Contacts of the helix formed by residues 172 - 178 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.7 18.5 - - + +
147A GLU* 4.8 7.9 - - - +
168A LEU* 2.9 60.9 + - - +
169A THR* 3.7 4.7 - - - +
171A GLY* 1.3 72.3 - - - +
173A MET* 1.3 60.6 + - - +
175A HIS* 3.2 6.1 + - - +
176A HIS* 2.9 37.2 + - + +
189A GLU* 3.7 34.0 + - - +
192A ARG* 6.0 0.8 - - - +
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Residues in contact with MET 173 (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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169A THR* 2.9 33.3 + - + +
170A LEU* 3.5 11.4 - - - +
172A ARG* 1.3 74.3 - - - +
174A VAL* 1.3 66.1 + - - +
176A HIS* 3.2 4.4 + - - +
177A LEU* 2.9 30.1 + - - +
186A CYS* 3.3 48.0 - - + +
189A GLU* 4.2 8.3 - - + -
190A ALA* 3.7 17.5 - - + +
221A LEU* 3.6 33.7 - - + -
224A TYR* 5.5 0.4 - - - -
225A PHE* 4.2 4.5 - - + -
254A LEU* 3.9 22.4 - - + -
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Residues in contact with VAL 174 (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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133A LEU* 4.0 13.9 - - + -
136A ALA* 3.9 21.3 - - + -
137A LEU* 4.4 2.5 - - + -
140A LEU* 5.2 0.2 - - + -
170A LEU 2.9 19.2 + - - +
171A GLY* 3.7 8.1 - - - +
173A MET* 1.3 74.5 - - - +
175A HIS* 1.3 59.1 + - + +
177A LEU* 3.3 6.6 + - - +
178A ILE* 3.0 51.0 + - + +
253A MET* 4.0 36.8 - - + -
254A LEU* 4.5 5.8 - - + -
257A ALA* 5.1 7.6 - - + -
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Residues in contact with HIS 175 (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 ALA* 2.9 34.7 + - + -
139A THR* 3.2 35.7 + - - -
140A LEU* 3.6 21.6 + - + +
143A PRO* 3.9 17.7 - - + +
146A LEU* 3.7 24.0 - - + +
171A GLY 3.1 18.7 + - - +
172A ARG* 3.5 10.5 - - - +
173A MET 3.2 0.2 - - - -
174A VAL* 1.3 74.0 - - - +
176A HIS* 1.3 61.0 + - - +
179A GLY* 2.9 27.0 + - - -
181A ARG* 3.4 15.6 + - - +
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Residues in contact with HIS 176 (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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172A ARG* 2.9 29.1 + - + +
173A MET* 3.2 10.1 + - - +
175A HIS* 1.3 77.2 - - - +
177A LEU* 1.3 60.6 + - - +
179A GLY 3.6 0.2 - - - -
180A GLY 3.1 3.6 + - - -
181A ARG* 2.7 67.9 + - + +
182A GLY 4.3 1.3 - - - +
185A ALA* 3.6 41.8 + - + +
186A CYS* 4.2 7.4 - - - -
189A GLU* 2.8 30.5 + - + -
192A ARG* 4.3 5.4 + - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ARG* 3.4 21.0 + - - +
173A MET 2.9 21.5 + - - +
174A VAL* 3.9 3.4 - - - +
176A HIS* 1.3 78.0 - - - +
178A ILE* 1.3 57.8 + - - +
180A GLY* 2.9 18.5 + - - -
182A GLY* 3.6 31.8 + - - +
183A MET 3.8 1.1 - - - +
186A CYS* 3.6 9.4 - - - -
224A TYR* 3.2 22.7 - - - +
254A LEU* 3.4 29.8 - - + +
257A ALA* 3.9 21.8 - - + +
258A THR* 3.2 28.0 - - + +
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Residues in contact with ILE 178 (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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6A VAL* 3.8 47.8 - - + +
9A ARG* 3.8 23.8 + - + +
10A ALA* 4.1 13.0 - - + -
13A ALA* 5.2 0.7 - - + -
137A LEU* 3.4 33.4 - - + -
140A LEU* 3.8 26.0 - - + -
174A VAL* 3.0 27.0 + - + +
177A LEU* 1.3 76.3 - - - +
179A GLY* 1.3 57.7 + - - +
180A GLY* 3.1 4.4 + - - -
257A ALA* 4.5 8.7 - - + -
293A LEU* 5.3 2.2 - - + -
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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