Contacts of the helix formed by residues 166 - 173 (chain A) in PDB entry 1PS9
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 TYR 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.4 25.6 - - + -
103A HIS 3.5 9.0 - - - +
104A THR* 3.4 33.7 - - + -
107A TYR* 3.6 26.9 - + + -
161A MET* 3.7 22.9 - - + +
162A GLY 6.1 0.2 - - - -
163A SER 3.2 21.8 + - - +
164A GLU* 3.9 13.2 - - + -
165A GLY* 1.3 74.4 - - - +
167A LEU* 1.3 69.0 + - - +
168A ILE 3.6 2.0 - - - +
169A ASN* 3.1 3.8 + - - +
170A GLU* 2.8 29.1 + - - +
252A HIS* 2.7 26.5 + + - -
704A MDE 3.5 33.6 - - + +
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Residues in contact with LEU 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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103A HIS* 3.2 47.9 + - + +
105A GLY* 3.7 6.9 - - - +
114A VAL 3.8 22.0 - - - +
115A ALA* 4.2 10.8 - - - -
116A PRO* 4.4 2.5 - - + -
131A LEU* 4.4 4.5 - - + -
139A LEU* 3.5 26.0 - - + -
143A PHE* 4.8 1.6 - - + -
166A TYR* 1.3 73.6 - - - +
168A ILE* 1.3 66.4 + - + +
170A GLU* 2.8 21.9 + - - +
171A PHE* 3.2 28.5 + - + -
193A PHE* 3.8 22.0 - - + -
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Residues in contact with ILE 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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103A HIS 4.9 0.4 + - - -
143A PHE* 4.0 20.6 - - + -
160A VAL* 3.5 31.4 - - + -
161A MET 3.7 16.4 + - - +
162A GLY* 3.7 9.2 - - - +
166A TYR 3.6 0.4 - - - -
167A LEU* 1.3 77.2 - - + +
169A ASN* 1.3 64.0 + - - +
171A PHE* 3.2 14.4 + - - +
172A LEU* 3.6 11.7 + - + +
193A PHE* 3.5 28.0 - - + -
194A ALA* 3.6 31.1 + - + +
197A VAL* 4.5 9.4 - - + -
213A TYR* 3.6 16.4 - - + +
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Residues in contact with ASN 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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162A GLY 3.4 21.4 + - - +
163A SER* 3.3 11.9 - - - -
164A GLU 3.3 1.9 + - - -
165A GLY* 2.8 29.6 + - - +
166A TYR* 3.1 12.6 + - - +
168A ILE* 1.3 79.7 - - - +
170A GLU* 1.3 61.6 + - - +
172A LEU* 3.0 28.3 + - - +
173A THR* 3.6 7.1 + - - +
216A SER* 3.5 10.8 + - - -
219A ASP* 3.5 17.2 + - - -
251A TRP* 3.0 20.3 + - - +
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Residues in contact with GLU 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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104A THR 3.9 1.4 - - - +
105A GLY* 3.8 0.5 - - - -
106A ARG* 3.1 44.5 + - + +
107A TYR 4.3 0.3 + - - -
115A ALA* 3.6 6.1 - - - +
116A PRO* 3.5 25.8 - - + +
165A GLY* 2.8 23.7 - - - +
166A TYR* 2.8 31.3 + - - +
167A LEU* 2.8 9.8 + - - +
169A ASN* 1.3 75.2 - - - +
171A PHE* 1.3 63.5 + - - +
172A LEU 3.3 0.5 + - - -
173A THR* 3.4 9.8 + - - +
176A THR* 2.5 40.4 + - + +
177A ASN* 3.6 5.2 - - - +
251A TRP* 4.7 1.8 - - + -
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Residues in contact with PHE 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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116A PRO* 3.5 27.6 - - + -
131A LEU* 3.8 21.5 - - + -
136A ILE* 3.9 27.6 - - + -
167A LEU* 3.2 30.9 + - + -
168A ILE 3.2 7.4 + - - +
170A GLU* 1.3 76.6 - - - +
172A LEU* 1.3 58.6 + - - +
177A ASN* 2.9 37.2 + - - +
179A ARG* 4.4 3.6 - - - -
183A TRP* 4.1 18.6 - + + -
190A ARG* 3.1 28.0 - - - +
193A PHE* 3.4 45.8 - + + -
194A ALA 5.9 0.2 - - - +
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Residues in contact with LEU 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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162A GLY 4.6 2.2 - - - +
168A ILE* 3.7 16.6 - - + +
169A ASN* 3.0 24.1 + - - +
171A PHE* 1.3 79.3 - - + +
173A THR* 1.3 61.3 + - + +
187A TYR* 3.9 21.0 - - + +
190A ARG* 3.0 47.3 + - - +
191A MET* 3.7 17.0 - - + -
194A ALA* 4.7 4.7 - - + -
213A TYR* 4.2 11.2 - - - +
215A LEU* 5.8 0.4 - - + -
216A SER* 5.9 3.1 - - - +
229A GLU* 5.5 0.3 - - - +
233A LEU* 3.5 34.1 - - + -
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Residues in contact with THR 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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169A ASN* 3.6 7.0 + - - +
170A GLU 3.4 1.6 + - - +
171A PHE 3.5 0.2 - - - -
172A LEU* 1.3 81.0 - - + +
174A LEU* 1.3 58.8 + - - +
175A ARG* 2.9 7.2 + - - -
176A THR* 3.1 17.0 + - - -
177A ASN* 2.8 29.1 + - - +
190A ARG* 4.3 1.8 - - - +
219A ASP* 3.5 26.0 - - - +
223A ASP 3.6 10.1 - - - -
224A GLY* 3.7 14.6 - - - -
225A GLY* 3.8 5.8 - - - +
251A TRP* 3.3 26.4 - - + -
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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