Contacts of the strand formed by residues 283 - 287 (chain B) in PDB entry 2FQ6
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 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B LEU* 3.4 31.6 - - + +
278B ALA* 4.9 3.8 - - - +
280B HIS* 3.1 15.5 + - + +
281B PRO 3.2 0.6 - - - -
282B GLN* 1.3 79.3 - - - +
284B ALA* 1.3 63.7 + - - +
285B ARG 3.7 22.9 - - - +
286B VAL* 3.9 13.2 - - + -
313B PHE* 3.9 15.3 - - + -
314B VAL 3.8 5.2 - - - +
315B LEU* 4.6 0.4 - - - +
316B LYS* 3.5 13.2 - - - -
391B PHE* 3.5 33.2 - - + -
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Residues in contact with ALA 284 (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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283B VAL* 1.3 73.8 - - - +
285B ARG* 1.3 62.1 + - + +
314B VAL* 2.7 25.7 + - + +
315B LEU 3.8 13.9 - - - +
316B LYS* 3.8 21.9 - - + +
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Residues in contact with ARG 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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160B THR* 6.3 0.6 - - - +
283B VAL* 3.6 3.7 - - - +
284B ALA* 1.3 82.2 - - + +
286B VAL* 1.3 69.1 + - - +
287B ASN* 3.2 35.0 + - - +
293B GLY 5.0 12.1 - - - +
294B SER* 6.0 0.7 - - - +
295B LYS* 6.0 1.2 - - - +
313B PHE* 3.4 5.2 - - - +
314B VAL* 2.9 41.6 + - + +
365B ASP* 2.6 60.3 + - - +
366B PHE* 3.7 11.4 - - - +
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Residues in contact with VAL 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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274B ALA* 3.8 8.7 - - + +
277B LEU* 3.9 12.6 - - + -
278B ALA* 3.6 35.7 - - + +
283B VAL* 3.9 5.8 - - + -
285B ARG* 1.3 82.9 - - - +
287B ASN* 1.3 65.1 + - - +
288B HIS 3.5 6.4 + - - +
291B LEU* 3.7 28.3 - - + +
292B PRO 5.6 0.7 - - - +
293B GLY 5.0 1.4 - - - +
294B SER* 3.9 14.6 + - - -
311B PHE* 3.9 30.1 - - + -
312B SER 3.9 2.9 - - - +
313B PHE* 4.1 3.6 - - + -
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Residues in contact with ASN 287 (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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160B THR* 3.5 25.1 + - - +
161B MET* 3.3 11.9 - - + +
285B ARG* 3.2 35.3 + - - +
286B VAL* 1.3 70.0 - - - +
288B HIS* 1.3 59.5 + - - +
289B PRO 4.2 0.7 - - - -
294B SER* 3.5 11.7 + - - +
295B LYS 5.8 0.9 + - - -
311B PHE* 3.4 0.7 - - - +
312B SER* 2.7 54.6 + - - +
313B PHE* 4.5 0.2 - - - +
314B VAL* 4.0 14.3 - - - +
370B LEU* 4.0 16.0 - - - +
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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