Contacts of the helix formed by residues 328 - 333 (chain W) in PDB entry 4UJ3
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 328 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324W ILE* 2.8 19.3 + - - +
326W GLN 3.6 0.6 - - - -
327W GLU* 1.3 83.2 - - - +
329W ILE* 1.3 65.0 + - - +
330W PHE 3.6 1.3 - - - -
331W PRO* 3.3 3.7 - - - +
332W CYS* 3.2 28.1 + - - +
445W ARG* 2.4 56.9 + - - +
448W MET* 3.2 34.2 - - + +
449W SER* 3.6 18.0 + - - -
452W LYS* 4.8 2.6 + - - +
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Residues in contact with ILE 329 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324W ILE* 3.1 25.6 + - + +
325W TYR* 3.9 33.2 - - + +
328W ASP* 1.3 73.2 - - - +
330W PHE* 1.3 69.1 + - - +
332W CYS* 3.2 2.4 + - - +
333W LEU* 3.1 35.6 + - + +
345W LEU* 4.1 14.6 - - + -
414W VAL* 3.8 29.4 - - + -
417W PHE* 4.3 7.6 - - + -
418W PHE* 3.4 32.3 - - + -
448W MET* 4.2 6.7 - - - -
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Residues in contact with PHE 330 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316W ARG* 4.3 20.0 - - - -
325W TYR* 3.0 49.2 + + + -
326W GLN* 3.4 36.1 - - - +
329W ILE* 1.3 77.4 - - + +
331W PRO* 1.3 74.7 - - + +
333W LEU* 3.0 15.5 + - + +
334W THR* 3.1 18.2 + - - +
345W LEU* 4.8 15.3 - - + -
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Residues in contact with PRO 331 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326W GLN 3.5 15.5 - - - +
327W GLU 3.4 20.4 - - - +
328W ASP 3.3 16.8 - - - +
330W PHE* 1.3 96.1 - - + +
332W CYS* 1.3 56.0 + - - -
334W THR* 3.4 16.3 + - - +
410W ARG* 2.8 21.4 + - - -
452W LYS* 3.6 25.9 - - + +
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Residues in contact with CYS 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328W ASP 3.2 18.6 + - - +
329W ILE 3.6 4.9 - - - +
330W PHE 3.2 0.8 - - - -
331W PRO* 1.3 78.9 - - - +
333W LEU* 1.3 60.0 + - - +
334W THR 3.3 1.7 + - - -
335W PHE* 3.4 13.7 - - - -
410W ARG* 3.1 32.8 + - - +
414W VAL* 3.8 20.0 - - + -
448W MET* 3.3 36.6 - - - -
451W ALA* 3.8 13.5 - - - -
452W LYS* 3.8 12.1 - - - +
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Residues in contact with LEU 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329W ILE* 3.1 21.9 + - + +
330W PHE* 3.0 8.6 + - + +
332W CYS* 1.3 81.0 - - + +
334W THR* 1.3 58.6 + - - +
335W PHE* 3.7 14.3 + - + -
341W ALA* 3.9 21.7 - - - +
344W VAL* 4.6 9.0 - - + -
345W LEU* 3.5 51.1 - - + -
348W VAL* 4.4 11.9 - - + -
411W ILE* 4.4 26.9 - - + -
414W VAL* 4.4 19.5 - - + -
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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