Contacts of the helix formed by residues 122 - 128 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L ASP 3.9 8.7 - - - +
121L ILE* 1.3 79.2 - - - +
123L PHE* 1.3 65.3 + - - +
124L ASP* 2.8 27.3 + - - +
125L GLU* 2.9 39.1 + - - +
126L LEU* 3.0 12.1 + - - +
209L VAL* 4.2 3.4 - - - -
213L ARG* 4.2 6.7 - - - +
57O VAL* 4.9 3.1 - - + -
84O ALA* 3.8 35.4 - - + +
87O CYS* 4.1 13.0 - - + -
164O TYR* 5.2 1.3 - - - +
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Residues in contact with PHE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L THR* 1.3 72.0 - - - +
124L ASP* 1.3 61.3 + - - +
126L LEU* 3.4 5.0 + - - +
127L TYR* 3.3 41.9 + + - -
203L HIS* 3.8 32.8 - + - -
205L LEU* 3.5 30.8 - - + +
206L ASN* 3.3 28.0 - - - -
209L VAL* 3.8 14.5 - - + +
213L ARG* 5.2 0.6 - - - +
87O CYS* 4.5 9.9 + - - +
88O TYR 4.9 0.4 - - - +
89O GLY* 3.6 18.4 - - - +
90O ASP* 3.9 11.7 - - + -
166O ILE* 3.7 31.0 - - + -
167O GLY 3.8 5.8 - - - -
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Residues in contact with ASP 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L THR* 2.8 23.0 + - - +
123L PHE* 1.3 77.9 - - - +
125L GLU* 1.3 79.8 + - - +
127L TYR* 3.3 25.9 + - - +
128L ASN* 3.6 6.6 + - - +
87O CYS* 3.8 12.6 - - - -
111O VAL* 4.8 16.0 - - + +
132O TRP* 5.6 2.8 - - - -
134O LEU* 5.0 5.6 - - + -
164O TYR* 4.5 3.5 + - - -
166O ILE* 3.9 20.9 - - + +
225O GLY 5.2 4.9 - - - +
227O ILE* 4.1 25.9 - - + +
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Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L ARG* 5.7 0.3 + - - -
116L LEU* 5.6 0.2 - - - +
118L ALA* 5.4 2.1 - - - +
121L ILE* 3.4 17.9 - - + +
122L THR* 2.9 38.5 + - - +
124L ASP* 1.3 83.4 - - - +
126L LEU* 1.3 65.5 + - - +
128L ASN* 3.3 16.4 + - - +
129L ALA* 3.6 10.0 + - - +
55O ARG* 2.9 39.7 + - - -
57O VAL* 4.1 7.4 - - - +
225O GLY 5.9 2.9 - - - +
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Residues in contact with LEU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L LEU* 4.7 2.0 - - + -
112L LEU* 5.2 6.5 - - + -
116L LEU* 4.2 23.3 - - + -
121L ILE* 4.0 13.1 - - + +
122L THR 3.0 11.2 + - - +
123L PHE 3.6 7.4 - - - +
124L ASP 3.3 0.4 - - - -
125L GLU* 1.3 75.6 - - - +
127L TYR* 1.3 59.1 + - - +
129L ALA* 2.8 25.1 + - + +
130L ILE* 3.4 11.9 + - + +
205L LEU* 3.8 35.7 - - + +
208L ALA* 3.4 47.8 - - + +
209L VAL* 4.0 8.3 - - + +
212L ALA* 4.4 2.7 - - + -
228L ILE* 5.5 1.3 - - + -
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Residues in contact with TYR 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L PHE* 3.3 36.8 + + - -
124L ASP* 3.3 12.5 + - - +
125L GLU 3.3 0.2 - - - -
126L LEU* 1.3 78.7 - - - +
128L ASN* 1.3 61.2 + - - +
129L ALA 3.1 1.4 + - - -
130L ILE* 3.3 25.4 + - + +
173L PRO* 4.6 21.5 - - + +
176L LEU 4.8 2.3 + - - -
178L LEU* 4.3 19.5 + - + +
203L HIS* 4.5 7.3 + - - -
205L LEU* 3.6 24.2 - - + +
132O TRP* 4.8 14.0 - + + +
134O LEU* 4.1 16.2 - - + -
167O GLY 3.8 11.2 - - - -
168O GLY* 4.0 11.3 - - - -
169O PRO* 4.1 3.5 - - + +
170O ALA* 3.9 37.8 + - + -
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Residues in contact with ASN 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L ASN* 2.6 25.3 + - - +
114L ARG* 3.1 31.4 + - - +
124L ASP 3.6 5.5 + - - +
125L GLU* 3.3 11.3 + - - +
126L LEU 3.2 1.0 - - - -
127L TYR* 1.3 78.8 - - - +
129L ALA* 1.3 49.7 + - - +
130L ILE 3.5 1.6 - - - +
111O VAL* 6.4 0.9 - - + -
131O GLU* 3.0 34.1 + - - +
132O TRP* 3.0 31.7 - - + +
172O ARG* 5.1 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