Contacts of the helix formed by residues 336 - 347 (chain B) in PDB entry 1W1J
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 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ASP* 4.8 6.9 - - - +
335B SER* 1.3 73.5 - - - +
337B GLU* 1.3 71.8 + - + +
339B LEU* 3.5 3.0 + - - +
340B ASP* 3.2 22.9 + - - +
350B ARG* 3.4 40.6 + - - +
444B LYS* 4.6 16.5 + - - -
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Residues in contact with GLU 337 (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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335B SER* 3.4 18.0 + - - +
336B ASP* 1.3 88.4 + - + +
338B GLU* 1.3 58.5 + - + +
339B LEU 3.2 0.2 - - - -
340B ASP* 3.2 13.5 + - - +
341B LYS* 3.1 33.5 + - - +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR 6.1 0.4 - - - +
328B SER* 3.5 23.4 + - - -
330B ARG* 3.3 32.5 + - - -
334B LEU* 4.6 12.6 - - + -
335B SER* 2.6 37.0 + - - +
336B ASP 3.3 0.8 - - - -
337B GLU* 1.3 77.4 - - + +
339B LEU* 1.3 59.1 + - - +
341B LYS* 3.7 27.7 - - + +
342B ILE* 3.4 30.0 + - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B HIS* 4.4 15.9 - - + +
314B ILE* 4.4 8.6 - - + +
315B LEU* 3.5 37.2 - - + -
334B LEU* 3.9 27.6 - - + +
335B SER 3.3 18.4 + - - +
336B ASP* 3.9 3.4 - - - +
337B GLU 3.2 0.6 - - - -
338B GLU* 1.3 76.0 - - - +
340B ASP* 1.3 61.4 + - - +
341B LYS 3.1 0.9 - - - -
342B ILE* 3.3 6.1 + - + +
343B ALA* 2.9 27.4 + - - +
350B ARG* 3.6 40.9 - - - +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO 4.8 2.6 - - - +
285B LYS* 5.6 1.4 - - - -
336B ASP* 3.2 18.5 + - - +
337B GLU* 3.2 12.0 + - - +
339B LEU* 1.3 78.6 - - - +
341B LYS* 1.3 57.8 + - - +
343B ALA* 3.4 6.5 - - - +
344B LYS* 2.9 31.9 + - - +
350B ARG* 3.5 27.0 + - - +
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Residues in contact with LYS 341 (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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337B GLU* 3.1 16.9 + - - +
338B GLU* 3.7 36.0 - - + +
339B LEU 3.1 0.6 - - - -
340B ASP* 1.3 77.9 - - - +
342B ILE* 1.3 59.9 + - + +
344B LYS* 3.5 34.4 - - + +
345B GLN* 3.1 36.4 + - - +
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Residues in contact with ILE 342 (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* 4.1 9.9 - - + +
315B LEU* 4.3 12.6 - - + -
318B ALA* 3.8 24.2 - - + -
327B TYR* 3.7 45.8 - - + +
334B LEU* 4.1 20.0 - - + -
338B GLU 3.4 16.7 + - - +
339B LEU* 3.3 9.9 + - + +
341B LYS* 1.3 75.4 - - + +
343B ALA* 1.3 63.8 + - - +
345B GLN* 3.8 9.6 - - - +
346B LEU* 3.3 34.2 + - + +
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Residues in contact with ALA 343 (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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284B PRO 5.5 1.6 - - - +
314B ILE* 4.0 9.6 - - + +
339B LEU 2.9 16.3 + - - +
340B ASP* 3.4 11.7 - - - +
341B LYS 3.2 0.2 - - - -
342B ILE* 1.3 77.2 - - - +
344B LYS* 1.3 65.2 - - - +
345B GLN 3.3 0.2 + - - -
347B ASN* 3.2 16.1 + - - -
348B LEU 3.0 31.4 + - - +
349B GLY* 4.0 15.7 - - - +
350B ARG* 4.6 6.5 - - + +
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP 2.9 20.2 + - - +
341B LYS* 3.5 38.0 - - + +
343B ALA* 1.3 75.3 - - - +
345B GLN* 1.3 72.9 + - - +
347B ASN* 3.7 11.2 + - - +
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Residues in contact with GLN 345 (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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327B TYR* 3.6 31.8 - - - -
341B LYS* 3.1 30.3 + - - +
342B ILE* 3.5 12.5 - - - +
344B LYS* 1.3 88.7 - - - +
346B LEU* 1.3 65.4 + - + +
347B ASN* 3.2 5.4 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 4.5 2.9 - - + -
318B ALA* 4.0 25.1 - - + +
321B LEU* 3.8 27.6 - - + -
327B TYR* 4.1 13.5 - - + +
342B ILE* 3.3 35.5 + - + +
345B GLN* 1.3 83.7 - - + +
347B ASN* 1.3 67.8 + - - +
348B LEU* 3.6 29.0 + - + +
390B PRO* 5.3 7.3 - - - +
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Residues in contact with ASN 347 (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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282B THR* 4.0 7.8 - - - +
343B ALA 3.2 4.6 + - - -
344B LYS* 3.7 8.6 + - - +
345B GLN 3.2 8.1 + - - +
346B LEU* 1.3 80.3 - - - +
348B LEU* 1.3 64.6 + - - +
384B TYR* 3.7 32.2 + - + +
390B PRO* 5.7 11.4 - - + +
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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