Contacts of the helix formed by residues 139 - 145 (chain A) in PDB entry 2WOK
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 TYR 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.8 10.3 - - - -
137A PRO* 3.6 16.7 - - + -
138A THR* 1.3 78.3 - - - +
140A LEU* 1.3 61.8 + - + +
141A ILE 3.4 0.5 + - - -
142A PRO* 3.5 16.8 - - - +
143A LEU* 3.7 15.8 - - + +
180A PHE* 5.7 1.8 - + + -
186A LEU* 3.7 23.1 - - + -
189A GLN* 3.9 10.8 - - - +
453A TRP* 4.6 3.5 - - - -
456A ASP* 2.5 43.9 + - + +
457A PHE* 3.8 25.0 - + - -
461A TYR* 5.0 11.4 - + - -
462A GLY* 5.0 1.1 + - - -
466A PRO* 4.3 23.4 - - + +
472A GLN* 5.6 7.6 - - - -
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Residues in contact with LEU 140 (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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124A VAL* 4.0 32.3 - - + -
127A VAL* 4.9 13.9 - - + -
128A PHE* 4.6 3.4 - - + -
137A PRO 5.5 0.2 + - - -
138A THR 3.0 1.6 + - - -
139A TYR* 1.3 76.0 - - + +
141A ILE* 1.3 65.4 + - - +
143A LEU* 3.3 3.6 + - + +
144A LEU* 3.1 43.1 + - + +
183A PHE* 3.5 33.0 - - + -
186A LEU* 4.1 16.8 - - + +
187A MET* 3.6 19.7 - - + -
189A GLN* 6.1 1.3 - - - +
191A CYS* 4.7 19.7 - - - -
192A ALA* 4.8 4.5 - - + -
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Residues in contact with ILE 141 (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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127A VAL* 3.6 34.5 - - + +
128A PHE* 3.7 38.1 - - + +
130A GLN* 4.2 9.2 - - + -
138A THR* 3.0 31.3 + - + +
140A LEU* 1.3 77.1 - - - +
142A PRO* 1.4 66.6 - - + +
145A ASP* 2.8 45.2 + - + +
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Residues in contact with PRO 142 (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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138A THR 3.4 12.6 - - - +
139A TYR* 3.5 12.1 - - - +
141A ILE* 1.4 94.1 - - + +
143A LEU* 1.3 53.4 + - + +
144A LEU 3.3 0.4 + - - -
145A ASP* 4.3 6.7 - - + +
177A THR* 2.8 27.9 + - - +
178A ARG* 3.4 27.3 + - - +
472A GLN* 5.9 4.9 - - - +
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Residues in contact with LEU 143 (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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139A TYR* 3.7 12.6 - - + +
140A LEU* 3.3 7.8 + - - +
141A ILE 3.1 1.0 - - - -
142A PRO* 1.3 80.8 - - + +
144A LEU* 1.3 61.5 + - + +
175A ARG 4.2 0.2 - - - +
176A LEU* 3.2 19.5 - - + -
177A THR* 2.8 29.3 + - - +
178A ARG* 3.8 36.8 - - + +
180A PHE* 3.9 37.9 - - + -
183A PHE* 4.3 10.3 - - + -
186A LEU* 3.4 34.1 - - + -
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Residues in contact with LEU 144 (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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124A VAL* 3.5 32.1 - - + -
128A PHE* 4.0 11.0 - - + -
140A LEU* 3.1 29.0 + - + +
143A LEU* 1.3 84.7 - - + +
145A ASP* 1.3 61.0 + - - +
146A ASP 3.7 1.7 + - - -
161A LEU* 3.8 8.4 - - + +
163A SER* 2.7 52.5 + - - +
164A VAL* 4.0 9.2 - - + -
174A PHE* 4.0 15.9 - - + -
175A ARG 4.0 3.1 - - - +
176A LEU* 3.7 26.9 - - + -
177A THR* 4.4 2.5 - - - +
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Residues in contact with ASP 145 (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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128A PHE* 3.7 16.4 - - + -
141A ILE* 2.8 28.0 + - + +
142A PRO* 4.3 5.7 + - + +
143A LEU 3.8 0.2 - - - -
144A LEU* 1.3 76.0 - - - +
146A ASP* 1.3 66.3 + - - +
147A PRO* 3.3 13.9 - - + +
150A PRO* 3.6 11.3 - - - +
151A TYR* 2.8 38.6 + - - +
161A LEU* 4.9 1.3 - - - -
177A THR* 3.4 16.1 - - - +
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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