Contacts of the helix formed by residues 175 - 182 (chain H) in PDB entry 2WW9
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 HIS 175 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166H VAL* 4.3 23.1 - - + -
169H LEU* 3.5 39.3 + - + +
170H LYS* 4.2 10.4 + - + +
173H GLY* 4.7 1.8 - - - -
174H ALA* 1.4 77.1 - - - +
176H SER* 1.4 63.3 + - - +
177H ASP 3.2 1.5 - - - +
178H LEU* 3.1 33.1 + - - +
179H LEU* 3.3 40.5 + - + +
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Residues in contact with SER 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H ARG* 6.1 2.9 - - - -
143H GLU* 5.4 12.4 - - - +
174H ALA 2.9 9.0 + - - -
175H HIS* 1.4 77.0 - - - +
177H ASP* 1.4 58.9 + - - +
178H LEU 3.3 0.2 - - - -
179H LEU* 3.2 19.4 + - - +
180H LYS* 3.1 25.5 + - - +
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Residues in contact with ASP 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H HIS* 3.0 35.4 - - - +
141H ARG* 3.2 29.1 + - - +
174H ALA* 4.1 12.9 - - - -
175H HIS 4.0 0.6 - - - +
176H SER* 1.4 79.8 - - - +
178H LEU* 1.4 62.7 + - + +
180H LYS* 3.1 43.4 + - - +
181H VAL* 3.5 5.4 - - - +
204H GLY* 3.8 18.7 - - - -
205H PRO* 4.1 2.8 - - - +
247H PHE* 4.0 14.3 - - + -
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Residues in contact with LEU 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LEU* 3.8 35.2 - - + -
174H ALA* 4.4 5.4 - - + -
175H HIS* 3.1 30.2 + - - +
177H ASP* 1.4 76.6 - - + +
179H LEU* 1.4 64.1 + - + +
180H LYS 3.3 0.4 - - - -
181H VAL* 3.5 10.3 + - - +
182H LEU* 3.6 10.4 + - - +
205H PRO* 4.1 33.0 - - + -
222H VAL* 3.7 21.5 - - + -
223H PRO* 3.6 42.8 - - + +
225H VAL* 4.2 5.4 - - + -
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Residues in contact with LEU 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H HIS* 3.4 43.1 - - + +
176H SER* 3.2 18.0 + - - +
178H LEU* 1.4 77.5 - - + +
180H LYS* 1.4 61.9 + - - +
181H VAL 3.3 0.2 - - - -
182H LEU* 3.3 34.0 + - + +
183H LYS* 3.2 29.7 + - - +
223H PRO* 6.3 0.2 - - + -
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Residues in contact with LYS 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H GLY 3.7 22.0 + - - +
140H HIS* 4.4 1.8 - - - +
141H ARG* 6.1 1.3 - - + +
176H SER 3.1 11.0 + - - +
177H ASP* 3.1 52.4 + - - +
178H LEU 3.3 0.4 - - - -
179H LEU* 1.4 76.6 - - - +
181H VAL* 1.4 63.6 + - - +
183H LYS* 3.3 28.8 + - + +
202H ARG* 3.8 21.3 - - - -
203H ARG 3.5 17.4 + - - -
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Residues in contact with VAL 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H ASP 3.5 15.0 - - - +
178H LEU* 3.5 10.7 + - - +
179H LEU 3.3 0.8 - - - -
180H LYS* 1.4 82.6 - - - +
182H LEU* 1.4 54.5 + - - +
183H LYS 3.2 4.3 + - - +
186H LYS* 3.4 27.7 - - - +
201H GLN* 4.9 10.6 - - + +
202H ARG* 4.1 16.4 - - + +
203H ARG 3.4 28.5 - - - +
204H GLY* 4.4 5.6 - - - -
223H PRO* 4.0 12.8 - - + +
224H GLY* 4.0 21.5 - - - +
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Residues in contact with LEU 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H LEU 3.6 9.1 + - - +
179H LEU* 3.3 35.7 - - + +
180H LYS 3.3 0.6 - - - -
181H VAL* 1.4 74.5 - - - +
183H LYS* 1.4 69.7 + - - +
186H LYS* 3.9 20.2 - - + +
223H PRO* 3.8 26.9 - - + +
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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