
130H ILE* 3.3 26.9 + - + +
173H PRO* 4.6 20.6 - - + +
176H LEU 4.8 2.0 + - - -
178H LEU* 4.3 18.3 + - + +
203H HIS* 4.5 8.0 + - - -
205H LEU* 3.6 23.9 - - + +
132I TRP* 4.7 12.2 - + + +
134I LEU* 3.9 20.9 - - + -
167I GLY 3.5 20.4 - - - -
168I GLY* 3.7 17.2 - - - -
169I PRO* 4.0 3.5 - - - +
170I ALA* 3.8 30.8 + - + -
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Residues in contact with ASN 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H ASN* 2.6 24.6 + - - -
114H ARG* 3.1 31.7 + - - +
124H ASP 3.6 6.1 + - - +
125H GLU* 3.3 12.7 + - - +
126H LEU 3.2 0.8 - - - -
127H TYR* 1.3 78.2 - - - +
129H ALA* 1.3 49.5 + - - +
130H ILE 3.5 1.5 - - - +
111I VAL* 6.0 1.8 - - + -
131I GLU* 3.1 32.8 + - - +
132I TRP* 2.7 38.9 - - + +
172I ARG* 4.9 1.2 - - - +
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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