Contacts of the strand formed by residues 161 - 169 (chain D) in PDB entry 2WJZ
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 GLU 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D VAL* 5.7 0.5 - - - +
112D LYS 4.8 0.9 - - - +
113D LEU* 3.3 22.5 - - + +
114D ARG* 2.8 67.7 + - + +
115D SER* 4.3 2.6 + - - -
144D ARG* 3.0 38.1 + - - +
156D THR 3.5 2.1 - - - +
157D GLU* 3.2 2.2 + - - -
158D TYR* 2.9 38.5 + - - +
159D ASP 3.1 2.2 - - - +
160D GLY* 1.3 78.2 - - - +
162D ILE* 1.3 64.6 + - - +
163D PHE* 3.8 4.5 - - + -
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Residues in contact with ILE 162 (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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114D ARG* 5.7 0.2 - - - +
144D ARG* 3.6 14.4 + - - -
155D THR* 3.6 33.9 - - + +
156D THR 3.4 4.9 - - - +
157D GLU* 4.2 14.8 - - + +
160D GLY 3.9 5.6 + - - +
161D GLU* 1.3 76.3 - - - +
163D PHE* 1.3 63.4 + - - +
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Residues in contact with PHE 163 (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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113D LEU* 4.2 13.0 - - + -
120D HIS* 4.2 4.9 - + - -
139D PHE* 4.5 2.5 - + - -
141D HIS* 3.5 34.3 - + - -
144D ARG* 3.6 36.6 - - + +
155D THR* 3.6 7.6 - - - -
156D THR* 3.0 65.1 + - + -
158D TYR* 4.3 17.7 - - + -
161D GLU* 3.8 8.5 - - + -
162D ILE* 1.3 76.4 - - - +
164D PRO* 1.3 83.2 - - + +
165D SER* 3.1 14.9 + - - -
176D GLN* 4.4 4.0 - - + -
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Residues in contact with PRO 164 (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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87D MET* 3.4 16.1 - - + +
144D ARG* 3.7 8.3 - - - +
145D ALA* 3.4 25.5 + - + +
147D CYS* 4.1 20.2 - - - +
152D VAL* 4.2 16.2 - - + -
154D GLY 3.4 9.4 - - - +
163D PHE* 1.3 95.3 - - + +
165D SER* 1.3 60.6 + - - +
166D ALA 3.1 15.9 - - - +
167D VAL* 4.0 15.0 - - + -
176D GLN* 4.5 2.1 - - - +
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Residues in contact with SER 165 (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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87D MET* 4.6 0.9 - - - -
126D VAL* 3.4 14.4 - - - +
139D PHE* 3.7 20.0 - - - -
154D GLY 3.1 2.6 + - - -
155D THR 3.2 15.2 + - - -
156D THR* 2.7 35.1 + - - -
163D PHE* 3.1 7.1 + - - -
164D PRO* 1.3 73.2 - - - +
166D ALA* 1.3 58.6 + - - +
176D GLN* 2.9 35.8 + - - +
177D PHE* 3.6 7.0 - - - -
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Residues in contact with ALA 166 (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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87D MET* 4.6 0.9 - - - -
126D VAL* 4.8 0.2 - - + -
128D PHE* 3.5 25.8 - - + -
152D VAL* 3.9 1.2 - - - -
153D LEU* 2.9 22.3 + - + -
154D GLY* 3.1 28.3 + - - +
164D PRO* 3.1 3.1 - - - +
165D SER* 1.3 80.8 - - - +
167D VAL* 1.3 67.0 + - - +
174D GLY 3.2 11.7 - - - +
175D PHE* 4.0 9.2 - - + -
177D PHE* 4.7 1.1 - - + -
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Residues in contact with VAL 167 (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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87D MET* 3.9 17.9 - - + -
90D LEU* 4.6 2.5 - - + -
91D PHE* 4.0 18.8 - - + -
106D ILE* 3.4 28.5 - - + -
145D ALA* 5.1 0.2 - - + -
147D CYS* 3.7 24.7 - - - -
151D HIS 3.2 15.9 - - - +
153D LEU* 3.6 7.5 - - - +
164D PRO* 4.0 6.1 - - + -
166D ALA* 1.3 78.2 - - - +
168D ARG* 1.3 67.5 + - - +
173D LEU* 3.5 2.3 - - - -
174D GLY* 2.8 38.6 + - - +
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Residues in contact with ARG 168 (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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106D ILE* 4.4 0.4 - - - -
129D LYS* 5.3 4.4 - - - +
130D ASP* 2.5 44.0 + - - -
131D THR* 4.1 4.9 + - - -
132D PHE* 5.1 3.0 - - - -
150D GLU 4.1 7.3 + - - +
151D HIS* 2.8 33.9 + - - +
152D VAL 4.9 7.7 + - - -
153D LEU* 3.9 34.3 - - + +
167D VAL* 1.3 79.3 - - - +
169D LYS* 1.3 62.3 + - - +
170D GLY* 3.7 20.8 + - - +
172D ILE 3.3 5.2 - - - -
173D LEU* 3.5 23.6 - - + +
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Residues in contact with LYS 169 (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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104D SER 5.3 0.8 + - - -
105D LEU 3.0 28.1 + - - +
106D ILE* 3.6 24.3 - - + +
107D GLU* 2.7 34.1 + - - +
151D HIS* 3.4 25.4 - - + +
168D ARG* 1.3 71.8 - - - +
170D GLY* 1.3 63.4 + - - +
171D ARG 3.3 1.4 + - - -
172D ILE* 3.0 31.5 + - + +
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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