Contacts of the helix formed by residues 122 - 128 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 4.8 3.4 - - + -
84A ALA* 3.7 35.4 - - + +
87A CYS* 3.8 14.1 - - + -
164A TYR* 5.0 1.6 - - - +
120D ASP 3.8 8.1 - - - +
121D ILE* 1.3 79.8 - - - +
123D PHE* 1.3 65.0 + - - +
124D ASP* 2.8 24.2 + - - +
125D GLU* 3.0 42.1 + - - +
126D LEU* 3.0 10.9 + - - +
209D VAL* 4.3 4.0 - - - -
213D ARG* 4.2 5.6 - - - +
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Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A CYS* 4.3 10.1 + - - -
88A TYR 4.7 0.4 - - - +
89A GLY* 3.5 19.7 - - - +
90A ASP* 3.8 13.2 - - + -
166A ILE* 3.5 31.6 - - + -
167A GLY 3.6 15.9 - - - -
122D THR* 1.3 72.6 - - - +
124D ASP* 1.3 62.2 + - - +
126D LEU* 3.3 5.7 + - - +
127D TYR* 3.3 31.5 + + - -
203D HIS* 3.8 31.4 - + - -
205D LEU* 3.5 31.2 - - + +
206D ASN* 3.4 26.7 - - - -
209D VAL* 3.8 14.1 - - + +
213D ARG* 5.2 0.8 - - - +
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A CYS* 3.8 2.4 - - - -
111A VAL* 4.6 14.3 - - + +
132A TRP* 5.5 2.9 - - - -
134A LEU* 4.8 8.0 - - + +
164A TYR* 4.3 3.6 + - - -
166A ILE* 3.6 31.2 - - + +
225A GLY 5.2 4.0 - - - +
227A ILE* 3.9 28.6 - - + +
122D THR* 2.8 22.2 + - - +
123D PHE* 1.3 77.3 - - - +
125D GLU* 1.3 75.4 + - - +
127D TYR* 3.3 24.9 + - - +
128D ASN* 3.6 6.9 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.0 38.1 + - - -
57A VAL* 3.9 10.9 - - - +
225A GLY 5.7 4.4 - - - +
114D ARG* 5.7 0.7 + - - -
116D LEU* 5.5 0.2 - - - +
118D ALA* 5.4 1.6 - - - +
121D ILE* 3.5 17.4 - - + +
122D THR* 3.0 36.7 + - - +
124D ASP* 1.3 82.9 - - - +
126D LEU* 1.3 66.1 + - - +
128D ASN* 3.3 16.3 + - - +
129D ALA* 3.6 10.2 + - - +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.7 2.0 - - + -
112D LEU* 5.2 7.2 - - + -
116D LEU* 4.2 23.8 - - + -
121D ILE* 4.1 9.8 - - + +
122D THR 3.0 11.6 + - - +
123D PHE 3.6 8.3 - - - +
124D ASP 3.2 0.2 - - - -
125D GLU* 1.3 75.6 - - - +
127D TYR* 1.3 65.3 + - - +
129D ALA* 2.8 19.3 + - + +
130D ILE* 3.4 12.1 + - + +
205D LEU* 3.8 36.6 - - + +
208D ALA* 3.4 46.4 - - + +
209D VAL* 4.1 8.1 - - + +
212D ALA* 4.4 5.8 - - + -
228D ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TRP* 4.6 14.9 - + + +
134A LEU* 3.9 17.9 - - + -
167A GLY 3.6 19.3 - - - -
168A GLY* 3.8 11.6 - - - -
169A PRO* 3.9 3.5 - - - +
170A ALA* 3.7 40.2 + - + -
123D PHE* 3.3 28.4 + + - -
124D ASP* 3.3 11.2 - - - +
125D GLU 3.3 0.2 - - - -
126D LEU* 1.3 79.8 - - - +
128D ASN* 1.3 60.9 + - - +
129D ALA 3.1 1.0 + - - -
130D ILE* 3.3 27.2 + - + +
173D PRO* 4.6 18.6 - - + +
176D LEU 4.8 2.0 + - - -
178D LEU* 4.3 18.1 + - + +
203D HIS* 4.5 7.6 + - - -
205D LEU* 3.6 24.6 - - + +
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Residues in contact with ASN 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 6.1 1.8 - - + -
131A GLU* 2.9 33.5 + - - +
132A TRP* 2.8 36.9 - - + +
172A ARG* 4.9 1.2 - - - +
113D ASN* 3.3 16.6 + - - +
114D ARG* 3.1 35.1 + - - +
124D ASP 3.6 6.1 + - - +
125D GLU* 3.3 12.2 + - - +
126D LEU 3.1 0.6 - - - -
127D TYR* 1.3 78.0 - - - +
129D ALA* 1.3 57.4 + - - +
130D 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