Contacts of the helix formed by residues 330 - 338 (chain A) in PDB entry 2WOK
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 ASP 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ALA 3.4 0.8 + - - -
329A ALA* 1.3 68.5 - - - +
331A LYS* 1.3 59.0 + - - +
332A ILE 3.3 3.1 + - - -
333A LEU* 3.0 28.9 + - + +
334A LEU* 2.9 33.5 + - - +
372A ARG* 3.0 63.8 + - - +
412A SER* 3.1 21.8 + - - +
415A ARG* 3.7 12.2 + - - +
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Residues in contact with LYS 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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329A ALA* 4.2 18.4 - - + -
330A ASP* 1.3 72.2 - - - +
332A ILE* 1.3 58.4 + - - +
334A LEU* 3.6 4.8 + - - +
335A GLN* 3.0 29.3 + - - +
347A LEU* 3.8 21.6 - - + +
348A THR 2.9 30.5 + - - +
349A THR* 4.2 12.1 - - + +
367A THR* 3.7 30.5 - - + +
371A LEU* 3.1 19.1 + - + +
524A LEU* 4.8 5.1 - - + +
525A PRO 3.4 18.2 + - - +
526A LEU* 3.9 24.7 + - + +
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Residues in contact with ILE 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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330A ASP* 3.2 5.8 + - - +
331A LYS* 1.3 75.6 - - - +
333A LEU* 1.3 60.0 + - - +
335A GLN* 3.4 8.8 + - - +
336A ASP* 2.9 49.6 + - - +
347A LEU* 4.2 22.2 - - + -
370A ASP 3.7 21.3 - - - +
371A LEU* 4.0 17.9 - - + +
372A ARG* 3.9 25.6 - - - +
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Residues in contact with LEU 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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330A ASP* 3.0 29.5 + - + +
332A ILE* 1.3 77.9 - - - +
334A LEU* 1.3 57.5 + - - +
336A ASP* 3.4 11.7 + - + +
337A ALA* 2.9 26.7 + - - +
372A ARG* 4.3 10.5 - - - +
408A ALA* 3.8 31.2 - - + +
411A GLU* 3.7 39.5 - - + +
412A SER* 4.2 7.0 - - - +
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Residues in contact with LEU 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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305A HIS* 5.8 0.5 - - - -
329A ALA* 4.0 17.9 - - + -
330A ASP 2.9 28.5 + - - +
331A LYS* 3.9 6.3 - - + +
333A LEU* 1.3 75.8 - - - +
335A GLN* 1.3 64.7 + - - +
337A ALA* 3.2 4.5 + - - +
338A ARG* 3.2 21.0 + - - +
405A VAL* 3.6 19.2 - - + +
408A ALA* 3.4 24.7 - - + -
409A VAL* 3.6 30.1 - - + +
412A SER* 4.5 5.8 - - - +
524A LEU* 5.3 1.8 - - + -
526A LEU* 3.7 37.3 - - + +
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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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331A LYS 3.0 18.5 + - - +
332A ILE* 3.8 10.4 - - - +
334A LEU* 1.3 76.2 - - - +
336A ASP* 1.3 59.6 + - - +
338A ARG* 3.1 7.8 + - - +
339A GLY 3.0 12.5 + - - -
340A GLY* 2.9 23.7 + - - -
341A PRO* 5.7 3.6 - - - +
344A GLY* 3.3 20.0 + - - +
345A GLY 3.0 26.9 + - - -
347A LEU* 3.4 40.6 - - + +
526A LEU* 6.1 0.2 - - - +
527A VAL* 4.0 14.7 - - + +
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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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332A ILE* 2.9 35.9 + - - +
333A LEU* 3.5 12.7 - - + +
334A LEU 3.3 0.2 - - - -
335A GLN* 1.3 78.9 - - - +
337A ALA* 1.3 60.2 + - - +
339A GLY* 3.3 8.7 + - - -
340A GLY* 3.3 36.4 - - - +
341A PRO* 3.4 13.5 - - - +
372A ARG* 5.5 2.3 + - - -
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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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333A LEU 2.9 13.8 + - - +
334A LEU 3.5 9.4 - - - +
335A GLN 3.2 0.4 - - - -
336A ASP* 1.3 76.8 - - - +
338A ARG* 1.3 59.1 + - - +
339A GLY 3.4 0.4 + - - -
401A LYS* 4.6 3.6 - - - +
404A LEU* 3.5 55.1 - - + +
405A VAL* 3.9 10.4 - - - +
408A ALA* 4.0 8.1 - - + -
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Residues in contact with ARG 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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305A HIS* 3.5 25.4 - - + -
334A LEU 3.2 12.7 + - - +
335A GLN* 3.1 10.8 + - - +
337A ALA* 1.3 76.1 - - - +
339A GLY* 1.3 54.4 + - - +
343A ASN 4.1 2.6 - - - +
344A GLY* 3.7 12.1 - - - +
401A LYS* 4.4 17.6 - - - +
402A PHE* 3.7 21.6 - - - -
405A VAL* 3.9 12.3 - - + -
452A ASP* 2.7 25.6 + - - -
527A VAL* 4.5 8.3 - - + -
529A ASP* 2.4 46.3 + - - +
3B PRO* 5.7 1.2 - - - +
5B PHE* 5.3 5.3 - - - -
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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