Contacts of the strand formed by residues 159 - 167 (chain A) in PDB entry 2C0O
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.3 21.9 - - + +
124A PHE* 3.9 20.6 - + - -
149A ILE* 3.9 14.6 - - + -
150A ARG 3.1 15.0 - - - +
151A ASP* 3.4 19.7 - - - -
152A SER* 3.9 2.3 - - - +
157A GLY 5.1 7.0 - - - -
158A SER* 1.3 90.8 - - - +
160A SER* 1.3 69.3 + - - +
178A LYS* 4.1 1.7 - - - +
179A ILE* 2.9 38.4 + - + +
181A THR* 5.4 4.6 - - + +
187A PHE* 4.3 21.8 - + - -
198A LEU* 4.1 23.1 - - + -
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Residues in contact with SER 160 (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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148A MET 3.5 1.7 - - - +
149A ILE* 3.2 4.9 - - - -
150A ARG* 2.9 64.1 + - - +
152A SER* 3.2 5.7 - - - -
159A TYR* 1.3 79.5 + - - +
161A LEU* 1.3 61.1 + - - +
177A TYR 3.4 11.7 + - - -
178A LYS* 4.1 3.8 - - - +
179A ILE* 3.7 7.0 - - - -
501A PTR 2.8 29.4 + - - -
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Residues in contact with LEU 161 (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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147A PHE* 4.1 12.6 - - + -
148A MET 3.5 11.2 - - - +
149A ILE* 3.8 12.3 - - + -
160A SER* 1.3 73.1 - - - +
162A SER* 1.3 78.6 + - - +
163A VAL* 3.7 21.3 - - + -
175A LYS 3.5 0.7 - - - +
176A HIS* 3.2 7.3 - - - +
177A TYR* 2.8 43.7 + - + +
179A ILE* 3.7 13.2 - - + +
189A ILE* 3.8 23.6 - - + -
201A LEU* 4.6 12.1 - - + -
205A TYR* 5.3 0.9 - - + -
212A LEU* 4.4 19.1 - - + -
216A LEU* 4.1 10.5 - - + -
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Residues in contact with SER 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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133A ALA* 4.4 1.1 - - - -
137A LEU* 3.6 24.1 - - - +
146A SER 3.8 0.2 - - - +
147A PHE* 3.0 28.1 - - - +
148A MET* 2.9 22.4 + - - -
150A ARG* 3.1 18.3 + - - -
160A SER 3.9 0.2 + - - -
161A LEU* 1.3 70.6 + - - +
163A VAL* 1.3 62.9 + - - +
174A VAL* 3.9 3.1 - - - -
175A LYS 3.3 2.7 - - - -
176A HIS* 2.6 30.2 + - - -
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Residues in contact with VAL 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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145A GLY* 4.2 7.0 - - - +
146A SER 3.5 6.7 - - - +
161A LEU* 3.7 23.8 - - + -
162A SER* 1.3 80.9 - - - +
164A ARG* 1.3 75.7 + - - +
165A ASP* 3.5 2.0 + - + +
174A VAL* 3.4 5.7 - - - -
175A LYS* 2.9 36.9 + - + +
177A TYR* 4.2 18.6 - - + -
212A LEU* 4.7 4.7 - - + -
214A GLN* 3.8 25.1 - - + +
215A LYS 4.7 0.2 - - - +
216A LEU* 3.8 23.6 - - + -
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Residues in contact with ARG 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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137A LEU* 3.4 33.6 + - + +
138A LEU* 4.1 16.7 + - + +
139A ALA 4.0 6.5 + - - -
142A ASN* 3.2 32.8 + - - +
143A MET* 3.3 27.1 + - - +
144A LEU* 4.7 2.1 - - - +
145A GLY* 2.9 27.2 + - - -
146A SER* 2.7 21.2 + - - +
163A VAL* 1.3 72.9 - - - +
165A ASP* 1.3 62.6 + - - +
172A ASP* 3.1 37.8 + - - +
173A THR 3.6 12.1 - - - +
174A VAL* 4.5 10.0 - - + +
214A GLN* 3.6 7.6 - - - +
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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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144A LEU* 3.7 7.0 - - - -
163A VAL* 3.5 5.8 + - + +
164A ARG* 1.3 76.6 - - - +
166A TYR* 1.3 89.3 + - - +
172A ASP* 3.6 9.3 - - - +
173A THR* 2.9 37.5 + - - +
175A LYS* 3.4 29.2 + - + -
213A CYS* 3.4 24.4 - - + +
214A GLN* 2.8 28.7 + - + -
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Residues in contact with TYR 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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144A LEU* 3.4 19.5 - - + +
165A ASP* 1.3 96.7 + - - +
167A ASP* 1.3 91.3 + - - +
168A PRO* 4.2 13.9 + - + +
171A GLY* 3.5 17.7 - - - -
172A ASP* 3.8 29.2 - - - +
173A THR* 4.6 0.4 - - - -
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Residues in contact with ASP 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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166A TYR* 1.3 85.5 - - - +
168A PRO* 1.3 79.5 - - - +
169A ARG* 3.7 6.5 + - - +
170A GLN* 3.0 34.5 - - + +
171A GLY 2.7 44.1 + - - +
173A THR* 4.4 12.4 - - + +
175A LYS* 5.5 7.4 - - - +
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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