Contacts of the strand formed by residues 246 - 253 (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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 2.9 27.4 + - - +
140A CYS 4.5 4.2 + - - -
143A LEU 2.9 7.8 + - - -
144A ILE* 3.6 22.6 - - - +
145A ASP* 2.8 26.5 + - - +
245A ALA* 1.3 72.1 - - - +
247A LYS* 1.3 58.5 + - - +
248A VAL* 3.6 8.4 + - + -
276A LEU* 3.5 31.6 - - + -
335A ILE* 4.0 20.0 - - + +
339A THR* 4.6 5.4 + - - -
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 3.6 8.7 - - + +
231A ARG 5.8 1.0 + - - -
235A TYR* 3.8 39.8 - - + +
245A ALA* 3.3 13.3 + - + +
246A THR* 1.3 72.9 - - - +
248A VAL* 1.3 62.0 + - - +
273A ASP* 3.0 47.3 + - - +
274A ASN* 3.7 9.9 + - - +
275A ILE* 3.6 20.7 - - + +
276A LEU* 2.9 28.0 + - - +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 3.6 26.2 - - + -
145A ASP 2.8 13.4 + - - +
146A VAL* 3.3 21.9 - - + -
147A VAL 2.8 20.3 + - - -
235A TYR* 2.7 19.5 + - - -
246A THR* 4.1 13.2 - - + +
247A LYS* 1.3 78.8 - - - +
249A MET* 1.3 60.8 + - - +
250A VAL* 4.5 0.9 - - + -
276A LEU* 3.4 13.9 - - + +
278A PHE* 3.9 27.8 - - + -
332A ILE* 4.4 11.4 - - + -
335A ILE* 5.8 4.3 - - + -
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.2 6.3 - - + +
149A VAL* 3.7 27.4 - - + -
227A ILE* 3.4 37.0 - - + +
230A ALA* 4.2 13.7 - - - -
231A ARG* 5.4 0.9 - - - -
235A TYR* 3.2 15.0 - - - +
248A VAL* 1.3 73.1 - - - +
250A VAL* 1.3 64.1 + - - +
251A VAL* 3.5 22.4 - - + -
270A CYS* 4.7 4.5 - - - -
275A ILE* 3.7 14.8 - - + -
276A LEU 2.8 10.0 + - - +
277A ARG* 3.3 25.1 - - + -
278A PHE* 2.8 28.6 + - - +
303A ILE* 5.1 0.2 - - + -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 4.0 22.4 - - + -
147A VAL 2.9 7.1 + - - -
148A VAL* 3.4 17.3 - - + +
149A VAL 2.8 33.1 + - - +
165A PHE* 5.1 2.9 - - + -
169A PHE* 4.3 15.0 - - + -
248A VAL* 4.5 6.3 - - + -
249A MET* 1.3 76.5 - - - +
251A VAL* 1.3 57.5 + - - +
252A VAL* 4.0 18.7 + - + -
278A PHE* 3.6 16.4 - - + +
280A ILE* 4.3 6.1 - - + -
328A LEU* 3.9 24.7 - - + -
332A ILE* 4.6 3.4 - - + -
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Residues in contact with VAL 251 (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* 3.4 16.8 - - + +
187A TYR* 4.7 5.8 - - - +
223A THR* 4.3 24.2 - - + -
227A ILE* 4.2 13.0 - - + -
249A MET* 3.5 35.4 - - + -
250A VAL* 1.3 74.3 - - - +
252A VAL* 1.3 61.0 + - - +
253A THR* 4.8 7.1 - - + +
277A ARG* 5.6 0.4 - - + -
278A PHE 2.9 16.5 + - - +
279A GLY* 3.7 2.0 - - - -
280A ILE* 2.8 33.3 + - - +
300A ILE* 5.1 2.5 - - + +
303A ILE* 4.4 16.2 - - + -
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 4.9 4.5 - - + -
149A VAL 3.0 9.2 + - - +
150A CYS* 3.7 21.3 - - - -
151A ASP* 2.8 30.4 + - + +
162A VAL* 5.7 1.8 - - + -
165A PHE* 4.3 15.5 - - + -
187A TYR* 4.2 1.2 - - - -
250A VAL* 4.2 20.4 - - + +
251A VAL* 1.3 74.8 - - - +
253A THR* 1.3 63.4 + - - +
280A ILE* 3.6 20.2 - - + +
282A VAL* 3.8 23.8 - - + -
321A LEU* 4.6 13.9 - - + -
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP* 2.9 21.0 + - - -
156A ILE* 5.5 0.4 - - - -
187A TYR* 3.2 23.1 + - - +
221A THR* 3.8 2.1 - - - +
223A THR* 4.2 3.2 + - + +
251A VAL* 4.8 7.9 - - + +
252A VAL* 1.3 74.3 - - - +
254A ASP* 1.3 58.4 + - - +
255A GLY 3.2 16.1 + - - +
280A ILE 3.1 7.0 + - - +
281A ALA* 3.6 1.6 - - - -
282A VAL* 2.8 27.2 + - - -
296A LEU* 4.3 5.8 - - + +
300A ILE* 3.3 39.7 - - + -
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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
------------------------------------------------------------
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