Contacts of the helix formed by residues 179 - 187 (chain A) in PDB entry 1LUA
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ALA* 1.3 81.2 - - + +
180A ASP* 1.3 68.3 + - - +
181A ALA* 3.9 13.1 - - - +
182A SER* 2.5 60.0 + - - -
183A ARG* 3.0 23.1 + - - +
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Residues in contact with ASP 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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179A ASP* 1.3 77.3 - - - +
181A ALA* 1.3 56.9 + - - +
183A ARG* 3.1 31.0 + - - +
184A ALA* 2.8 29.4 + - - +
203A LEU 5.0 3.5 - - - +
204A LEU* 5.9 0.3 - - - +
205A PRO* 5.3 12.6 - - + -
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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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179A ASP* 3.2 14.0 + - - +
180A ASP* 1.3 80.2 + - - +
182A SER* 1.3 64.0 + - - +
184A ALA* 3.0 18.5 + - - +
185A GLU* 3.1 16.2 + - - +
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Residues in contact with SER 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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176A GLU 4.6 3.1 - - - -
177A THR* 3.1 25.4 - - - +
178A ALA 3.1 2.1 + - - -
179A ASP* 2.5 49.2 + - - -
181A ALA* 1.3 73.5 - - - +
183A ARG* 1.3 60.9 + - - +
185A GLU* 3.1 11.1 + - - +
186A ALA* 3.0 23.7 + - - +
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Residues in contact with ARG 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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126A LEU* 4.2 25.5 - - + +
127A ALA 5.8 1.8 - - - +
152A ARG* 5.0 2.2 - - - +
177A THR* 3.7 31.7 + - - +
178A ALA 4.5 3.0 + - - -
179A ASP* 3.0 34.8 + - - +
180A ASP* 3.1 35.7 + - - +
182A SER* 1.3 79.0 + - - +
184A ALA* 1.3 59.8 + - - +
186A ALA* 3.7 2.8 + - - +
187A VAL* 3.4 27.4 + - - +
202A GLU 3.9 17.2 + - - -
203A LEU* 3.0 49.1 + - - +
204A LEU* 4.2 3.6 - - + +
456A NAP 4.5 13.3 + - - -
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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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180A ASP 2.8 12.3 + - - +
181A ALA* 3.0 12.7 + - - +
183A ARG* 1.3 75.7 - - - +
185A GLU* 1.3 64.0 + - + +
187A VAL* 3.5 13.8 + - - +
188A LYS* 3.5 22.3 - - - +
204A LEU* 4.7 0.4 - - - -
208A ALA* 4.4 29.3 - - + +
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Residues in contact with GLU 185 (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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181A ALA 3.1 13.6 + - - +
182A SER* 3.1 12.6 + - - +
184A ALA* 1.3 74.9 - - + +
186A ALA* 1.3 64.2 + - - +
187A VAL 3.1 2.2 - - - -
188A LYS* 3.0 57.8 + - - +
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Residues in contact with ALA 186 (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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122A LYS* 3.3 22.2 + - - -
124A VAL* 3.6 13.6 - - + +
126A LEU* 4.9 1.1 - - + -
148A VAL* 5.7 3.4 - - + +
150A CYS* 4.3 15.3 - - - -
175A ALA* 5.6 3.8 - - + -
177A THR* 4.0 20.2 - - + -
182A SER 3.0 14.4 + - - +
183A ARG* 4.0 5.4 - - - +
184A ALA 3.5 0.2 - - - -
185A GLU* 1.3 77.4 - - - +
187A VAL* 1.3 60.4 + - - +
188A LYS 3.5 0.2 + - - -
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Residues in contact with VAL 187 (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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124A VAL* 4.5 11.7 - - + -
126A LEU* 4.3 6.5 - - + -
183A ARG 3.4 14.5 + - - +
184A ALA 3.6 9.4 - - - +
185A GLU 3.1 0.6 - - - -
186A ALA* 1.3 76.9 - - - +
188A LYS* 1.3 63.7 + - + +
189A GLY 3.3 0.5 + - - -
190A ALA* 3.2 18.1 + - - +
193A VAL* 4.0 24.9 - - + -
204A LEU* 3.9 18.4 - - + -
208A ALA 3.9 14.1 - - - +
212A GLU* 4.0 5.8 - - + +
215A ILE* 3.4 30.1 - - + -
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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