Contacts of the helix formed by residues 335 - 346 (chain B) in PDB entry 1JFZ
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 PHE 335 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B LEU* 3.2 54.5 - - + -
286B LYS* 3.7 18.2 - - + -
287B LEU* 4.1 14.4 - - + -
309B PHE* 3.7 29.6 - + - -
313B TRP* 3.7 20.9 - + - -
331B PHE* 3.0 30.9 + + - +
334B LEU* 1.3 98.6 - - + +
336B LYS* 1.3 67.9 + - - +
337B GLU 3.0 3.6 - - - -
338B ASP* 3.3 6.3 + - + +
339B ILE* 3.0 33.2 + - + +
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Residues in contact with LYS 336 (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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254B LEU* 4.1 27.6 - - + +
258B TYR* 3.2 43.0 + - - -
332B TYR* 2.8 47.6 + - + +
334B LEU 3.8 0.2 - - - -
335B PHE* 1.3 72.0 - - - +
337B GLU* 1.3 65.6 + - - +
339B ILE* 3.3 1.6 + - - +
340B LEU* 3.1 39.5 + - + +
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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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332B TYR 4.6 0.2 + - - -
333B LYS 6.0 1.1 - - - +
334B LEU 4.8 6.5 - - - +
335B PHE 4.4 3.1 - - - -
336B LYS* 1.3 81.4 - - - +
338B ASP* 1.3 72.6 + - - +
339B ILE 3.4 0.2 + - - -
340B LEU* 3.7 6.7 + - - +
341B SER* 3.3 21.5 + - - -
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Residues in contact with ASP 338 (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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279B PHE* 4.1 9.8 - - + -
282B LEU* 3.5 29.0 - - + +
283B LEU* 4.7 5.6 - - + -
286B LYS* 3.9 25.2 - - - -
334B LEU 5.1 0.5 - - - +
335B PHE* 3.3 7.3 + - - +
337B GLU* 1.3 86.9 - - - +
339B ILE* 1.3 66.7 + - - +
341B SER* 3.5 9.3 + - - +
342B ALA* 3.2 24.4 + - - +
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Residues in contact with ILE 339 (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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251B ILE* 4.7 15.7 - - + +
254B LEU* 4.0 33.9 - - + -
255B LEU 5.4 0.2 - - - +
274B LEU* 4.4 13.3 - - + +
279B PHE* 4.1 24.0 - - + -
283B LEU* 5.0 2.5 - - + -
331B PHE* 3.9 22.0 - - + -
335B PHE* 3.0 40.3 + - + +
336B LYS 3.8 2.7 - - - +
338B ASP* 1.3 77.7 - - - +
340B LEU* 1.3 68.3 + - - +
342B ALA* 3.2 3.4 + - - +
343B ILE* 3.1 36.4 + - + +
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Residues in contact with LEU 340 (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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254B LEU* 4.7 9.4 - - + -
258B TYR* 3.3 60.1 - - + -
336B LYS* 3.1 33.7 + - + +
337B GLU* 4.0 6.3 - - - +
339B ILE* 1.3 74.4 - - - +
341B SER* 1.3 66.0 + - - +
343B ILE* 2.8 29.1 + - + +
344B LYS* 3.2 17.6 + - - +
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Residues in contact with SER 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 3.3 15.8 + - - -
338B ASP* 3.5 11.0 + - - +
340B LEU* 1.3 78.6 - - - +
342B ALA* 1.3 63.9 + - - +
344B LYS* 2.8 42.4 - - - +
345B GLU* 2.8 23.3 + - - +
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Residues in contact with ALA 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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270B LEU* 4.5 3.5 - - - +
273B TYR* 4.3 16.1 - - + -
274B LEU* 3.9 22.9 - - + +
279B PHE* 4.5 6.5 - - + -
338B ASP 3.2 16.2 + - - +
339B ILE 3.5 4.9 - - - +
341B SER* 1.3 81.0 + - - +
343B ILE* 1.3 57.7 + - - +
345B GLU* 4.0 9.3 - - - +
346B GLY* 3.1 23.6 + - - -
347B ARG* 4.1 4.7 + - - +
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Residues in contact with ILE 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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255B LEU* 4.2 27.6 - - + +
258B TYR* 4.3 10.8 - - + +
259B SER* 4.0 22.4 - - - +
260B PRO* 4.3 9.6 - - + +
266B PHE* 5.1 5.7 - - - -
270B LEU* 3.8 27.8 - - + +
274B LEU* 4.2 7.9 - - + -
339B ILE* 3.1 33.9 + - + +
340B LEU* 2.8 26.3 + - + +
342B ALA* 1.3 76.3 - - - +
344B LYS* 1.3 67.0 + - + +
346B GLY* 3.3 12.8 + - - -
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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
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260B PRO* 6.1 1.3 - - - -
340B LEU* 3.2 12.0 + - - +
341B SER* 2.8 42.3 + - - +
343B ILE* 1.3 80.8 - - + +
345B GLU* 1.3 73.4 + - + +
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Residues in contact with GLU 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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341B SER* 2.8 38.3 + - - +
342B ALA* 3.7 6.7 + - - +
344B LYS* 1.3 85.6 - - + +
346B GLY* 1.3 67.6 + - - +
347B ARG* 5.4 4.9 - - + +
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Residues in contact with GLY 346 (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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266B PHE* 5.9 2.7 - - - -
270B LEU* 3.4 22.7 - - - -
342B ALA 3.1 11.7 + - - -
343B ILE 3.3 5.6 + - - -
344B LYS 3.2 2.2 - - - -
345B GLU* 1.3 82.8 - - - +
347B ARG* 1.3 63.3 + - - +
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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