Contacts of the helix formed by residues 122 - 128 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ASP 3.8 8.7 - - - +
121C ILE* 1.3 78.3 - - - +
123C PHE* 1.3 65.7 + - - +
124C ASP* 2.8 23.7 + - - +
125C GLU* 3.0 42.7 + - - +
126C LEU* 3.0 12.0 + - - +
209C VAL* 4.3 3.6 - - - -
213C ARG* 4.2 5.8 - - - +
57D VAL* 4.7 3.8 - - + -
84D ALA* 3.8 35.7 - - + +
87D CYS* 3.9 13.2 - - + -
164D TYR* 4.9 1.3 - - - +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C THR* 1.3 73.8 - - - +
124C ASP* 1.3 60.8 + - - +
126C LEU* 3.4 4.9 + - - +
127C TYR* 3.3 33.2 + + - -
203C HIS* 3.8 32.1 - + - -
205C LEU* 3.5 32.8 - - + +
206C ASN* 3.4 26.0 - - - -
209C VAL* 3.8 15.0 - - + +
213C ARG* 5.2 0.4 - - - +
87D CYS* 4.3 11.6 - - - -
88D TYR 4.8 0.4 - - - +
89D GLY* 3.5 17.9 - - - +
90D ASP* 3.9 13.5 - - + -
166D ILE* 3.6 30.5 - - + -
167D GLY 3.6 16.2 - - - -
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Residues in contact with ASP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C THR* 2.8 21.6 + - - -
123C PHE* 1.3 79.8 - - - +
125C GLU* 1.3 76.1 + - - +
127C TYR* 3.3 25.0 - - - +
128C ASN* 3.6 7.1 + - - +
57D VAL* 6.1 0.5 - - - +
87D CYS* 3.8 2.6 - - - -
111D VAL* 4.6 17.4 - - + +
132D TRP* 5.4 3.1 - - - -
134D LEU* 4.8 5.6 - - + +
164D TYR* 4.3 4.3 + - - -
166D ILE* 3.7 29.6 - - + +
225D GLY 5.1 4.7 - - - +
227D ILE* 3.9 28.4 - - + +
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ARG* 5.7 0.5 + - - -
118C ALA* 5.4 1.6 - - - +
121C ILE* 3.4 17.1 - - + +
122C THR* 3.0 36.6 + - - +
124C ASP* 1.3 82.5 - - - +
126C LEU* 1.3 65.4 + - - +
128C ASN* 3.3 16.6 + - - +
129C ALA* 3.6 10.6 + - - +
55D ARG* 3.0 38.9 + - - -
57D VAL* 3.9 11.3 - - - +
225D GLY 5.6 5.9 - - - +
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU* 4.7 2.0 - - + -
112C LEU* 5.2 6.7 - - + -
116C LEU* 4.2 24.2 - - + -
121C ILE* 4.0 13.3 - - + +
122C THR 3.0 11.1 + - - +
123C PHE 3.6 8.5 - - - +
124C ASP 3.3 0.2 - - - -
125C GLU* 1.3 74.3 - - - +
127C TYR* 1.3 64.6 + - - +
129C ALA* 2.8 19.4 + - + +
130C ILE* 3.4 11.5 + - + +
205C LEU* 3.7 36.8 - - + +
208C ALA* 3.5 47.1 - - + +
209C VAL* 4.1 8.5 - - + +
212C ALA* 4.4 2.2 - - + -
228C ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PHE* 3.3 29.6 + + - -
124C ASP* 3.3 12.6 - - - +
125C GLU 3.3 0.4 - - - -
126C LEU* 1.3 78.5 - - - +
128C ASN* 1.3 59.2 + - - +
129C ALA 3.1 1.4 + - - -
130C ILE* 3.3 26.9 + - + +
173C PRO* 4.6 17.3 - - + +
176C LEU 4.8 1.8 + - - -
178C LEU* 4.2 19.3 - - + +
203C HIS* 4.6 7.3 + - - -
205C LEU* 3.6 25.4 - - + +
132D TRP* 4.5 16.1 - + + +
134D LEU* 3.8 17.0 - - + -
167D GLY 3.6 20.1 + - - -
168D GLY* 3.8 11.8 - - - -
169D PRO* 3.9 3.5 - - - +
170D ALA* 3.7 41.1 + - + -
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Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASN* 3.0 14.6 + - - +
114C ARG* 3.1 36.4 + - - +
124C ASP 3.6 6.3 + - - +
125C GLU* 3.3 12.2 + - - +
126C LEU 3.2 1.2 - - - -
127C TYR* 1.3 77.1 - - - +
129C ALA* 1.3 56.2 + - - +
130C ILE 3.5 1.3 - - - +
111D VAL* 6.0 2.2 - - + -
131D GLU* 2.8 37.6 + - - +
132D TRP* 2.8 34.8 - - + +
172D ARG* 4.8 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