Contacts of the helix formed by residues 177 - 184 (chain A) in PDB entry 2PWY
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 VAL 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU* 3.9 23.6 - - + -
155A GLU* 3.5 28.3 - - + +
169A LEU* 3.6 35.4 - - + -
171A LEU* 4.4 7.6 - - + -
173A GLU 5.0 2.2 - - - +
174A PRO* 3.1 19.2 + - + +
176A LYS* 1.3 80.4 - - + +
178A LEU* 1.3 59.1 - - - +
179A GLU 3.3 3.1 - - - -
180A LYS* 3.4 8.4 + - + +
181A ALA* 2.8 29.1 + - + +
501A SAH 3.8 13.7 - - - +
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Residues in contact with LEU 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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169A LEU* 5.1 1.3 - - + -
174A PRO 3.6 15.3 - - - +
175A TRP* 3.4 23.7 + - - +
176A LYS 3.5 0.2 - - - -
177A VAL* 1.3 76.2 - - - +
179A GLU* 1.3 60.5 + - - +
181A ALA* 4.2 2.0 - - - -
182A ALA* 2.8 32.6 + - - +
191A LEU* 3.9 26.2 - - + -
204A LEU* 3.9 19.5 - - + -
207A ALA* 3.9 3.1 - - + -
208A ALA* 3.8 24.5 - - - +
211A HIS* 3.7 33.2 - - + +
213A PHE* 3.8 13.4 - - + -
249A LEU* 4.2 7.0 - - + -
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Residues in contact with GLU 179 (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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175A TRP 4.9 0.4 + - - -
176A LYS 5.1 3.5 + - - +
177A VAL 3.3 0.8 - - - -
178A LEU* 1.3 79.6 - - - +
180A LYS* 1.3 63.8 + - - +
182A ALA* 3.8 3.8 - - - +
183A LEU* 3.1 22.0 + - - +
211A HIS* 3.7 21.8 - - + +
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Residues in contact with LYS 180 (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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154A LEU* 3.5 24.2 - - + +
155A GLU* 3.2 32.1 + - - -
156A GLU 4.4 1.6 - - - -
157A ALA 2.8 29.9 + - - +
159A LEU* 3.5 28.9 - - + +
177A VAL* 3.4 9.7 + - - +
178A LEU 3.4 0.4 - - - -
179A GLU* 1.3 80.7 - - - +
181A ALA* 1.3 57.2 + - - +
183A LEU* 3.2 20.6 + - + +
184A ALA* 3.0 27.8 + - - +
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Residues in contact with ALA 181 (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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98A LEU* 4.8 4.9 - - + +
154A LEU* 5.5 2.0 - - + +
167A VAL* 4.1 18.2 - - + +
177A VAL* 2.8 25.0 + - + +
178A LEU* 3.9 3.8 - - - +
180A LYS* 1.3 73.4 - - - +
182A ALA* 1.3 57.5 + - - +
184A ALA* 3.8 4.8 - - - +
185A LEU* 3.0 34.7 + - - +
191A LEU* 3.5 32.1 - - + -
213A PHE* 4.1 3.1 - - + -
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Residues in contact with ALA 182 (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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178A LEU 2.8 22.5 + - - +
179A GLU* 3.8 5.4 - - - +
181A ALA* 1.3 72.8 - - - +
183A LEU* 1.3 63.6 + - - +
185A LEU 3.8 4.3 - - - +
211A HIS* 4.9 1.3 - - + +
212A PRO* 3.9 30.1 - - + -
213A PHE* 3.7 21.4 - - + -
251A ARG* 2.8 31.3 + - - +
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Residues in contact with LEU 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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159A LEU* 4.4 18.2 - - + +
161A GLU* 3.3 49.9 - - + +
162A ALA* 2.9 22.7 + - - -
179A GLU 3.1 13.2 + - - +
180A LYS* 3.4 28.9 - - + +
182A ALA* 1.3 80.6 - - - +
184A ALA* 1.3 58.4 + - - +
185A LEU 4.4 0.5 - - - +
251A ARG* 5.1 2.2 + - - +
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Residues in contact with ALA 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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98A LEU* 3.8 12.8 - - + -
159A LEU* 3.8 20.4 - - + -
160A GLU 4.0 10.3 - - - -
162A ALA 3.2 0.9 + - - -
163A ALA 3.0 26.7 + - - -
164A TYR* 3.1 30.6 + - + -
167A VAL* 4.9 0.9 - - + -
180A LYS 3.0 15.9 + - - +
181A ALA 3.3 3.6 + - - +
183A LEU* 1.3 77.7 - - - +
185A LEU* 1.3 58.2 + - - +
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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