Contacts of the helix formed by residues 328 - 333 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E ILE* 2.9 16.7 + - - +
326E GLN 3.5 0.2 - - - -
327E GLU* 1.3 88.2 - - - +
329E ILE* 1.3 67.1 + - - +
330E PHE 3.6 0.7 - - - -
331E PRO* 3.2 11.3 - - - +
332E CYS* 3.3 18.4 + - - +
445E ARG* 2.6 52.7 + - - +
448E MET* 3.5 31.2 - - + +
449E SER* 3.4 20.7 + - - -
452E LYS* 5.2 2.1 - - - +
452K LYS* 3.9 0.7 + - - -
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Residues in contact with ILE 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E ILE* 3.0 17.3 + - + +
325E TYR* 3.3 46.0 + - + +
328E ASP* 1.3 74.4 - - - +
330E PHE* 1.3 66.8 + - + +
332E CYS* 3.2 16.0 + - - +
333E LEU* 3.2 17.2 + - + +
345E LEU* 4.2 14.8 - - + -
414E VAL* 4.0 18.8 - - + +
417E PHE* 4.2 15.5 - - + -
418E PHE* 3.7 27.6 - - + -
448E MET* 4.3 14.8 - - - -
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Residues in contact with PHE 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E ARG* 5.0 16.2 - - - -
325E TYR* 2.8 63.9 + + + +
326E GLN* 4.0 13.7 - - + +
329E ILE* 1.3 72.6 - - + +
331E PRO* 1.3 69.7 - - + +
333E LEU* 3.2 14.6 + - + +
334E THR* 3.1 16.3 + - - -
345E LEU* 4.1 23.3 - - + -
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Residues in contact with PRO 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E GLN 3.3 18.2 - - - +
327E GLU 3.3 21.1 - - - +
328E ASP 3.2 16.6 - - - +
330E PHE* 1.3 97.0 - - + +
332E CYS* 1.3 56.7 + - - -
334E THR* 3.4 17.8 + - - +
410E ARG* 3.0 20.1 + - - -
452E LYS* 3.7 25.4 - - + +
298K ASP* 4.5 1.4 - - - +
327K GLU* 4.2 12.3 - - - +
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Residues in contact with CYS 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E ASP 3.3 13.9 + - - +
329E ILE 3.2 11.0 + - - +
331E PRO* 1.3 79.9 - - - +
333E LEU* 1.3 58.1 + - - +
334E THR 3.3 1.1 + - - -
335E PHE* 3.6 10.0 - - - -
410E ARG* 3.1 41.5 + - + +
414E VAL* 3.9 14.8 - - + -
448E MET* 3.2 41.5 - - - -
451E ALA* 4.0 9.6 - - - -
452E LYS* 3.9 11.7 - - - +
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Residues in contact with LEU 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E ILE* 3.2 22.6 + - + +
330E PHE* 3.2 9.1 + - + +
332E CYS* 1.3 80.0 - - - +
334E THR* 1.3 59.3 + - - +
335E PHE* 3.8 13.0 - - + -
341E ALA* 3.6 28.1 - - - +
344E VAL* 4.7 6.7 - - + -
345E LEU* 4.0 45.1 - - + +
348E VAL* 5.0 6.1 - - + -
411E ILE* 3.8 36.6 - - + -
414E VAL* 4.6 15.3 - - + -
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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
------------------------------------------------------------
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