Contacts of the strand formed by residues 147 - 152 (chain A) in PDB entry 2WJW
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 LYS 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A TRP 3.7 0.4 - - - -
146A ASP* 1.3 90.4 + - - +
148A PHE* 1.3 67.6 + - - +
174A GLN* 3.4 35.2 - - + +
202A LYS* 3.7 32.5 + - + +
203A LYS* 4.7 9.1 + - - +
204A GLU* 3.1 21.9 - - - +
206A ARG* 3.9 19.9 + - - +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.9 22.0 - - + -
145A TRP* 3.6 28.5 - + + -
147A LYS* 1.3 84.2 - - - +
149A ALA* 1.3 71.9 + - - +
150A TYR* 4.7 1.6 - - + -
164A VAL* 4.1 8.1 - - + -
173A TRP* 3.7 36.6 - + + -
174A GLN 3.1 5.6 + - - +
175A VAL* 3.4 37.8 - - + -
176A THR 3.0 22.2 + - - -
204A GLU* 3.3 13.0 + - - +
206A ARG* 3.3 15.3 - - + +
208A ILE* 3.6 22.9 - - + -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PHE* 1.3 80.7 - - - +
150A TYR* 1.3 60.1 + - - +
151A LEU* 3.9 9.6 - - + -
176A THR 3.3 9.4 - - - +
199A LEU* 3.8 31.2 - - + -
204A GLU* 3.4 16.1 + - + +
206A ARG 2.9 11.2 + - - +
207A VAL* 3.5 5.6 - - + -
208A ILE 2.8 26.2 + - - -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 4.6 1.3 - - + -
148A PHE* 4.1 3.5 + - + -
149A ALA* 1.3 73.5 - - - +
151A LEU* 1.3 62.0 + - - +
152A TYR* 3.4 30.4 - + + +
160A THR* 3.4 8.1 - - + +
161A LEU* 3.4 44.9 + - + +
164A VAL* 4.2 22.0 - - + -
175A VAL* 3.9 20.6 - - + -
176A THR 2.8 8.4 + - - +
177A ALA* 4.3 3.4 - - + -
178A ILE 3.0 25.8 + - - +
208A ILE* 3.8 29.4 - - + -
210A ASP* 2.4 41.4 + - + -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA* 4.2 14.8 - - + -
150A TYR* 1.3 78.2 - - - +
152A TYR* 1.3 58.0 + - - +
178A ILE* 3.5 32.1 - - + +
180A VAL* 3.9 14.1 - - + -
195A LEU* 4.4 20.6 - - + -
196A PHE* 5.7 1.1 - - + -
199A LEU* 4.6 4.9 - - + -
207A VAL* 3.9 23.1 - - + -
208A ILE 2.9 14.9 + - - +
209A LEU* 3.7 7.4 - - + -
210A ASP* 2.8 28.3 + - - +
211A CYS* 4.4 4.1 - - - -
219A ILE* 4.1 30.5 - - + -
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TYR* 3.4 39.9 - + + +
151A LEU* 1.3 74.6 - - - +
153A ASP* 1.3 64.9 + - - +
154A SER* 4.9 1.3 - - - -
157A GLY 4.7 2.7 - - - -
158A LEU* 3.3 33.4 - - + +
161A LEU* 3.9 25.3 - - + +
177A ALA* 4.1 7.5 + - + +
178A ILE 3.2 15.0 + - - -
179A ASN* 3.2 45.8 + - + +
180A VAL* 2.6 34.3 + - - -
181A GLY 3.4 1.2 + - - -
210A ASP* 3.2 11.9 - - + +
211A CYS* 4.5 3.6 - - - -
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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