Contacts of the strand formed by residues 278 - 285 (chain F) in PDB entry 4BQ7
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 278 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F LEU* 4.2 25.8 - - + -
220F PHE* 5.3 0.6 - - + -
271F MET 3.8 0.7 - - - +
272F HIS* 3.9 0.3 - - - -
273F ALA* 2.9 37.6 + - + +
276F ILE* 2.7 40.5 + - + +
277F GLY* 1.4 71.7 - - - +
279F THR* 1.3 73.1 + - - +
280F VAL* 4.3 9.4 - - + -
293F ILE* 4.4 3.6 - - + -
294F ARG 3.3 10.5 - - - +
295F MET* 3.3 22.4 - - + +
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Residues in contact with THR 279 (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 GLU* 4.7 0.4 - - + +
271F MET 3.4 11.0 - - - +
272F HIS* 4.0 24.0 + - + +
274F ARG* 5.2 3.1 + - - -
277F GLY 4.4 1.8 + - - -
278F THR* 1.3 75.1 + - - +
280F VAL* 1.3 69.7 + - - +
281F PHE* 3.4 40.3 - - + -
292F ALA 4.5 0.2 - - - -
293F ILE* 3.4 4.5 - - - +
294F ARG* 2.9 56.3 + - - +
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F LEU* 4.8 4.5 - - + -
197F VAL* 5.4 0.9 - - + -
218F ILE* 3.9 28.9 - - + -
220F PHE* 4.4 18.4 - - + -
269F VAL 3.9 0.9 - - - +
270F GLU* 3.5 3.3 - - - +
271F MET* 2.9 47.0 + - + +
278F THR* 4.3 14.6 - - + -
279F THR* 1.3 79.0 - - - +
281F PHE* 1.3 60.8 + - - +
282F VAL* 4.2 3.8 - - + -
291F LEU* 3.5 30.1 - - + -
292F ALA 3.4 3.8 - - - +
293F ILE* 4.3 13.0 - - + -
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Residues in contact with PHE 281 (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 TYR* 3.9 29.2 - + + -
269F VAL 3.7 2.2 - - - -
270F GLU* 3.3 38.4 - - + -
272F HIS* 5.5 0.2 - + - -
279F THR* 3.4 31.9 - - + -
280F VAL* 1.3 73.1 - - - +
282F VAL* 1.3 63.1 + - - +
290F THR 3.9 0.2 - - - +
291F LEU* 3.4 7.1 - - - +
292F ALA* 2.8 58.3 + - + +
294F ARG* 5.3 10.8 - - + -
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Residues in contact with VAL 282 (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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216F ILE* 4.1 24.5 - - + -
218F ILE* 4.3 1.3 - - + -
232F TYR* 4.5 7.4 - - + +
234F ALA* 4.1 18.8 - - + -
239F LEU* 3.9 20.1 - - + +
268F TYR* 3.4 2.3 - - - -
269F VAL* 2.9 36.6 + - + +
271F MET* 4.1 20.2 - - + -
280F VAL* 4.2 2.2 - - + -
281F PHE* 1.3 79.2 - - - +
283F ARG* 1.3 66.5 + - - +
289F LEU* 5.1 1.6 - - + -
290F THR 3.5 8.5 - - - +
291F LEU* 3.7 19.7 - - + -
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Residues in contact with ARG 283 (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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239F LEU* 3.7 11.7 - - - -
268F TYR* 3.2 61.2 + - + +
282F VAL* 1.3 75.5 - - - +
284F GLN* 1.3 63.1 + - - +
285F VAL* 3.6 30.3 - - + +
289F LEU* 3.4 5.8 - - - +
290F THR* 2.8 49.6 + - - +
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Residues in contact with GLN 284 (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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236F THR* 3.9 8.8 - - - +
237F ASP* 2.8 49.0 + - - +
239F LEU* 3.8 18.5 - - + +
283F ARG* 1.3 79.5 + - - +
285F VAL* 1.3 60.5 + - - +
286F GLY 2.8 29.6 + - - +
287F ARG* 3.5 6.9 - - - +
288F TYR 3.3 13.0 - - - +
289F LEU* 3.9 10.3 - - + -
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Residues in contact with VAL 285 (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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283F ARG* 3.6 43.2 + - + +
284F GLN* 1.3 71.5 - - - +
286F GLY* 1.3 63.2 + - - +
287F ARG 3.4 0.5 + - - -
288F TYR* 2.8 27.7 + - - +
290F THR* 3.8 26.9 - - + -
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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