Contacts of the helix formed by residues 122 - 128 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1K MET* 4.5 1.1 - - + -
57R VAL* 4.7 3.4 - - + -
84R ALA* 3.7 34.5 - - + +
87R CYS* 3.9 14.6 - - + -
164R TYR* 4.9 2.0 - - - +
120T ASP 3.9 9.0 - - - +
121T ILE* 1.3 79.5 - - - +
123T PHE* 1.3 64.3 + - - +
124T ASP* 2.8 23.1 + - - +
125T GLU* 3.0 42.6 + - - +
126T LEU* 3.0 12.0 + - - +
209T VAL* 4.3 3.4 - - - -
213T ARG* 4.3 4.3 - - - +
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Residues in contact with PHE 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R CYS* 4.3 10.4 + - - -
88R TYR 4.7 0.2 - - - +
89R GLY* 3.4 18.6 - - - +
90R ASP* 3.8 14.1 - - + -
166R ILE* 3.5 31.9 - - + -
167R GLY 3.5 15.7 - - - -
122T THR* 1.3 72.0 - - - +
124T ASP* 1.3 60.5 + - - +
126T LEU* 3.4 5.0 + - - +
127T TYR* 3.3 32.5 + + - -
203T HIS* 3.8 31.4 - + - -
205T LEU* 3.5 30.2 - - + +
206T ASN* 3.4 27.8 - - - -
209T VAL* 3.8 16.1 - - + +
213T ARG* 5.3 0.4 - - - +
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Residues in contact with ASP 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R CYS* 3.8 2.8 - - - -
111R VAL* 4.5 17.5 - - + +
132R TRP* 5.4 3.3 - - - -
134R LEU* 4.8 5.8 - - + -
164R TYR* 4.4 3.6 + - - -
166R ILE* 3.6 30.2 - - + +
225R GLY 5.1 4.7 - - - +
227R ILE* 3.8 28.3 - - + +
122T THR* 2.8 22.9 + - - +
123T PHE* 1.3 80.2 - - - +
125T GLU* 1.3 76.6 + - - +
127T TYR* 3.3 25.6 + - - +
128T ASN* 3.6 6.2 + - - +
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Residues in contact with GLU 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R ARG* 3.0 38.4 + - - -
57R VAL* 3.9 11.1 - - - +
225R GLY 5.6 5.6 - - - +
114T ARG* 5.7 0.5 + - - -
116T LEU* 5.5 0.2 - - - +
118T ALA* 5.4 1.7 - - - +
121T ILE* 3.4 18.1 - - + +
122T THR* 3.0 34.9 + - - +
124T ASP* 1.3 82.7 - - - +
126T LEU* 1.3 64.3 + - - +
128T ASN* 3.3 16.1 + - - +
129T ALA* 3.6 9.9 + - - +
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Residues in contact with LEU 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T LEU* 4.7 1.8 - - + -
112T LEU* 5.2 6.7 - - + -
116T LEU* 4.2 24.7 - - + -
121T ILE* 4.0 12.5 - - + +
122T THR 3.0 10.7 + - - +
123T PHE 3.6 7.6 - - - +
124T ASP 3.3 0.2 - - - -
125T GLU* 1.3 75.4 - - - +
127T TYR* 1.3 60.6 + - - +
129T ALA* 2.8 23.0 + - + +
130T ILE* 3.4 12.8 + - + +
205T LEU* 3.8 37.0 - - + +
208T ALA* 3.5 45.1 - - + +
209T VAL* 4.1 9.4 - - + +
212T ALA* 4.4 3.1 - - + -
228T ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132R TRP* 4.5 16.1 - + + +
134R LEU* 3.8 17.7 - - + -
167R GLY 3.6 19.9 + - - -
168R GLY* 3.8 12.3 - - - -
169R PRO* 3.9 3.3 - - - +
170R ALA* 3.6 40.8 + - + -
123T PHE* 3.3 29.0 + + - -
124T ASP* 3.3 11.4 - - - +
125T GLU 3.3 0.4 - - - -
126T LEU* 1.3 79.3 - - - +
128T ASN* 1.3 61.3 + - - +
129T ALA 3.1 1.4 + - - -
130T ILE* 3.3 25.8 + - + +
173T PRO* 4.6 18.0 - - + +
176T LEU 4.8 2.4 + - - -
178T LEU* 4.3 18.4 + - + +
203T HIS* 4.5 7.3 + - - -
205T LEU* 3.6 24.6 - - + +
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Residues in contact with ASN 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131R GLU* 2.9 34.1 + - - +
132R TRP* 2.8 36.4 - - + +
172R ARG* 4.8 1.8 - - - +
113T ASN* 2.6 24.8 + - - -
114T ARG* 3.1 33.5 + - - +
124T ASP 3.6 5.3 + - - +
125T GLU* 3.3 13.3 + - - +
126T LEU 3.2 0.8 - - - -
127T TYR* 1.3 78.7 - - - +
129T ALA* 1.3 49.8 + - - +
130T ILE 3.5 1.9 - - - +
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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