Contacts of the strand formed by residues 275 - 282 (chain B) 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 ILE 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ARG* 3.9 24.0 - - + +
235B TYR* 3.7 42.2 - - + +
247B LYS* 3.5 20.4 - - + +
249B MET* 3.7 26.5 - - + +
270B CYS* 2.9 28.3 + - + +
271B ASN* 4.9 0.7 - - - +
273B ASP* 3.9 19.3 - - + +
274B ASN* 1.3 74.5 - - - +
276B LEU* 1.3 62.6 + - - +
277B ARG* 3.0 29.0 + - + -
305B SER* 3.9 1.4 + - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B THR* 4.6 9.6 - - + -
247B LYS 2.9 15.3 + - - +
248B VAL* 3.3 11.1 - - + +
249B MET 2.8 26.9 + - - +
274B ASN 3.8 4.2 + - - +
275B ILE* 1.3 72.8 - - - +
277B ARG* 1.3 59.4 + - - +
278B PHE* 4.8 1.3 - - + -
305B SER* 3.7 10.1 - - - +
311B TYR* 3.9 29.2 - - + +
335B ILE* 3.7 37.7 - - + -
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ILE* 5.8 1.6 - - - -
249B MET* 3.4 17.9 - - + +
251B VAL* 5.6 1.8 - - + -
267B ILE* 4.1 20.1 - - - +
270B CYS* 3.6 34.4 - - - +
271B ASN* 2.9 38.0 + - - +
275B ILE* 3.0 31.8 + - + +
276B LEU* 1.3 76.3 - - - +
278B PHE* 1.3 65.4 + - - +
302B ALA 5.4 0.4 + - - -
303B ILE* 2.8 39.2 + - + +
304B ALA* 3.6 3.5 + - - -
305B SER* 2.9 52.4 + - - +
306B ILE* 5.1 2.8 - - - +
311B TYR* 3.2 13.1 - - - +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 4.0 24.9 - - + -
249B MET 2.9 9.5 + - - +
250B VAL* 3.6 14.1 - - + -
251B VAL* 2.8 31.6 + - - +
276B LEU* 4.4 3.6 - - + -
277B ARG* 1.3 77.5 - - - +
279B GLY* 1.3 59.4 + - - +
280B ILE* 5.2 4.0 - - + -
303B ILE* 5.5 0.4 - - - -
304B ALA* 4.9 0.2 - - - -
310B ARG 3.8 2.2 - - - -
311B TYR* 3.2 47.6 - + - +
313B PHE* 4.3 6.5 - + + -
328B LEU* 3.7 24.2 - - + -
331B GLN* 3.6 31.2 - - + -
332B ILE* 3.9 24.2 - - + -
335B ILE* 4.5 13.0 - - + -
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Residues in contact with GLY 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 3.5 8.1 - - - -
278B PHE* 1.3 73.7 - - - +
280B ILE* 1.3 63.9 + - - +
300B ILE* 3.5 21.8 - - - -
303B ILE* 4.9 2.9 - - - -
304B ALA* 4.1 10.9 - - - +
311B TYR 2.9 9.5 + - - +
312B PHE* 3.5 4.7 - - - -
313B PHE* 2.9 26.3 + - - +
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Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.8 31.0 - - + -
250B VAL* 4.4 6.5 - - + -
251B VAL 2.6 17.1 + - - +
252B VAL* 3.5 16.6 - - + +
253B THR* 3.2 25.6 + - - +
278B PHE* 5.2 2.2 - - + -
279B GLY* 1.3 77.8 - - - +
281B ALA* 1.3 66.0 + - - +
282B VAL* 3.7 0.8 + - + +
300B ILE* 3.7 4.6 - - - +
313B PHE* 3.4 25.8 - - + +
315B VAL* 4.5 8.3 - - + -
321B LEU* 3.8 23.1 - - + -
324B LYS* 5.7 3.1 - - + -
328B LEU* 4.0 20.6 - - + -
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B THR 3.7 4.5 - - - -
280B ILE* 1.3 72.3 - - - +
282B VAL* 1.3 60.1 + - - +
283B LEU* 3.7 6.1 + - + +
296B LEU* 4.0 15.7 - - + -
297B ILE* 4.7 5.8 - - + -
300B ILE* 4.0 23.0 - - + +
312B PHE* 4.0 19.1 - - + -
313B PHE 2.9 9.2 + - - +
314B ASN* 3.4 5.3 - - + +
315B VAL* 2.9 27.7 + - - +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ILE* 4.7 7.0 - - + -
252B VAL* 4.0 22.0 - - + -
253B THR 2.9 27.6 + - - +
254B ASP* 3.2 36.1 - - + +
280B ILE* 4.5 0.9 - - + +
281B ALA* 1.3 73.0 - - - +
283B LEU* 1.3 81.3 + - - +
285B TYR 5.1 0.2 + - - -
286B LEU 5.7 0.2 + - - -
296B LEU* 4.0 4.0 - - - +
315B VAL* 3.6 11.2 - - + +
317B ASP 4.0 4.7 - - - +
318B GLU* 3.9 34.1 - - + +
321B LEU* 4.9 11.2 - - + -
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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
------------------------------------------------------------
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