Contacts of the helix formed by residues 180 - 187 (chain A) in PDB entry 1LTQ
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ARG* 3.7 23.4 + - - +
177A GLY* 3.0 22.0 + - - +
178A PRO 4.9 0.4 - - - +
179A TYR* 1.3 76.3 - - - +
181A LEU* 1.3 62.6 + - - +
182A GLU* 3.2 7.8 + - - +
183A LYS* 3.3 48.7 + - - +
184A CYS 4.0 0.2 + - - -
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Residues in contact with LEU 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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167A ASP* 4.5 0.9 - - - +
176A ARG* 4.0 11.7 - - - +
179A TYR* 3.5 14.0 + - - +
180A ASP* 1.3 72.9 - - - +
182A GLU* 1.3 61.5 + - - +
183A LYS 2.9 7.8 + - - -
184A CYS* 2.9 30.1 + - + -
213A ARG* 3.6 37.7 - - + +
214A GLU* 3.8 27.4 - - + +
224A TYR* 3.4 50.2 - - + -
227A MSE 3.9 2.3 - - - +
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Residues in contact with GLU 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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180A ASP* 3.2 7.7 - - - +
181A LEU* 1.3 77.1 - - - +
183A LYS* 1.3 77.1 + - + +
185A ASP* 3.5 10.1 - - - +
223A LYS* 6.3 0.4 - - + -
224A TYR* 3.8 20.3 + - - +
227A MSE 4.3 14.2 - - - +
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Residues in contact with LYS 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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175A GLY 6.0 0.4 - - - +
176A ARG* 3.8 19.9 - - + -
180A ASP* 3.3 38.2 + - - +
181A LEU 2.9 0.8 - - - -
182A GLU* 1.3 90.2 - - + +
184A CYS* 1.3 56.0 + - - +
185A ASP* 3.0 13.3 + - - -
186A THR* 2.8 37.0 + - + +
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Residues in contact with CYS 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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176A ARG* 3.5 24.9 - - - +
180A ASP 4.0 0.4 + - - -
181A LEU* 2.9 32.1 + - - +
182A GLU 3.6 0.2 - - - -
183A LYS* 1.3 74.2 - - - +
185A ASP* 1.3 60.6 + - - +
186A THR 3.1 6.4 + - - -
187A ASP* 2.9 27.4 + - - +
213A ARG* 3.5 30.2 + - - +
224A TYR* 4.9 3.6 - - - -
227A MSE 4.1 24.9 - - - -
228A THR* 4.4 4.5 - - - -
231A TRP* 4.1 7.3 - - - +
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Residues in contact with ASP 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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182A GLU 3.5 19.6 - - - +
183A LYS* 3.6 6.6 - - - -
184A CYS* 1.3 81.7 + - - +
186A THR* 1.3 68.2 + - - +
187A ASP 3.4 0.4 - - - -
227A MSE 4.7 23.4 - - + +
231A TRP* 4.3 10.5 - - + -
235A ILE* 3.9 20.6 - - - +
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Residues in contact with THR 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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174A ASN* 3.5 31.4 + - - +
176A ARG* 4.4 6.6 - - - +
183A LYS* 2.8 29.2 + - + +
184A CYS 3.1 0.4 - - - -
185A ASP* 1.3 93.5 - - - +
187A ASP* 1.3 66.4 + - - +
188A VAL* 3.5 2.3 + - - +
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Residues in contact with ASP 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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171A ALA* 3.8 19.1 - - + -
172A LYS 3.4 6.5 - - - +
173A MSE 3.0 27.4 - - - +
174A ASN 4.3 4.9 - - - +
176A ARG* 3.1 24.8 + - - -
184A CYS* 2.9 19.3 - - - +
185A ASP 3.4 2.3 - - - +
186A THR* 1.3 80.4 + - - +
188A VAL* 1.3 59.2 + - - +
213A ARG* 2.9 24.9 + - - -
231A TRP* 2.7 28.0 + - + +
235A ILE* 4.5 5.4 - - - +
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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