Contacts of the strand formed by residues 171 - 179 (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 GLY 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TYR* 3.8 19.7 - - - -
167A ASP* 2.7 52.4 + - - +
168A PRO 4.2 1.2 + - - -
170A GLN* 1.3 74.3 - - - +
172A ASP* 1.3 64.0 + - - -
173A THR* 3.4 3.9 + - - +
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Residues in contact with ASP 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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138A LEU* 3.8 24.2 - - + +
144A LEU* 5.2 4.2 + - - +
164A ARG* 3.1 35.3 + - - +
165A ASP 3.6 11.2 - - - +
166A TYR* 3.8 22.8 - - - +
170A GLN 4.2 1.8 + - - +
171A GLY* 1.3 70.0 - - - -
173A THR* 1.3 62.1 + - - +
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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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138A LEU* 4.6 4.9 - - - -
164A ARG* 3.6 5.5 - - - +
165A ASP* 2.9 42.1 + - - +
167A ASP* 4.4 12.3 - - + +
170A GLN* 5.1 10.1 - - + +
171A GLY 3.8 9.7 + - - +
172A ASP* 1.3 77.4 - - - +
174A VAL* 1.3 73.5 + - - +
175A LYS* 4.3 17.4 + - - -
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Residues in contact with VAL 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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134A GLU* 3.9 36.1 - - + +
137A LEU* 3.7 44.4 - - + -
138A LEU* 4.0 10.1 - - + +
162A SER* 3.9 5.2 - - - -
163A VAL 3.4 9.2 - - - +
164A ARG* 4.6 4.3 - - + -
173A THR* 1.3 80.8 - - - +
175A LYS* 1.3 68.6 + - - +
176A HIS* 3.6 32.2 + - + +
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Residues in contact with LYS 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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161A LEU 3.5 0.5 - - - +
162A SER* 3.3 5.5 - - - -
163A VAL* 2.9 36.7 + - + +
165A ASP* 3.4 28.8 + - + -
167A ASP* 5.5 8.3 - - - +
173A THR* 4.3 19.8 + - - +
174A VAL* 1.3 73.3 - - - +
176A HIS* 1.3 65.5 + - - +
177A TYR* 4.0 14.8 - - + +
213A CYS* 4.0 23.0 - - + -
500A GLN 5.6 0.2 - - - -
502A GLU* 3.2 38.8 - - + +
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Residues in contact with HIS 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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130A ARG* 3.6 37.1 + - + +
133A ALA* 4.6 2.5 - - + -
134A GLU* 4.1 12.2 + - - -
150A ARG* 2.8 14.4 + - - +
161A LEU 3.2 5.4 - - - +
162A SER* 2.6 28.5 + - - -
174A VAL* 3.6 32.3 + - + +
175A LYS* 1.3 75.3 - - - +
177A TYR* 1.3 62.2 + - - +
500A GLN 3.7 19.1 + - - +
501A PTR 3.3 28.0 - - + -
502A GLU* 2.9 32.2 + - - +
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Residues in contact with TYR 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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160A SER* 3.4 4.9 - - - -
161A LEU* 2.8 49.0 + - + +
163A VAL* 4.2 19.3 - - + -
175A LYS* 4.0 17.6 - - + +
176A HIS* 1.3 75.3 - - - +
178A LYS* 1.3 61.9 + - - +
189A ILE* 3.9 15.7 - - + -
212A LEU* 3.7 32.9 - - + -
213A CYS* 2.9 37.6 + - + +
214A GLN 5.9 0.4 - - - -
501A PTR 4.1 2.7 - - - -
502A GLU* 3.4 35.7 + - + +
503A GLU 4.8 0.2 - - - -
504A ILE* 3.8 29.8 - - + -
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Residues in contact with LYS 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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152A SER* 3.7 2.2 + - - +
154A THR* 3.1 19.2 + - - -
155A THR* 2.9 23.4 + - - +
159A TYR 4.1 3.1 - - - +
160A SER* 4.1 4.3 - - - +
177A TYR* 1.3 74.4 - - - +
179A ILE* 1.3 60.4 + - - +
180A ARG* 3.3 35.8 + - + +
189A ILE* 3.3 24.8 - - - +
501A PTR 3.1 50.8 + - + +
502A GLU 5.1 2.8 + - - +
463B GLU* 3.3 34.3 - - + +
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Residues in contact with ILE 179 (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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149A ILE* 3.7 41.7 - - + -
158A SER* 4.6 3.3 + - - -
159A TYR* 2.9 28.7 + - + +
160A SER* 3.7 4.0 - - - +
161A LEU* 3.7 22.9 - - + +
177A TYR 3.6 0.2 + - - -
178A LYS* 1.3 72.3 - - - +
180A ARG* 1.3 72.4 + - - +
181A THR* 4.0 7.6 + - + +
187A PHE* 3.8 37.0 - - + -
188A TYR 3.9 3.6 - - - +
189A ILE* 3.9 18.6 - - + -
198A LEU* 4.3 9.9 - - + -
201A LEU* 4.1 9.0 - - + -
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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