Contacts of the strand formed by residues 161 - 170 (chain A) in PDB entry 1Z57
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ASP 3.5 1.4 - - - +
156A VAL* 3.2 4.4 - - - -
157A LEU* 2.7 51.4 + - + +
158A SER* 4.1 2.5 - - - -
160A ARG* 1.2 103.1 + - + +
162A GLU* 1.3 60.7 + - - +
163A ILE 3.7 0.5 + - - -
178A CYS* 3.8 17.3 - - + -
179A ILE 3.3 2.9 - - - -
180A ASP* 3.4 31.5 + - + -
188A VAL* 3.8 18.6 - - + -
190A VAL* 4.6 4.7 - - + -
228A LEU* 5.7 0.7 - - - +
229A GLU* 2.5 39.5 + - - +
231A PHE* 3.5 28.9 - + - -
240A VAL* 3.8 20.6 - - + +
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Residues in contact with GLU 162 (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 GLY* 4.4 16.6 - - - +
155A ASP 3.5 7.6 - - - +
156A VAL* 4.4 10.5 - - + +
160A ARG 3.7 1.0 + - - -
161A TYR* 1.3 73.0 - - - +
163A ILE* 1.3 69.1 + - - +
164A VAL* 3.3 8.5 + - + +
178A CYS* 3.1 3.2 - - - -
179A ILE* 2.9 50.3 + - + +
181A HIS* 2.7 43.6 + - + +
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Residues in contact with ILE 163 (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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150A ILE 3.9 8.7 - - - +
151A CYS* 3.6 38.1 - - - +
152A GLN 3.5 21.1 - - - +
153A SER* 3.6 8.8 - - - +
154A GLY* 2.9 24.1 + - - -
155A ASP* 2.9 22.1 + - + +
157A LEU* 4.0 14.6 - - + -
162A GLU* 1.3 72.0 - - - +
164A VAL* 1.3 65.9 + - - +
165A ASP 3.9 16.8 - - - +
166A THR* 5.9 0.2 - - - +
176A VAL* 4.0 16.4 - - + -
177A GLU 3.7 7.9 - - - +
178A CYS* 3.9 16.2 - - - -
192A ILE* 4.6 0.7 - - + -
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Residues in contact with VAL 164 (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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153A SER* 3.5 16.6 + - - -
162A GLU* 3.3 13.9 + - - +
163A ILE* 1.3 78.8 - - - +
165A ASP* 1.3 61.4 + - + +
177A GLU* 2.8 47.9 + - + +
178A CYS* 4.4 3.8 - - - +
179A ILE* 3.5 28.3 - - + -
187A HIS* 4.5 11.7 - - + -
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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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153A SER* 4.5 4.9 - - - -
163A ILE* 3.9 5.7 - - - +
164A VAL* 1.3 80.8 - - + +
166A THR* 1.3 77.6 + - - +
167A LEU* 5.2 3.4 - - + +
176A VAL* 3.4 8.2 - - - +
177A GLU* 2.8 46.3 + - + +
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Residues in contact with THR 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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151A CYS 4.6 3.8 + - - -
163A ILE* 5.9 0.2 - - - +
165A ASP* 1.3 88.8 + - - +
167A LEU* 1.3 64.6 + - - +
168A GLY* 3.7 19.1 - - - +
169A GLU* 5.7 2.5 - - + -
174A LYS* 4.0 30.1 + - - -
175A VAL 3.6 11.7 - - - +
176A VAL* 4.1 6.5 - - - +
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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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1A DBQ 3.9 33.3 - - + +
165A ASP* 5.2 3.8 - - - +
166A THR* 1.3 77.6 - - - +
168A GLY* 1.3 55.5 + - - +
175A VAL* 2.8 15.2 + - + +
176A VAL 3.9 5.2 - - - -
177A GLU* 3.8 44.0 - - + +
189A ALA* 4.0 8.7 - - + -
243A LEU* 3.5 28.5 - - + -
244A LEU 5.4 2.9 - - - +
246A LEU* 6.0 2.1 - - - +
250A ASP* 4.6 9.2 - - - +
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Residues in contact with GLY 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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1A DBQ 5.3 4.7 - - - -
166A THR* 3.7 7.6 - - - +
167A LEU* 1.3 82.2 - - - +
169A GLU* 1.3 59.3 + - - +
172A PHE* 5.6 0.4 - - - -
174A LYS* 3.3 5.2 - - - +
175A VAL* 2.8 35.6 + - - +
250A ASP* 5.6 3.6 - - - -
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Residues in contact with GLU 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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166A THR* 5.7 2.2 - - + -
168A GLY* 1.3 75.5 - - - +
170A GLY* 1.3 59.3 + - - +
172A PHE* 4.6 3.4 - - - -
173A GLY 3.4 11.9 - - - +
174A LYS* 4.1 8.1 - - + +
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Residues in contact with GLY 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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169A GLU* 1.3 74.8 - - - +
171A ALA* 1.3 67.7 + - - +
172A PHE* 3.1 20.6 - - - -
173A GLY* 2.9 18.8 + - - +
194A LYS* 4.5 4.3 + - - -
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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