Contacts of the helix formed by residues 182 - 188 (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 ASP 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.0 23.1 + - + -
181A SER* 1.3 92.4 + - - +
183A PHE* 1.3 64.9 + - - +
184A ASP 3.3 2.7 - - - -
185A HIS* 2.9 32.5 + - + +
186A LEU* 3.6 2.8 + - - +
457A PHE* 3.8 8.6 - - + -
459A THR* 2.6 40.8 + - - +
461A TYR* 3.5 17.9 + - - +
498A LEU* 5.3 0.4 - - - -
506A ARG* 4.7 8.7 + - - -
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Residues in contact with PHE 183 (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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99A TRP* 3.4 37.0 - + + -
101A TYR* 3.5 15.0 - + - -
140A LEU* 3.5 22.4 - - + -
143A LEU* 4.3 7.4 - - + -
144A LEU* 5.2 0.4 - - + -
174A PHE* 3.7 41.5 - + + -
176A LEU* 3.5 28.0 - - + -
180A PHE* 3.2 12.1 + + - +
181A SER 3.3 3.2 + - - -
182A ASP* 1.3 77.2 - - - +
184A ASP* 1.3 62.7 + - - +
186A LEU* 3.0 23.6 + - + +
187A MET* 3.1 41.4 + - + +
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Residues in contact with ASP 184 (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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68A MET* 3.7 29.2 - - + +
81A PRO* 3.9 22.7 - - + +
89A PRO* 4.0 6.8 - - - +
90A GLY 3.2 20.3 + - - +
99A TRP* 3.6 16.7 - - + -
101A TYR* 2.7 32.2 + - - -
181A SER 5.1 0.2 + - - -
182A ASP 3.2 1.2 + - - -
183A PHE* 1.3 75.8 - - - +
185A HIS* 1.3 63.4 + - + +
187A MET* 3.2 5.1 + - - +
188A ALA* 3.1 18.5 + - - +
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Residues in contact with HIS 185 (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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70A TYR* 2.7 28.6 + + - +
79A LEU 3.3 25.8 + - - -
80A VAL* 5.3 0.2 - - - -
81A PRO* 3.4 19.7 - - + +
182A ASP* 2.9 24.5 + - + +
184A ASP* 1.3 79.9 - - + +
186A LEU* 1.3 62.9 + - - +
188A ALA* 3.1 12.7 + - - +
189A GLN* 3.4 15.7 + - - +
457A PHE* 3.8 18.8 - - + +
458A PRO* 3.7 11.2 - - + +
459A THR* 3.3 33.4 - - + +
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Residues in contact with LEU 186 (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 24.5 - - + -
140A LEU* 4.1 25.5 - - + +
143A LEU* 3.4 33.0 - - + -
180A PHE* 3.6 20.2 - - + -
182A ASP 4.2 0.2 - - - +
183A PHE* 3.0 13.9 + - + +
185A HIS* 1.3 75.6 - - - +
187A MET* 1.3 63.7 + - + +
189A GLN* 3.4 31.6 + - - +
191A CYS* 5.2 0.3 - - - -
192A ALA* 3.7 10.7 - - - +
457A PHE* 3.7 35.7 - - + -
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Residues in contact with MET 187 (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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66A THR* 3.3 22.9 - - - +
67A LEU* 3.8 23.6 + - + -
68A MET* 3.6 14.2 - - + +
101A TYR* 3.5 27.6 - - + +
120A VAL* 5.1 0.4 - - - -
124A VAL* 4.6 2.7 - - + -
140A LEU* 3.6 25.8 - - + -
174A PHE* 3.8 26.5 - - + -
183A PHE* 3.1 34.6 + - + +
184A ASP 3.2 8.7 + - - +
186A LEU* 1.3 81.0 - - - +
188A ALA* 1.3 58.3 + - - +
189A GLN 3.4 0.2 - - - -
192A ALA* 3.9 19.6 - - + +
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Residues in contact with ALA 188 (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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66A THR* 4.1 8.4 + - - +
68A MET* 3.1 25.1 - - + +
69A ALA* 4.1 6.3 - - - -
70A TYR* 3.7 29.1 - - + -
81A PRO* 4.6 2.9 - - + -
184A ASP 3.1 10.6 + - - +
185A HIS* 3.1 11.1 + - - +
187A MET* 1.3 77.6 - - - +
189A GLN* 1.3 62.2 + - - +
190A PRO* 3.9 2.8 - - - +
1561A GOL 4.7 5.8 + - - -
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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