Contacts of the helix formed by residues 327 - 334 (chain B) in PDB entry 2WFD
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 327 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311B MSE 4.7 9.5 - - + -
312B LYS 3.6 22.7 - - - +
313B TYR* 4.2 2.4 - - - +
314B ILE* 4.8 0.2 - - - -
326B CYS* 1.3 82.2 - - - +
328B GLN* 1.3 62.9 + - + +
329B LYS* 3.9 17.5 - - + +
330B ALA* 3.1 9.0 + - - +
331B ALA* 3.0 24.4 + - - +
382B GLU* 5.0 16.0 - - + +
385B GLY 4.8 1.6 + - - -
386B THR 3.0 21.9 + - - -
387B GLY* 3.7 8.5 - - - -
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Residues in contact with GLN 328 (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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312B LYS 4.7 2.2 + - - +
313B TYR 5.2 0.2 - - - -
314B ILE* 3.5 42.3 - - + +
326B CYS 3.8 1.0 + - - -
327B THR* 1.3 77.5 - - + +
329B LYS* 1.3 57.3 + - - +
331B ALA* 3.4 7.5 + - + +
332B ARG* 3.0 33.9 + - - +
346B VAL* 5.5 5.4 - - + +
348B VAL* 4.8 14.0 - - + +
351B GLU* 5.5 1.4 - - - +
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Residues in contact with LYS 329 (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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465A GLU* 5.7 4.5 - - - -
327B THR* 3.9 13.3 - - + +
328B GLN* 1.3 77.2 - - - +
330B ALA* 1.3 63.8 + - - +
332B ARG* 3.5 7.2 - - - +
333B ASN* 3.4 19.6 + - - +
382B GLU* 3.6 25.8 + - + +
383B ASP* 3.6 26.0 + - - +
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Residues in contact with ALA 330 (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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326B CYS* 3.9 10.8 - - - -
327B THR* 3.1 15.1 + - - +
329B LYS* 1.3 76.4 - - - +
331B ALA* 1.3 65.5 + - - +
333B ASN* 3.3 5.7 + - - +
334B MSE 3.0 28.6 + - + +
385B GLY 4.0 8.0 + - - +
386B THR* 3.8 30.5 - - - -
507B TYR* 4.0 13.3 + - - +
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Residues in contact with ALA 331 (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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314B ILE* 4.6 1.8 - - + -
316B PHE* 3.5 42.9 - - + -
326B CYS* 4.0 0.6 - - - -
327B THR 3.0 11.8 + - - +
328B GLN* 3.5 12.6 - - - +
329B LYS 3.3 0.2 - - - -
330B ALA* 1.3 76.7 - - - +
332B ARG* 1.3 52.0 + - - +
334B MSE 2.9 7.6 + - - +
335B SER* 2.8 33.3 + - - -
346B VAL* 4.1 18.2 - - + +
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Residues in contact with ARG 332 (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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328B GLN* 3.0 18.3 + - - +
329B LYS* 3.5 12.1 - - - +
331B ALA* 1.3 74.3 - - - +
333B ASN* 1.3 63.0 + - - +
335B SER* 2.5 26.7 + - - -
336B TYR* 3.3 42.5 + - + -
344B GLY* 2.9 31.2 + - - -
346B VAL* 3.9 32.1 - - + +
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Residues in contact with ASN 333 (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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465A GLU* 5.7 1.6 - - - +
469A LEU* 3.6 23.9 - - - +
329B LYS 3.4 8.4 + - - +
330B ALA* 3.3 9.8 + - - +
331B ALA 3.3 0.2 - - - -
332B ARG* 1.3 80.1 - - - +
334B MSE 1.3 62.5 + - - +
336B TYR* 3.4 13.3 + - - -
337B GLN* 3.2 17.8 + - - +
507B TYR* 3.1 24.9 + - - +
508B MSE 2.8 29.5 + - - +
509B GLU* 4.0 11.6 - - - +
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Residues in contact with MSE 334 (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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266B LEU* 3.4 29.4 - - + -
290B VAL* 3.6 17.3 - - + -
316B PHE* 4.0 21.5 - - + -
324B PHE* 4.6 4.9 - - - -
326B CYS* 4.1 12.8 - - - -
330B ALA* 3.0 18.5 + - + +
331B ALA* 2.9 11.3 + - - +
333B ASN* 1.3 74.3 - - - +
335B SER* 1.3 64.0 + - - +
337B GLN* 3.1 20.0 + - - +
339B PHE* 3.2 50.4 + - + +
386B THR* 3.8 17.9 - - + -
507B TYR* 3.5 21.1 - - + -
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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