Contacts of the helix formed by residues 174 - 182 (chain A) in PDB entry 3PU3
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 LEU 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 4.1 3.4 - - + +
150A GLU* 3.5 30.3 - - + +
153A VAL* 3.8 23.1 - - + -
154A GLY 3.6 26.2 - - - +
155A PRO 3.4 1.6 + - - -
157A ARG* 2.9 15.7 + - + +
159A VAL* 3.9 25.1 - - + -
173A LYS* 1.3 72.4 - - - +
175A LYS* 1.3 56.8 + - - +
177A PHE* 3.2 14.5 + - + +
178A VAL* 2.8 43.8 + - + +
192A VAL* 5.3 2.7 - - + -
195A LEU* 4.6 11.2 - - + -
239A ILE* 5.0 9.0 - - + -
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Residues in contact with LYS 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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46A EDO 3.3 26.6 + - - -
150A GLU* 3.1 21.9 - - - +
155A PRO* 2.9 27.0 + - + +
156A GLU* 2.6 30.4 + - - +
173A LYS* 4.0 14.9 - - + +
174A LEU* 1.3 77.8 - - - +
176A GLU* 1.3 63.0 + - - +
178A VAL* 3.4 1.7 + - - +
179A ASP* 2.9 28.1 + - - +
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Residues in contact with GLU 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 MET* 3.9 31.9 - - - +
173A LYS* 3.1 18.6 + - + +
175A LYS* 1.3 83.3 - - + +
177A PHE* 1.3 65.3 + - - +
179A ASP* 3.3 8.4 + - + +
180A TYR* 3.0 21.6 + - + +
188A ARG* 5.1 6.4 + - - -
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Residues in contact with PHE 177 (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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146A VAL* 5.5 0.9 - - + -
159A VAL* 4.7 1.6 - - + -
161A VAL* 4.1 16.6 - - + -
172A MET* 3.4 19.0 - - + -
173A LYS 3.1 9.3 + - - +
174A LEU* 3.7 13.5 - - + +
176A GLU* 1.3 76.8 - - - +
178A VAL* 1.3 55.8 + - + +
180A TYR* 3.0 22.9 + + - +
181A TYR* 2.7 41.3 + + + -
190A LEU* 3.4 38.8 - - + -
191A ASN 4.1 6.7 - - - -
192A VAL* 3.9 24.7 - - + -
239A ILE* 3.8 47.3 - - + -
241A VAL* 5.2 0.4 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 4.1 15.3 - - + +
147A SER* 5.0 1.6 - - - -
150A GLU* 3.1 52.7 - - + +
174A LEU* 2.8 31.4 + - + +
175A LYS 3.6 0.2 - - - +
177A PHE* 1.3 74.5 - - + +
179A ASP* 1.3 65.5 + - - +
181A TYR* 3.0 7.7 + - - +
182A TYR* 3.0 46.9 + - + -
239A ILE* 6.1 0.7 - - + -
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Residues in contact with ASP 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 LYS 2.9 14.7 + - - +
176A GLU* 3.4 13.2 - - + +
177A PHE 3.2 0.2 - - - -
178A VAL* 1.3 78.2 - - - +
180A TYR* 1.3 65.8 + - - +
182A TYR* 3.4 4.9 + - - +
183A SER* 3.3 16.6 + - - -
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Residues in contact with TYR 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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172A MET* 5.8 1.3 - - - -
176A GLU* 3.0 12.0 + - + +
177A PHE* 3.0 27.3 + + - +
179A ASP* 1.3 76.7 - - - +
181A TYR* 1.3 76.1 + - - +
183A SER* 2.5 32.5 + - - -
186A ARG* 3.8 19.1 - - + +
187A LYS 5.6 0.2 - - - -
188A ARG* 2.4 64.6 + - + +
189A VAL* 3.4 1.4 - - - -
190A LEU* 2.8 56.1 + - + -
241A VAL* 3.8 21.8 - - + +
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Residues in contact with TYR 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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146A VAL* 3.3 39.0 - - + +
177A PHE* 2.7 23.6 + + + +
178A VAL* 3.0 12.3 + - - +
180A TYR* 1.3 81.6 - - + +
182A TYR* 1.3 81.6 + + - +
183A SER 4.0 1.2 - - - +
186A ARG* 2.8 46.7 + - - +
239A ILE* 3.9 22.0 - - + -
240A CYS 4.9 2.7 - - - -
241A VAL* 4.0 14.6 - - + -
263A LYS* 5.0 10.5 + - - -
328A ASP* 3.5 33.0 + - + +
329A CYS 4.9 3.4 + - - -
330A LEU* 6.1 0.5 - - - +
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Residues in contact with TYR 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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145A TYR* 3.7 7.8 - - - +
146A VAL* 3.5 10.9 + - + +
147A SER* 3.1 43.4 + - - -
178A VAL* 3.0 40.1 + - + +
179A ASP* 3.4 5.6 + - - +
180A TYR 3.1 0.4 - - - -
181A TYR* 1.3 98.9 - + - +
183A SER* 1.3 64.9 + - - +
184A THR* 3.6 3.3 + - - -
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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