Contacts of the strand formed by residues 333 - 339 (chain A) in PDB entry 2W8B
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 GLN 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A ARG* 2.7 45.7 + - - +
312A PRO* 3.4 38.8 - - - +
313A GLN* 3.6 3.0 - - - +
330A GLU 3.9 0.7 + - - +
331A GLY 3.6 1.8 - - - -
332A SER* 1.3 75.7 + - - +
334A ASN* 1.3 73.1 + - - +
335A GLN* 2.7 28.6 + - - +
349A VAL 4.6 0.2 - - - -
350A SER* 3.7 1.0 + - - -
351A SER* 2.9 43.7 + - - -
113H GLY* 5.2 6.7 - - - -
117H TYR* 5.8 0.4 - - - -
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A PRO 3.0 7.4 + - - -
313A GLN* 2.9 52.2 + - - +
314A VAL* 3.9 2.0 - - + -
328A THR* 3.7 27.6 - - + +
329A TRP 4.4 0.2 - - - -
330A GLU* 2.8 29.7 + - - +
333A GLN* 1.3 76.1 - - - +
335A GLN* 1.3 66.7 + - - +
348A MET* 3.4 17.4 - - - +
349A VAL 3.4 5.8 - - - +
350A SER* 2.7 30.5 + - - -
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.9 0.4 - - - +
305A THR* 3.4 24.5 - - + -
312A PRO* 4.0 3.4 - - + -
314A VAL* 3.8 11.5 - - - +
333A GLN* 2.7 38.6 + - - +
334A ASN* 1.3 77.5 - - - +
336A ASP* 1.3 72.3 + - + +
337A ALA 3.5 2.0 - - - -
348A MET* 3.7 1.9 - - - +
349A VAL* 3.0 36.4 + - + +
351A SER* 4.3 6.0 + - - -
113H GLY* 4.0 7.3 - - - -
114H THR* 2.9 45.8 + - + +
117H TYR* 3.8 17.8 - - - +
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.1 37.8 + - - +
305A THR* 2.8 15.1 + - - -
335A GLN* 1.3 76.6 - - - +
337A ALA* 1.3 63.1 + - - +
348A MET* 3.9 1.0 - - - -
349A VAL* 3.7 2.2 - - + +
379A THR* 2.8 44.3 + - - +
380A PRO* 3.6 20.4 - - - +
114H THR* 3.6 22.4 - - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 4.6 8.3 + - - +
293A PRO 5.1 0.2 - - - +
294A THR* 3.3 26.9 - - + +
303A ALA* 4.8 0.2 - - + -
304A PHE* 5.4 1.8 - - - +
305A THR* 4.7 1.2 + - - -
314A VAL* 3.9 24.9 - - + -
336A ASP* 1.3 77.4 - - - +
338A ASP* 1.3 62.0 + - - +
346A MET* 3.9 24.0 - - - -
347A VAL 3.3 11.7 - - - +
348A MET* 4.1 3.4 - - + -
380A PRO 5.2 0.2 - - - +
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Residues in contact with ASP 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A THR* 3.4 13.6 + - - -
337A ALA* 1.3 76.3 - - - +
339A VAL* 1.3 67.9 + - - +
346A MET* 3.3 3.5 - - - -
347A VAL* 2.9 38.2 + - + -
380A PRO 3.6 20.2 - - - +
381A SER* 3.5 4.7 + - - -
382A LEU* 2.7 42.7 + - - +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A THR* 3.0 28.4 + - + +
295A TRP 3.5 24.4 - - - +
296A PHE* 4.2 28.9 - - + -
303A ALA* 3.9 16.4 - - + -
338A ASP* 1.3 80.5 + - - +
340A SER* 1.3 75.8 + - - +
341A SER* 4.7 0.2 - - - -
343A GLY* 4.2 11.9 - - - -
345A PHE 3.7 8.7 - - - +
346A MET* 3.9 12.3 - - + -
363A LEU* 4.3 4.7 - - + -
382A LEU* 4.0 4.2 - - - +
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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