Contacts of the helix formed by residues 179 - 187 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C THR 3.5 0.4 + - - -
178C ALA* 1.3 81.2 - - + +
180C ASP* 1.3 65.8 + - - +
181C ALA* 3.8 11.6 - - - +
182C SER* 2.8 29.8 + - - -
183C ARG* 3.1 34.8 + - - +
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Residues in contact with ASP 180 (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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179C ASP* 1.3 74.3 - - - +
181C ALA* 1.3 64.8 + - - +
183C ARG* 3.0 27.8 + - - +
184C ALA* 3.0 26.1 + - - +
202C GLU 5.5 1.7 - - - +
203C LEU 5.7 0.2 - - - +
205C PRO* 5.4 17.0 - - + +
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Residues in contact with ALA 181 (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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179C ASP* 3.3 12.5 + - - +
180C ASP* 1.3 81.0 - - - +
182C SER* 1.3 57.4 + - - +
184C ALA* 3.5 6.0 + - - +
185C GLU* 3.1 26.4 + - - +
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Residues in contact with SER 182 (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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176C GLU 4.6 3.6 - - - -
177C THR* 3.7 28.0 - - - +
178C ALA* 4.0 3.5 + - - +
179C ASP* 2.8 25.2 + - - -
181C ALA* 1.3 71.6 - - - +
183C ARG* 1.3 61.1 + - - +
185C GLU* 3.2 7.5 + - - +
186C ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 183 (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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126C LEU* 4.2 18.9 - - + +
127C ALA 6.0 0.9 - - - +
152C ARG* 4.3 8.5 - - - +
177C THR* 3.6 38.1 + - - +
178C ALA 4.5 1.0 + - - -
179C ASP* 3.1 30.7 + - - +
180C ASP* 3.0 29.9 + - - +
182C SER* 1.3 76.8 - - - +
184C ALA* 1.3 63.9 + - - +
186C ALA* 3.2 11.8 + - - +
187C VAL* 3.5 17.7 + - - +
202C GLU 5.3 3.6 + - - -
203C LEU* 3.5 55.6 + - - +
204C LEU* 5.5 1.6 - - + -
2456C NAP 4.3 14.3 + - - -
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Residues in contact with ALA 184 (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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180C ASP 3.0 17.4 + - - +
181C ALA* 3.8 6.1 - - - +
183C ARG* 1.3 79.5 - - - +
185C GLU* 1.3 63.2 + - - +
187C VAL* 3.6 20.4 + - - +
188C LYS* 3.6 17.5 - - - +
204C LEU* 5.4 1.1 - - - -
205C PRO* 6.2 0.4 - - + -
208C ALA* 4.2 25.5 - - + +
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Residues in contact with GLU 185 (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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181C ALA 3.1 16.7 + - - +
182C SER* 3.2 8.0 + - - +
184C ALA* 1.3 75.9 - - - +
186C ALA* 1.3 63.5 + - - +
187C VAL 3.2 1.4 + - - -
188C LYS* 3.2 51.5 + - - +
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Residues in contact with ALA 186 (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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122C LYS* 4.6 8.7 + - - -
124C VAL* 3.6 20.2 - - + +
126C LEU* 4.9 1.6 - - + -
148C VAL* 6.1 1.8 - - + -
150C CYS* 4.4 12.8 - - - -
175C ALA* 6.0 2.0 - - + -
177C THR* 3.9 20.0 - - + -
182C SER 2.9 16.4 + - - +
183C ARG* 3.2 7.1 + - - +
185C GLU* 1.3 78.8 - - - +
187C VAL* 1.3 59.6 + - - +
188C LYS 3.4 4.3 + - - +
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Residues in contact with VAL 187 (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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124C VAL* 4.1 13.2 - - + -
126C LEU* 4.2 10.8 - - + -
183C ARG 3.5 12.3 + - - +
184C ALA 3.6 14.4 - - - +
185C GLU 3.2 0.4 - - - -
186C ALA* 1.3 78.6 - - - +
188C LYS* 1.3 68.5 + - + +
189C GLY 3.3 0.5 + - - -
190C ALA* 3.0 21.3 + - - +
193C VAL* 3.8 37.7 - - + -
204C LEU* 4.2 9.6 - - + -
208C ALA 3.7 20.4 - - - +
212C GLU* 4.2 2.0 - - + +
215C ILE* 4.1 17.2 - - + +
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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