Contacts of the strand formed by residues 180 - 187 (chain A) in PDB entry 1AOX
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 THR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A SER 4.5 1.7 + - - -
144A ILE* 3.4 32.6 - - + +
146A VAL* 4.1 12.1 - - + -
173A LEU* 4.4 16.5 - - + +
174A ASP* 2.9 24.2 + - - +
175A ILE* 3.4 13.0 - - + +
176A GLY 3.1 22.2 + - - +
179A LYS* 1.3 81.5 - - - +
181A GLN* 1.3 70.8 + - - +
182A VAL* 4.3 9.0 - - + -
332A ILE* 5.5 1.8 - - + +
333A PHE* 5.4 4.5 - - - -
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Residues in contact with GLN 181 (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 ILE 2.9 7.0 + - - +
145A ASP* 3.2 19.3 + - - +
146A VAL* 2.9 26.5 + - - +
175A ILE* 5.1 0.4 - - - -
176A GLY 3.9 12.3 - - - +
177A PRO* 3.7 18.0 - - + +
179A LYS 4.0 0.2 + - - -
180A THR* 1.3 78.8 - - - +
182A VAL* 1.3 65.1 + - - +
197A LEU* 3.5 31.5 - - + +
198A ASN* 4.6 7.8 - - - +
200A TYR 5.6 2.8 - - - +
206A MET* 5.5 1.6 - - - -
240A GLY 2.9 28.8 + - - +
242A ARG* 3.3 22.5 + - - +
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Residues in contact with VAL 182 (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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146A VAL* 3.1 12.3 - - + +
148A VAL* 4.1 17.5 - - + -
169A PHE* 4.9 2.2 - - + -
170A VAL* 4.6 10.5 - - + -
173A LEU* 3.7 29.6 - - + -
175A ILE* 3.7 14.6 - - + -
180A THR* 4.3 3.1 - - + -
181A GLN* 1.3 81.9 - - - +
183A GLY* 1.3 71.2 + - - +
184A LEU* 5.7 0.2 - - - -
195A PHE* 3.2 23.5 - - + -
196A ASN 3.5 7.4 - - - +
197A LEU* 3.8 5.4 + - - -
206A MET* 3.4 28.2 - - - +
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Residues in contact with GLY 183 (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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146A VAL 2.8 10.2 + - - +
147A VAL* 4.3 10.1 - - - -
148A VAL* 2.9 29.1 + - - +
182A VAL* 1.3 77.8 - - - +
184A LEU* 1.3 60.4 + - - -
185A ILE* 4.3 0.7 - - - -
195A PHE* 3.5 13.5 - - - -
196A ASN* 3.9 9.6 - - - -
197A LEU* 3.9 5.6 - - - +
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Residues in contact with LEU 184 (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 VAL* 3.6 30.5 - - + +
150A CYS* 4.3 9.9 - - + -
166A LEU* 4.5 19.7 - - + -
182A VAL* 5.8 0.4 - - + -
183A GLY* 1.3 73.5 - - - -
185A ILE* 1.3 73.0 + - - +
186A GLN* 3.6 21.1 - - + +
193A VAL* 4.0 0.2 - - - -
194A VAL* 2.8 53.3 + - + -
195A PHE* 2.9 44.4 + - + +
210A THR* 4.9 5.8 - - + -
213A THR* 4.3 7.0 - - + +
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Residues in contact with ILE 185 (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 VAL* 4.0 13.2 - - + -
148A VAL 2.8 12.7 + - - +
149A VAL* 3.2 11.9 - - + -
150A CYS* 2.8 26.0 + - - -
183A GLY 5.6 0.2 - - - -
184A LEU* 1.3 79.6 - - - +
186A GLN* 1.3 73.1 + - - +
191A PRO* 4.4 12.3 - - + -
192A ARG 3.5 18.2 - - - +
193A VAL* 4.4 14.4 - - + -
195A PHE 5.5 0.9 - - - +
226A ALA* 5.0 7.2 - - + +
229A TYR* 4.0 15.3 - - + -
230A ALA* 3.8 36.3 - - + +
234A ALA* 4.0 10.3 - - + -
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Residues in contact with GLN 186 (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 CYS* 3.1 20.0 - - + +
152A GLU* 2.8 31.6 + - - +
159A TRP* 3.6 19.1 - - + -
166A LEU* 5.2 1.0 - - - +
184A LEU* 3.6 16.9 - - + +
185A ILE* 1.3 77.2 - - - +
187A TYR* 1.3 60.9 + - - +
191A PRO* 3.7 0.3 - - - +
192A ARG* 2.7 51.4 + - - +
194A VAL* 3.6 12.6 - - + +
213A THR* 2.5 25.8 + - - +
214A SER 2.8 27.3 + - - -
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Residues in contact with TYR 187 (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 VAL* 3.8 27.1 - - + -
150A CYS 2.9 16.2 + - - -
151A ASP* 3.3 28.3 - - + +
152A GLU* 2.8 36.2 + - - +
185A ILE* 5.1 0.4 - - + -
186A GLN* 1.3 77.6 - - - +
188A ALA* 1.3 67.5 + - - +
190A ASN 3.4 13.0 - - - +
191A PRO* 3.9 3.6 - - + -
221A THR* 4.0 11.4 - - + -
222A ASN 3.7 16.8 - - - -
223A THR* 2.9 46.4 + - + +
226A ALA* 3.5 16.2 - - + -
251A VAL* 4.7 1.8 - - + +
252A VAL 4.2 2.9 - - - -
253A THR* 3.2 23.9 + - - -
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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