Contacts of the strand formed by residues 292 - 300 (chain F) in PDB entry 6Q2J
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 VAL 292 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291F THR* 1.3 81.0 - - - +
293F VAL* 1.3 67.0 + - - +
294F ALA 4.6 0.7 - - - +
295F THR* 3.8 22.0 - - - +
355F ARG* 4.2 33.9 - - + +
356F LEU 3.7 6.1 - - - +
357F VAL* 4.9 5.6 - - + -
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Residues in contact with VAL 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F ALA* 3.3 32.9 - - + +
283F VAL* 4.1 20.9 - - + -
291F THR* 3.6 14.6 - - + +
292F VAL* 1.3 78.1 - - - +
294F ALA* 1.3 62.4 + - + +
329F PHE* 4.1 20.6 - - + -
356F LEU* 3.0 21.0 + - + +
358F LEU* 4.4 10.3 - - + -
395F VAL* 3.8 24.9 - - + -
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F ALA* 4.2 17.5 - - + +
280F SER 4.8 0.2 - - - -
281F ALA* 4.1 15.5 - - + +
292F VAL* 4.0 0.4 - - - -
293F VAL* 1.3 84.1 + - + +
295F THR* 1.3 64.7 + - - +
355F ARG* 3.3 5.2 - - - +
356F LEU* 3.2 24.7 + - + +
393F PHE* 3.6 28.3 - - + -
395F VAL* 5.6 1.1 - - + -
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Residues in contact with THR 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F ALA* 3.8 9.5 - - - +
292F VAL* 3.8 18.9 - - - +
294F ALA* 1.3 79.7 + - - +
296F LEU* 1.3 79.6 + - - +
297F ARG* 5.2 3.4 - - + -
353F ASP* 5.0 6.7 - - + +
354F TYR 3.3 12.8 - - - +
355F ARG* 3.8 26.0 + - - +
393F PHE* 4.1 0.6 - - - -
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Residues in contact with LEU 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F PHE* 5.3 0.2 - - + -
276F VAL* 3.7 27.4 - - + +
277F ASP 3.9 18.6 - - - +
278F THR 4.0 2.2 - - - +
279F ALA* 3.7 22.7 - - + +
295F THR* 1.3 79.8 - - - +
297F ARG* 1.3 67.5 + - - +
353F ASP* 3.6 3.3 - - - -
354F TYR* 2.9 35.0 + - - +
391F LEU* 3.7 38.4 - - + -
392F HIS 3.8 4.9 - - - +
393F PHE* 3.6 30.7 - - + -
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Residues in contact with ARG 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F PHE* 4.5 5.5 - - - -
273F PRO* 3.3 35.7 - - + +
276F VAL 5.3 1.7 - - - +
295F THR* 5.2 5.2 - - + -
296F LEU* 1.3 78.9 - - - +
298F VAL* 1.3 67.6 + - - +
351F VAL* 3.4 35.8 - - + +
352F HIS 3.2 6.1 - - - +
353F ASP* 3.3 19.9 + - - +
391F LEU* 5.3 0.3 - - - +
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Residues in contact with VAL 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F PRO* 3.7 29.4 - - + -
271F THR 4.3 4.0 - - - +
272F PHE* 5.0 0.7 - - + +
273F PRO* 5.0 0.7 - - - -
297F ARG* 1.3 79.7 - - - +
299F PHE* 1.3 63.8 + - - +
351F VAL* 3.4 7.7 - - - +
352F HIS* 2.9 49.9 + - + -
354F TYR* 3.7 26.2 - - + -
376F VAL* 4.8 7.9 - - + -
389F LEU* 3.7 23.1 - - + -
391F LEU* 4.3 15.5 - - + -
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Residues in contact with PHE 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F ALA 4.4 0.3 - - - +
270F PRO* 3.4 2.4 - - - +
271F THR* 2.8 52.8 + - - +
272F PHE 4.8 7.4 - - - +
273F PRO* 4.7 8.6 - - + +
298F VAL* 1.3 73.7 - - - +
300F ASP* 1.3 69.2 + - - +
301F ALA* 4.5 10.8 - - + -
338F THR* 5.6 3.8 - - + -
340F VAL* 4.6 25.1 - - + -
349F ALA* 3.9 25.8 - - + -
350F THR 3.8 1.1 - - - -
351F VAL* 4.0 23.8 - - + -
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Residues in contact with ASP 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F SER 3.0 10.5 - - - +
269F ALA 4.4 1.6 - - - +
270F PRO* 4.5 7.6 - - + -
299F PHE* 1.3 78.5 - - - +
301F ALA* 1.3 65.8 + - - +
302F ASP* 2.9 17.2 + - - +
314F TYR* 3.8 10.4 + - - -
349F ALA* 3.3 4.2 - - - +
350F THR* 2.9 48.3 + - - +
352F HIS* 3.9 12.3 + - + +
378F ASP* 2.2 30.6 - - - +
708F CA 2.3 19.0 - - - -
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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