Contacts of the helix formed by residues 122 - 128 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H VAL* 4.7 3.6 - - + -
84H ALA* 3.8 33.7 - - + +
87H CYS* 3.8 14.8 - - + -
164H TYR* 4.8 1.6 - - - +
120J ASP 3.8 8.7 - - - +
121J ILE* 1.3 79.3 - - - +
123J PHE* 1.3 65.4 + - - +
124J ASP* 2.8 26.3 + - - +
125J GLU* 2.9 44.5 + - - +
126J LEU* 3.0 11.6 + - - +
209J VAL* 4.3 3.1 - - - -
213J ARG* 4.3 4.9 - - - +
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Residues in contact with PHE 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H CYS* 4.3 11.7 - - - -
88H TYR 4.7 0.4 - - - +
89H GLY* 3.5 18.2 - - - +
90H ASP* 3.8 13.2 - - + -
166H ILE* 3.5 25.1 - - + -
167H GLY 3.4 23.1 - - - -
122J THR* 1.3 73.7 - - - +
124J ASP* 1.3 60.6 + - - +
126J LEU* 3.4 4.2 + - - +
127J TYR* 3.3 32.2 + + - -
203J HIS* 3.8 31.4 - + - -
205J LEU* 3.5 31.4 - - + +
206J ASN* 3.4 26.9 - - - -
209J VAL* 3.8 15.5 - - + +
213J ARG* 5.2 0.6 - - - +
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Residues in contact with ASP 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H CYS* 3.9 1.9 - - - -
111H VAL* 4.4 17.9 - - + +
132H TRP* 5.2 3.6 - - - -
134H LEU* 4.8 6.2 - - + +
164H TYR* 4.4 4.0 + - - -
166H ILE* 3.6 26.3 - - + +
225H GLY 5.1 4.5 - - - +
227H ILE* 3.8 33.9 - - + +
122J THR* 2.8 21.9 + - - -
123J PHE* 1.3 80.2 - - - +
125J GLU* 1.3 73.2 + - - +
127J TYR* 3.3 25.1 - - - +
128J ASN* 3.6 6.6 + - - +
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Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H ARG* 3.1 37.0 + - - -
57H VAL* 3.9 11.8 - - - +
225H GLY 5.5 6.6 - - - +
114J ARG* 5.7 0.5 + - - -
116J LEU* 5.5 0.3 - - - +
118J ALA* 5.5 1.4 - - - +
121J ILE* 3.4 17.3 - - + +
122J THR* 2.9 37.2 + - - +
124J ASP* 1.3 82.8 - - - +
126J LEU* 1.3 65.2 + - - +
128J ASN* 3.3 16.4 + - - +
129J ALA* 3.6 10.0 + - - +
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Residues in contact with LEU 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J LEU* 4.7 1.6 - - + -
112J LEU* 5.2 7.4 - - + -
116J LEU* 4.2 23.3 - - + -
121J ILE* 4.1 10.4 - - + +
122J THR 3.0 10.9 + - - +
123J PHE 3.6 8.3 - - - +
124J ASP 3.3 0.2 - - - -
125J GLU* 1.3 75.1 - - - +
127J TYR* 1.3 60.1 + - - +
129J ALA* 2.8 25.2 + - + +
130J ILE* 3.4 12.5 + - + +
205J LEU* 3.7 36.6 - - + +
208J ALA* 3.5 46.2 - - + +
209J VAL* 4.1 8.1 - - + +
212J ALA* 4.4 5.6 - - + -
228J ILE* 5.6 1.3 - - + -
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Residues in contact with TYR 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H TRP* 4.4 16.5 - + + +
134H LEU* 3.7 17.3 - - + -
167H GLY 3.6 20.0 - - - -
168H GLY* 3.7 12.8 - - - -
169H PRO* 3.8 3.8 - - - +
170H ALA* 3.5 41.1 + - + -
123J PHE* 3.3 27.2 + + - -
124J ASP* 3.3 11.9 - - - +
125J GLU 3.3 0.2 - - - -
126J LEU* 1.3 78.2 - - - +
128J ASN* 1.3 61.1 + - - +
129J ALA 3.1 1.2 + - - -
130J ILE* 3.3 26.1 + - + +
173J PRO* 4.6 17.1 - - + +
176J LEU 4.8 2.1 + - - -
178J LEU* 4.3 18.1 + - + +
203J HIS* 4.5 6.9 + - - -
205J LEU* 3.6 24.0 - - + +
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Residues in contact with ASN 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H VAL* 6.0 2.0 - - + -
131H GLU* 2.8 38.0 + - - +
132H TRP* 2.8 34.9 - - + +
172H ARG* 4.7 2.0 - - - +
113J ASN* 3.3 17.3 + - - +
114J ARG* 3.1 35.9 + - - +
124J ASP 3.6 5.2 + - - +
125J GLU* 3.3 11.1 + - - +
126J LEU 3.2 1.2 - - - -
127J TYR* 1.3 79.1 - - - +
129J ALA* 1.3 56.2 + - - +
130J 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