Contacts of the helix formed by residues 164 - 172 (chain A) in PDB entry 1U75
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 ASN 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASN 3.9 1.0 + - - -
163A MET* 1.3 73.2 - - - +
165A ASP* 1.3 65.0 + - - +
166A ARG* 3.2 20.2 + - - +
167A GLU* 2.9 33.5 + - - +
168A VAL* 3.0 17.9 + - - +
31C ARG* 3.4 22.8 + - + +
32C GLU* 3.2 30.8 + - - +
34C ASP* 2.9 35.7 + - - +
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Residues in contact with ASP 165 (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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155A ARG* 3.0 48.6 + - - +
164A ASN* 1.3 75.3 - - - +
166A ARG* 1.3 59.5 + - - +
168A VAL* 3.7 1.8 + - - +
169A VAL* 3.3 30.5 + - - +
243A LYS* 4.1 12.6 + - + +
244A TYR* 3.2 22.1 + - + -
247A ILE* 3.9 12.6 - - + +
32C GLU* 4.7 15.6 + - - +
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Residues in contact with ARG 166 (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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164A ASN* 3.2 10.4 + - - +
165A ASP* 1.3 79.0 - - - +
167A GLU* 1.3 63.9 + - + +
169A VAL 3.9 0.2 + - - -
170A ALA* 3.3 14.0 + - - +
247A ILE* 3.9 30.8 - - + +
250A GLU* 2.5 45.0 + - - -
251A TYR* 3.2 35.7 + - - +
257A LYS* 3.2 23.7 - - - +
261A ASP* 3.0 20.0 + - - +
264A LYS* 6.3 0.4 - - - +
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Residues in contact with GLU 167 (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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163A MET* 3.4 16.9 - - - -
164A ASN* 2.9 33.4 + - - +
166A ARG* 1.3 77.5 - - + +
168A VAL* 1.3 57.4 + - - +
170A ALA* 3.3 4.4 + - - +
171A LEU* 3.0 34.4 + - - +
261A ASP 5.7 0.4 - - - +
265A ALA* 4.0 16.8 - - + +
268A LYS* 2.9 34.5 + - - +
34C ASP* 2.7 28.4 - - - +
35C GLU* 5.1 1.9 - - - +
39C TYR* 3.8 9.5 + - - -
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Residues in contact with VAL 168 (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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154A VAL* 4.2 6.1 - - + -
155A ARG* 5.8 1.1 - - - +
158A PHE* 3.7 36.6 - - + -
163A MET* 4.0 6.5 - - + +
164A ASN 3.0 23.0 + - - +
165A ASP* 4.3 2.5 - - - +
167A GLU* 1.3 71.9 - - - +
169A VAL* 1.3 64.8 + - + +
171A LEU* 3.2 10.3 + - - +
172A MET* 2.9 49.0 + - + +
238A LEU* 4.9 1.1 - - + -
244A TYR* 3.6 34.8 - - + +
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Residues in contact with VAL 169 (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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165A ASP 3.3 19.3 + - - +
166A ARG 4.3 0.2 - - - +
168A VAL* 1.3 78.3 - - + +
170A ALA* 1.3 54.8 + - - +
172A MET* 3.5 12.9 + - - +
173A GLY 3.5 1.2 + - - -
203A TYR* 2.6 46.2 + - + -
238A LEU* 4.4 10.8 - - + -
244A TYR* 3.6 37.5 - - + +
247A ILE* 3.9 14.8 - - + -
248A VAL* 3.9 16.6 - - + +
251A TYR* 3.9 12.8 - - + -
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Residues in contact with ALA 170 (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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166A ARG 3.3 18.2 + - - +
167A GLU* 3.6 6.1 - - - +
168A VAL 3.2 0.6 - - - -
169A VAL* 1.3 78.9 - - - +
171A LEU* 1.3 60.6 + - - +
173A GLY 3.2 2.8 + - - -
203A TYR* 3.6 5.6 - - - -
251A TYR* 3.7 17.0 - - + +
258A PHE* 3.1 16.4 - - + -
261A ASP* 3.9 28.9 - - + +
262A PHE* 3.1 22.3 - - - +
265A ALA* 4.7 1.3 - - + -
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Residues in contact with LEU 171 (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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158A PHE* 4.3 14.1 - - + -
163A MET* 4.0 31.0 - - + -
167A GLU 3.0 20.9 + - - +
168A VAL* 3.2 5.4 + - - +
170A ALA* 1.3 71.6 - - - +
172A MET* 1.3 60.2 - - - +
173A GLY 3.1 5.5 + - - -
174A ALA* 3.3 22.0 + - - +
262A PHE* 4.0 6.5 - - + -
265A ALA* 4.0 7.4 - - + +
266A PHE* 4.0 33.0 - - + +
269A LEU* 4.1 18.4 - - + -
1001A ZNH 3.6 41.8 - - + +
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Residues in contact with MET 172 (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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154A VAL* 3.9 8.1 - - + -
158A PHE* 3.8 18.2 - - + -
168A VAL* 2.9 36.0 + - + +
169A VAL* 3.7 7.4 - - - +
170A ALA 3.3 0.6 - - - -
171A LEU* 1.3 71.9 - - - +
173A GLY* 1.3 58.4 + - - +
174A ALA 3.1 6.8 + - - -
175A HIS* 3.3 24.8 + - - +
202A PHE* 3.4 11.0 - - + -
234A THR 5.4 1.8 - - - +
235A ASP* 3.8 21.8 - - - +
238A LEU* 3.9 27.6 - - + -
1001A ZNH 3.5 53.6 - - + -
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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