Contacts of the strand formed by residues 280 - 286 (chain B) in PDB entry 7REQ
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 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B VAL* 3.4 21.3 - - + -
236B ILE* 3.5 29.6 - - + -
259B GLY 4.6 2.2 - - - +
262B TYR* 4.4 16.2 - - + -
263B VAL* 3.9 22.9 - - + -
266B LEU* 4.5 6.1 - - + -
276B ALA 3.2 24.9 - - - +
277B PHE 3.4 6.0 + - - +
278B ASP 3.6 0.4 - - - -
279B THR* 1.3 83.1 - - + +
281B ASN* 1.3 70.0 + - - +
282B PHE* 4.4 7.5 - - + -
304B TRP* 4.4 19.1 + - + -
321B ARG* 3.2 20.8 + - - +
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Residues in contact with ASN 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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163B LYS* 5.1 3.8 - - - +
196B ASN* 4.0 7.6 - - - +
232B ARG* 3.3 27.6 - - + +
234B VAL 2.7 11.5 + - - +
235B THR* 3.2 10.2 - - - +
236B ILE* 2.8 33.4 + - - +
279B THR 4.0 0.4 + - - -
280B ILE* 1.3 73.7 - - - +
282B PHE* 1.3 58.9 + - - +
321B ARG* 2.9 45.7 + - - +
323B ASN* 3.1 31.1 + - - +
356B GLU* 6.1 0.8 - - - +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B THR* 4.2 3.1 - - - -
236B ILE* 3.6 23.1 - - + +
238B ALA* 5.8 0.2 - - + -
255B ALA* 3.6 44.2 - - + -
256B LEU* 4.6 1.1 - - + -
280B ILE* 4.4 7.6 - - + -
281B ASN* 1.3 76.4 - - - +
283B ARG* 1.3 59.0 + - - +
284B VAL* 3.7 15.8 + - + -
300B LEU* 3.8 20.2 - - + -
304B TRP* 3.7 53.8 - + + -
320B ALA* 4.0 11.7 - - + -
321B ARG 3.0 19.4 + - - +
322B GLN* 3.6 4.4 - - + -
323B ASN* 2.9 29.5 + - - +
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Residues in contact with ARG 283 (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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137B LEU* 3.6 27.7 - - - +
165B GLU* 3.9 10.7 + - - -
167B PHE* 3.3 38.1 - - - +
198B GLY* 5.4 3.0 + - - -
235B THR* 3.6 32.5 + - + +
236B ILE 2.8 12.5 + - - +
237B ASP* 3.0 41.5 + - - +
238B ALA* 2.9 28.2 + - - +
239B ASN* 3.6 6.2 + - + -
282B PHE* 1.3 71.2 - - - +
284B VAL* 1.3 60.8 + - - +
323B ASN* 3.3 15.3 - - + +
325B ILE* 4.1 36.1 - - + -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA* 4.8 5.2 - - + -
239B ASN* 4.6 0.9 - - - -
251B GLU* 3.4 13.0 - - + +
282B PHE* 3.7 14.6 + - + -
283B ARG* 1.3 78.1 - - - +
285B THR* 1.3 59.3 + - - +
296B ARG* 4.4 5.8 - - + +
297B LEU* 3.6 26.5 - - + -
300B LEU* 3.9 19.5 - - + -
322B GLN* 3.5 29.6 - - + +
323B ASN 3.0 8.6 + - - +
324B ALA* 3.2 19.8 - - + -
325B ILE* 2.9 29.1 + - - +
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Residues in contact with THR 285 (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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239B ASN* 2.7 32.5 + - - +
242B HIS* 3.3 29.1 - - + +
251B GLU* 2.7 33.3 + - - -
284B VAL* 1.3 76.2 - - - +
286B ALA* 1.3 70.2 + - - +
287B THR* 4.2 1.1 - - + -
296B ARG* 2.8 36.5 + - - -
297B LEU* 4.3 5.4 - - - +
324B ALA* 5.2 0.2 - - - -
325B ILE 3.4 8.5 - - - +
327B SER* 3.8 8.5 - - - -
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Residues in contact with ALA 286 (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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284B VAL 3.9 0.4 + - - -
285B THR* 1.3 73.4 - - - +
287B THR* 1.3 59.9 + - - +
293B THR* 3.7 10.1 - - + -
297B LEU* 5.7 0.2 - - - -
324B ALA* 4.5 4.9 - - + -
325B ILE 2.9 14.2 + - - +
326B THR* 3.3 7.9 - - + -
327B SER 3.0 23.0 + - - -
346B ALA* 3.5 33.9 - - + +
350B ALA* 3.8 18.6 - - + -
358B ILE* 6.0 0.4 - - + -
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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