Contacts of the strand formed by residues 286 - 291 (chain B) in PDB entry 2DW1
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 ASN 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B VAL* 3.7 17.7 - - + -
201B GLU 3.3 2.4 + - - -
202B LEU* 3.4 17.1 - - + +
203B VAL 2.9 23.0 + - - -
274B ARG* 3.6 2.2 - - - +
284B HIS* 3.3 9.9 - - - -
285B ASP* 1.3 78.9 - - - +
287B ALA* 1.3 64.6 + - - +
288B GLN* 2.9 20.7 + - - +
307B MET* 3.5 13.7 - - + +
313B SER* 3.2 24.6 + - - -
335B MET* 3.6 12.2 - - - +
338B ASN* 3.1 27.2 + - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 4.1 0.4 - - - -
203B VAL 3.1 11.2 - - - +
205B VAL* 5.3 0.2 - - + -
270B PHE* 3.9 11.0 - - + -
274B ARG* 3.9 27.8 - - + +
278B LEU* 4.4 7.0 - - + -
284B HIS* 4.0 8.3 - - + +
286B ASN* 1.3 78.2 - - - +
288B GLN* 1.3 66.2 + - - +
313B SER 3.3 4.8 + - - -
314B THR* 3.2 30.9 - - + -
315B GLY 3.4 2.6 + - - -
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 3.7 10.1 - - + -
203B VAL 3.1 7.5 + - - -
204B LEU* 3.6 20.7 - - + +
205B VAL 3.0 24.3 + - - +
270B PHE* 3.8 3.6 - - - -
286B ASN* 2.9 22.9 - - - +
287B ALA* 1.3 80.5 - - - +
289B LEU* 1.3 60.6 + - - +
315B GLY* 3.0 33.0 + - - -
316B ILE 3.8 0.8 - - - +
317B ILE* 4.0 20.7 - - + +
331B MET* 4.5 4.5 - - + -
334B GLU* 3.8 15.0 - - - +
335B MET* 3.7 16.0 + - + +
338B ASN* 3.0 19.4 - - - +
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Residues in contact with LEU 289 (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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205B VAL* 3.3 35.7 - - + +
207B ASP* 4.3 6.5 - - + +
251B TRP* 4.2 11.4 - - + -
257B ILE* 4.0 12.1 - - + -
259B VAL* 5.0 8.1 - - + -
266B THR* 4.0 26.5 - - + -
270B PHE* 3.5 39.3 - - + -
288B GLN* 1.3 71.0 - - - +
290B LEU* 1.3 72.3 + - - +
291B THR* 3.8 4.5 + - + +
315B GLY 3.0 9.5 + - - -
316B ILE* 3.5 9.2 - - + +
317B ILE* 2.8 30.8 + - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.5 5.2 - - + -
205B VAL 2.6 16.6 + - - +
206B VAL* 3.7 4.4 - - + -
207B ASP* 3.0 30.7 + - - +
210B MET* 3.3 35.1 - - + +
224B ARG* 5.8 0.7 - - - +
225B MET* 3.3 37.0 - - + -
228B ILE* 5.5 0.9 - - + -
288B GLN 3.8 1.0 + - - -
289B LEU* 1.3 74.5 - - - +
291B THR* 1.3 60.7 + - - +
317B ILE* 3.4 29.2 - - + +
319B ASP* 4.9 10.1 - - + +
327B VAL* 4.8 11.4 - - + -
331B MET* 4.1 20.2 - - + -
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Residues in contact with THR 291 (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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207B ASP* 2.5 27.6 + - - -
210B MET* 4.1 4.3 - - - -
259B VAL* 3.4 10.8 - - + +
266B THR* 5.9 1.1 - - + -
289B LEU* 4.9 7.9 - - + +
290B LEU* 1.3 75.0 - - - +
292B ALA* 1.3 59.6 + - - +
293B ILE* 3.1 36.2 + - + +
295B LEU* 4.5 13.0 - - + -
316B ILE* 5.7 3.8 - - + -
317B ILE 2.9 19.4 + - - +
318B GLN* 3.3 5.7 - - - +
319B ASP 2.9 23.7 + - - -
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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
------------------------------------------------------------
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