Contacts of the helix formed by residues 327 - 334 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A MSE 4.6 11.1 - - + -
312A LYS 3.6 22.7 - - - +
313A TYR* 4.2 2.1 - - - +
314A ILE* 4.8 0.2 - - - -
326A CYS* 1.3 82.4 - - - +
328A GLN* 1.3 62.8 + - + +
329A LYS* 3.9 17.0 - - + +
330A ALA* 3.2 8.2 + - - +
331A ALA* 3.0 23.4 + - - +
382A GLU* 4.9 15.9 - - + +
385A GLY 4.7 2.0 + - - -
386A THR 3.0 22.4 + - - -
387A GLY* 3.6 8.7 + - - -
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Residues in contact with GLN 328 (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 LYS 4.8 2.2 + - - +
313A TYR 5.2 0.2 - - - -
314A ILE* 3.3 41.8 - - + +
326A CYS 3.8 0.8 + - - -
327A THR* 1.3 74.4 - - + +
329A LYS* 1.3 64.5 + - - +
331A ALA* 3.4 8.0 + - + +
332A ARG* 3.1 28.9 + - - +
346A VAL* 5.5 4.8 - - + +
348A VAL* 4.7 15.4 - - + +
351A GLU* 5.4 1.9 - - - +
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Residues in contact with LYS 329 (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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327A THR* 3.9 13.1 - - + +
328A GLN* 1.3 77.1 - - - +
330A ALA* 1.3 64.8 + - - +
332A ARG* 3.5 8.0 - - - +
333A ASN* 3.4 19.2 + - - +
382A GLU* 3.6 20.2 + - + +
383A ASP* 3.7 32.3 + - - +
465B GLU* 5.8 3.4 - - - -
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Residues in contact with ALA 330 (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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326A CYS* 3.9 10.3 - - - -
327A THR* 3.2 15.2 + - - +
329A LYS* 1.3 76.6 - - - +
331A ALA* 1.3 66.3 + - - +
333A ASN* 3.2 6.4 + - - +
334A MSE 2.9 27.5 + - + +
385A GLY 4.1 7.4 + - - +
386A THR* 3.8 32.3 - - + -
507A TYR* 4.1 13.3 + - - +
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Residues in contact with ALA 331 (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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314A ILE* 4.7 2.0 - - + -
316A PHE* 3.5 40.5 - - + -
326A CYS* 4.0 0.8 - - - -
327A THR 3.0 12.4 + - - +
328A GLN* 3.5 12.3 - - - +
330A ALA* 1.3 76.3 - - - +
332A ARG* 1.3 53.3 + - - +
334A MSE 2.8 8.6 + - - +
335A SER* 2.8 33.4 + - - -
346A VAL* 4.0 19.5 - - + +
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Residues in contact with ARG 332 (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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328A GLN* 3.1 16.2 + - - +
329A LYS* 3.5 13.0 - - - +
331A ALA* 1.3 76.8 - - - +
333A ASN* 1.3 62.6 - - - +
335A SER* 2.6 26.6 + - - -
336A TYR* 3.4 45.5 + - + -
344A GLY* 3.1 30.2 + - - -
346A VAL* 3.9 29.8 - - + +
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Residues in contact with ASN 333 (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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329A LYS 3.4 8.8 + - - +
330A ALA* 3.2 10.0 + - - +
332A ARG* 1.3 80.8 - - - +
334A MSE 1.3 60.9 + - - +
336A TYR* 3.4 14.9 + - - +
337A GLN* 3.0 22.1 + - - +
507A TYR* 3.1 25.7 + - - +
508A MSE 2.8 27.5 + - - +
509A GLU* 3.9 12.2 - - - +
469B LEU* 3.4 22.5 - - - +
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Residues in contact with MSE 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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266A LEU* 3.3 30.7 - - + -
290A VAL* 3.5 19.3 - - + -
316A PHE* 3.8 28.7 - - + -
324A PHE* 4.5 4.0 - - - -
326A CYS* 4.1 8.1 - - - -
330A ALA* 2.9 17.8 + - + +
331A ALA* 2.8 14.8 + - - +
333A ASN* 1.3 70.9 - - - +
335A SER* 1.3 61.5 + - - +
336A TYR 3.1 0.4 - - - -
337A GLN* 3.1 19.4 + - - +
339A PHE* 3.1 48.3 + - + +
386A THR* 4.0 16.2 - - + -
507A TYR* 3.6 19.3 - - + -
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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