Contacts of the helix formed by residues 171 - 178 (chain A) in PDB entry 1NUS
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 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A SER 4.3 0.4 + - - -
170A HIS* 1.3 73.8 - - - +
172A PRO* 1.4 57.0 - - - +
173A LYS* 3.2 1.4 - - - +
174A GLY* 2.7 43.1 + - - -
175A TYR* 3.0 22.3 + - - -
201B SER* 3.8 18.7 + - - +
203B THR* 3.7 10.7 - - + +
204B TYR* 3.5 22.7 - - + +
207B ARG* 2.8 46.0 + - - -
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Residues in contact with PRO 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.4 27.4 - - + -
139A LEU* 4.2 3.1 - - + +
164A CYS* 4.3 5.8 - - - -
166A GLY* 4.9 9.9 - - - +
170A HIS 3.2 11.0 - - - +
171A ASP* 1.4 87.4 - - - +
173A LYS* 1.3 58.2 + - + +
175A TYR* 3.2 15.3 + - + +
176A ILE* 2.9 36.5 + - - +
191A LEU* 3.8 28.0 - - + -
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Residues in contact with LYS 173 (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 ASP* 3.1 1.7 + - - +
172A PRO* 1.3 79.8 - - + +
174A GLY* 1.3 58.2 + - - +
176A ILE* 3.5 6.2 + - - +
177A ALA* 3.1 26.0 + - - +
191A LEU* 3.6 24.2 - - + +
193A LYS* 5.6 7.1 - - - +
207B ARG* 3.6 44.0 - - - +
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Residues in contact with GLY 174 (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 ASP* 2.7 32.0 + - - -
173A LYS* 1.3 70.7 - - - +
175A TYR* 1.3 64.0 + - - -
176A ILE 3.2 0.2 - - - -
177A ALA* 3.3 4.2 + - - -
178A GLU* 3.0 32.2 + - - +
203B THR* 3.6 13.2 - - - -
207B ARG* 4.0 11.7 - - - -
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Residues in contact with TYR 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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136A ALA 3.5 20.9 - - - -
139A LEU* 4.1 16.4 - - + +
140A LYS* 3.2 44.4 + - + +
143A GLN* 3.6 28.4 + - - +
169A SER 4.2 1.4 + - - -
170A HIS* 3.0 41.6 - - + -
171A ASP 3.0 16.1 + - - -
172A PRO* 3.6 20.0 - - + +
174A GLY* 1.3 75.8 - - - +
176A ILE* 1.3 64.1 + - - +
178A GLU* 3.5 3.6 + - - +
179A SER* 3.2 25.6 + - - -
182A LEU* 4.0 4.1 - - + +
201B SER* 5.2 0.9 + - - -
203B THR* 3.6 32.7 - - + -
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Residues in contact with ILE 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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139A LEU* 4.2 12.1 - - + -
172A PRO 2.9 21.2 + - - +
173A LYS* 3.8 6.3 - - - +
174A GLY 3.2 0.2 - - - -
175A TYR* 1.3 78.1 - - - +
177A ALA* 1.3 62.8 + - - +
179A SER 3.2 20.4 + - - +
182A LEU* 4.0 17.7 - - + +
183A ARG* 3.4 8.2 + - - +
186A GLN* 3.9 32.5 - - + +
189A ILE* 3.7 36.8 - - + +
191A LEU* 4.0 25.4 - - + -
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Residues in contact with ALA 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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173A LYS 3.1 17.0 + - - +
174A GLY* 3.8 6.5 - - - +
176A ILE* 1.3 77.6 - - - +
178A GLU* 1.3 64.2 + - + +
179A SER 3.2 1.7 + - - +
183A ARG* 3.7 33.6 + - - +
57B ASP* 5.4 0.7 - - - +
207B ARG* 5.6 5.4 - - + -
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Residues in contact with GLU 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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143A GLN* 5.2 5.6 + - - +
174A GLY* 3.0 22.7 + - - +
175A TYR* 3.9 3.8 - - - +
177A ALA* 1.3 78.4 - - + +
179A SER* 1.3 58.8 + - - +
180A PRO* 3.6 8.5 - - - +
56B LYS* 3.4 30.4 - - + +
57B ASP* 3.9 34.6 + - + +
203B THR* 4.4 7.1 + - - +
206B ARG* 2.6 55.1 + - - +
207B ARG 5.4 0.5 + - - -
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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