Contacts of the helix formed by residues 122 - 128 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Q ASP 3.8 8.1 - - - +
121Q ILE* 1.3 80.0 - - - +
123Q PHE* 1.3 65.7 + - - +
124Q ASP* 2.8 26.9 + - - +
125Q GLU* 3.0 40.5 + - - +
126Q LEU* 3.0 12.0 + - - +
209Q VAL* 4.3 3.8 - - - -
213Q ARG* 4.3 5.4 - - - +
57T VAL* 4.7 3.1 - - + +
84T ALA* 3.7 35.0 - - + +
87T CYS* 3.8 14.4 - - + -
164T TYR* 4.8 1.8 - - - +
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Residues in contact with PHE 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Q THR* 1.3 73.1 - - - +
124Q ASP* 1.3 61.6 + - - +
126Q LEU* 3.4 4.9 + - - +
127Q TYR* 3.3 32.8 + + - -
203Q HIS* 3.8 25.1 - + - -
205Q LEU* 3.4 36.8 - - + +
206Q ASN* 3.4 25.8 - - - -
209Q VAL* 3.8 15.8 - - + +
213Q ARG* 5.2 0.8 - - - +
87T CYS* 4.2 11.6 + - - -
88T TYR 4.7 0.2 - - - +
89T GLY* 3.5 18.4 - - - +
90T ASP* 3.8 13.5 - - + -
166T ILE* 3.5 31.0 - - + -
167T GLY 3.6 15.7 - - - -
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Residues in contact with ASP 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Q THR* 2.8 22.4 + - - -
123Q PHE* 1.3 79.5 - - - +
125Q GLU* 1.3 75.1 + - - +
127Q TYR* 3.4 22.7 - - - +
128Q ASN* 3.6 6.8 + - - +
87T CYS* 3.8 2.4 - - - -
111T VAL* 4.5 17.8 - - + +
132T TRP* 5.4 3.1 - - - -
134T LEU* 4.8 5.7 - - + +
164T TYR* 4.3 4.2 + - - -
166T ILE* 3.6 31.0 - - + +
225T GLY 5.2 4.5 - - - +
227T ILE* 3.8 27.9 - - + +
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Residues in contact with GLU 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q ARG* 5.7 0.3 + - - -
116Q LEU* 5.6 0.3 - - - +
118Q ALA* 5.4 1.4 - - - +
121Q ILE* 3.4 16.3 - - + +
122Q THR* 3.0 37.0 + - - +
124Q ASP* 1.3 82.9 - - - +
126Q LEU* 1.3 65.1 + - - +
128Q ASN* 3.3 16.4 + - - +
129Q ALA* 3.6 10.4 + - - +
55T ARG* 3.0 38.6 + - - -
57T VAL* 3.8 12.6 - - - +
225T GLY 5.6 6.3 - - - +
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Residues in contact with LEU 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LEU* 4.7 1.6 - - + -
112Q LEU* 5.2 7.2 - - + -
116Q LEU* 4.2 23.8 - - + -
121Q ILE* 4.1 12.5 - - + +
122Q THR 3.0 11.0 + - - +
123Q PHE 3.6 8.1 - - - +
124Q ASP 3.3 0.2 - - - -
125Q GLU* 1.3 75.4 - - - +
127Q TYR* 1.3 65.5 + - - +
129Q ALA* 2.8 18.8 + - + +
130Q ILE* 3.4 12.2 + - + +
205Q LEU* 3.7 36.3 - - + +
208Q ALA* 3.4 46.9 - - + +
209Q VAL* 4.1 9.0 - - + +
212Q ALA* 4.4 1.6 - - + -
228Q ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Q PHE* 3.3 37.9 + + - -
124Q ASP* 3.4 11.9 - - - +
126Q LEU* 1.3 78.8 - - - +
128Q ASN* 1.3 61.7 + - - +
129Q ALA 3.1 1.0 + - - -
130Q ILE* 3.3 27.9 + - + +
173Q PRO* 4.6 18.0 - - + +
176Q LEU 4.8 2.0 + - - -
178Q LEU* 4.3 18.9 + - + +
203Q HIS* 4.5 6.8 + - - -
205Q LEU* 3.6 24.1 - - + +
132T TRP* 4.6 15.6 - + + +
134T LEU* 3.8 16.8 - - + -
167T GLY 3.6 10.7 + - - -
168T GLY* 3.8 12.0 - - - -
169T PRO* 3.9 3.3 - - + +
170T ALA* 3.7 40.6 + - + -
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Residues in contact with ASN 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q ASN* 2.6 24.4 + - - -
114Q ARG* 3.1 33.1 + - - +
124Q ASP 3.6 6.3 + - - +
125Q GLU* 3.3 11.8 + - - +
126Q LEU 3.2 0.6 - - - -
127Q TYR* 1.3 78.3 - - - +
129Q ALA* 1.3 49.4 + - - +
130Q ILE 3.5 1.4 - - - +
111T VAL* 6.1 2.5 - - + -
131T GLU* 2.8 33.9 + - - +
132T TRP* 2.8 37.6 - - + +
172T ARG* 4.8 1.6 - - - +
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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