Contacts of the helix formed by residues 172 - 178 (chain C) in PDB entry 2WOE
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 ARG 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C LEU* 3.7 17.8 - - + +
147C GLU* 5.3 4.9 - - - +
168C LEU* 2.8 59.7 + - + +
169C THR* 3.7 4.5 - - - +
171C GLY* 1.3 71.2 - - - +
173C MET* 1.3 57.8 + - - +
175C HIS* 3.2 6.5 + - - +
176C HIS* 2.9 37.2 + - + +
189C GLU* 3.7 37.4 + - - +
192C ARG* 5.6 3.0 - - - +
196C GLN* 6.0 2.6 - - - +
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Residues in contact with MET 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C THR* 2.8 33.1 + - + +
170C LEU* 3.4 13.0 - - - +
172C ARG* 1.3 72.3 - - - +
174C VAL* 1.3 59.5 + - - +
176C HIS* 3.1 6.4 + - - +
177C LEU* 2.9 34.2 + - - +
186C CYS* 3.3 50.9 - - + +
189C GLU* 4.2 5.2 - - + -
190C ALA* 3.6 26.2 - - + +
221C LEU* 3.6 25.1 - - + -
224C TYR* 5.7 0.9 - - - -
225C PHE* 4.4 1.6 - - + -
254C LEU* 3.9 22.7 - - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LEU* 3.9 27.1 - - + -
136C ALA* 3.9 17.3 - - + -
137C LEU* 4.3 1.8 - - + -
170C LEU 2.9 18.7 + - - +
171C GLY 3.6 6.5 - - - +
173C MET* 1.3 74.1 - - - +
175C HIS* 1.3 60.7 + - + +
177C LEU* 3.3 7.4 + - - +
178C ILE* 2.9 53.5 + - + +
253C MET* 3.9 28.3 - - + -
254C LEU* 4.7 4.9 - - + -
257C ALA* 5.1 7.6 - - + -
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Residues in contact with HIS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ALA* 2.6 36.4 + - + -
139C THR* 3.0 37.3 + - - -
140C LEU* 3.5 22.6 + - + +
143C PRO* 4.0 16.3 - - + +
146C LEU* 3.7 23.7 - - + +
171C GLY 3.0 17.6 + - - +
172C ARG* 3.2 11.0 + - - +
174C VAL* 1.3 76.6 - - - +
176C HIS* 1.3 56.0 + - - +
179C GLY* 2.9 28.4 + - - -
181C ARG* 3.5 14.1 + - - +
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Residues in contact with HIS 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ARG* 2.9 26.7 + - + +
173C MET* 3.1 11.6 + - - +
175C HIS* 1.3 74.7 - - - +
177C LEU* 1.3 61.5 + - - +
179C GLY 3.3 1.4 + - - -
180C GLY 3.1 4.7 + - - -
181C ARG* 2.8 65.6 + - - +
182C GLY 4.3 1.1 - - - +
185C ALA* 3.6 43.0 + - + +
186C CYS* 4.2 6.7 - - - -
189C GLU* 2.9 30.5 + - + -
192C ARG* 4.6 5.1 + - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 3.4 23.0 + - - +
173C MET 2.9 20.4 + - - +
174C VAL* 3.8 1.8 - - - +
176C HIS* 1.3 74.2 - - - +
178C ILE* 1.3 65.2 + - - +
180C GLY* 3.1 11.6 + - - -
182C GLY* 3.6 24.5 + - - +
183C MET 3.9 0.9 - - - +
186C CYS* 3.5 18.6 - - - -
224C TYR* 3.3 22.2 - - - +
254C LEU* 3.4 28.7 - - + +
257C ALA* 3.8 22.7 - - + +
258C THR* 3.3 26.9 - - + +
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Residues in contact with ILE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 3.7 48.1 - - + +
9C ARG* 3.9 25.1 - - + +
10C ALA* 4.0 14.1 - - + -
13C ALA* 5.0 0.9 - - + -
137C LEU* 3.4 33.4 - - + -
140C LEU* 3.8 25.6 - - + -
174C VAL* 2.9 31.5 + - + +
177C LEU* 1.3 74.9 - - - +
179C GLY* 1.3 59.0 + - - +
180C GLY 3.3 1.0 + - - -
257C ALA* 4.3 8.5 - - + -
293C LEU* 5.6 1.3 - - + -
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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