Contacts of the helix formed by residues 343 - 348 (chain B) in PDB entry 4WB7
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 VAL 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B VAL* 3.6 29.4 - - + -
210B GLU* 3.9 39.7 - - + +
272B LYS* 5.9 0.2 - - - +
276B TRP* 3.8 24.4 - - + -
337B GLY* 4.6 7.5 + - - -
341B ASN 3.4 0.8 + - - +
342B GLY* 1.3 69.4 - - - -
344B ASN* 1.3 71.8 + - - +
345B ASP 3.2 0.2 - - - -
346B ILE* 2.9 21.6 + - + +
347B LYS* 3.0 19.7 + - + +
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Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 3.4 35.3 + - - +
3B ASP* 4.1 8.1 + - - +
6B GLN* 3.2 28.3 + - - +
341B ASN* 3.4 12.4 + - + +
342B GLY 3.2 1.0 - - - -
343B VAL* 1.3 84.3 - - - +
345B ASP* 1.3 57.5 + - - +
347B LYS* 4.0 12.7 + - - +
348B ASN* 2.9 43.1 + - - +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PHE* 3.4 41.4 - - + -
337B GLY 4.8 1.1 - - - +
339B LEU* 3.5 35.3 + - - +
341B ASN* 3.3 33.9 + - - +
342B GLY 3.4 10.6 + - - +
343B VAL 3.2 0.8 - - - -
344B ASN* 1.3 78.6 - - - +
346B ILE* 1.3 62.2 + - - +
348B ASN* 4.3 1.6 - - - -
349B HIS* 3.6 12.0 + - - +
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Residues in contact with ILE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.9 19.3 - - + -
276B TRP* 3.4 44.0 - - + -
279B LEU* 4.6 4.7 - - + -
323B LEU* 4.5 8.1 - - + -
327B LEU* 3.8 17.3 - - + -
336B PHE* 4.0 20.6 - - + -
337B GLY* 3.9 14.8 - - - +
343B VAL* 2.9 11.4 + - + +
345B ASP* 1.3 78.7 - - - +
347B LYS* 1.3 65.1 + - - +
349B HIS* 3.1 19.9 + - - +
352B PHE* 3.4 29.7 - - + -
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY 4.0 18.6 - - - +
206B VAL* 4.2 8.1 - - + -
207B LEU* 3.9 20.8 - - - +
210B GLU* 2.9 37.4 + - - -
343B VAL* 3.0 25.0 + - + +
344B ASN* 4.0 17.8 + - - +
346B ILE* 1.3 76.6 - - - +
348B ASN* 1.3 61.5 + - - +
349B HIS 3.3 0.9 + - - +
352B PHE* 3.8 11.3 - - - +
357B TRP* 3.4 55.7 + - + +
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 3.3 43.6 + - - -
2B LYS* 3.5 46.3 + - + +
3B ASP 4.6 0.6 - - - +
344B ASN* 2.9 30.2 + - - +
345B ASP* 4.3 1.8 - - - +
347B LYS* 1.3 76.1 - - - +
349B HIS* 1.3 66.5 + - - +
350B LYS* 3.6 2.3 + - - +
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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