Contacts of the helix formed by residues 330 - 340 (chain B) in PDB entry 2KZT
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 GLU 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B ASN 5.4 1.4 - - - +
326B HIS* 3.7 8.7 - - - +
327B LEU* 2.7 40.0 + - - +
328B VAL 3.0 3.9 - - - +
329B LYS* 1.3 79.0 - - - +
331B ILE* 1.3 69.5 + - + +
332B ASP 3.3 2.0 - - - +
333B MET* 3.4 20.4 + - - +
334B LEU* 3.9 10.5 + - + +
354B LEU* 3.5 33.4 - - + +
359B PHE* 4.5 16.9 - - + -
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Residues in contact with ILE 331 (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 LEU* 3.2 41.8 + - + +
330B GLU* 1.3 74.5 - - + +
332B ASP* 1.3 67.2 + - - +
334B LEU* 3.2 33.2 + - + +
335B LEU* 3.7 8.1 + - + +
359B PHE* 4.2 19.3 - - + -
362B GLU* 4.4 14.6 - - + +
363B LEU* 4.7 19.7 - - + +
366B GLU* 4.9 18.4 - - + +
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Residues in contact with ASP 332 (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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304A MET* 3.1 31.6 - - + +
327B LEU 4.6 1.4 + - - +
328B VAL* 6.2 0.4 - - - -
329B LYS 4.9 7.6 - - - +
330B GLU 4.2 0.6 - - - +
331B ILE* 1.3 78.7 - - - +
333B MET* 1.3 63.6 + - - +
335B LEU* 3.0 18.0 + - - +
336B LYS* 2.7 61.0 + - - +
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Residues in contact with MET 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLN* 5.1 9.4 - - - +
301A LEU* 4.6 15.7 - - + -
304A MET* 3.5 29.2 - - + -
329B LYS* 3.4 34.5 - - + +
330B GLU* 3.4 10.9 + - - +
331B ILE 3.3 0.2 - - - -
332B ASP* 1.3 77.9 - - - +
334B LEU* 1.3 65.1 - - + +
336B LYS* 3.3 0.7 + - - +
337B GLU* 2.9 36.3 + - + +
350B CYS* 6.2 7.9 - - + -
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Residues in contact with LEU 334 (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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330B GLU* 3.9 8.1 - - + +
331B ILE* 3.4 26.2 - - + +
332B ASP 3.2 0.6 - - - -
333B MET* 1.3 78.1 - - + +
335B LEU* 1.3 63.1 + - - +
337B GLU* 4.0 4.5 - - - +
338B TYR* 3.5 23.0 + - - +
347B ALA* 4.6 14.3 - - + +
350B CYS* 4.1 27.1 - - + +
351B LEU* 4.0 26.7 - - + +
354B LEU* 5.3 6.5 - - + -
363B LEU* 3.7 44.9 - - + -
386B LEU* 5.6 2.7 - - - +
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Residues in contact with LEU 335 (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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331B ILE* 4.0 13.7 - - + +
332B ASP* 3.0 16.9 + - - +
334B LEU* 1.3 74.7 - - - +
336B LYS* 1.3 63.2 + - + +
338B TYR* 3.2 5.4 + - - +
339B LEU* 2.9 31.2 + - - +
363B LEU* 4.1 17.7 - - + -
366B GLU* 3.4 39.0 - - + +
367B ALA* 4.5 10.1 - - + +
370B MET* 4.3 29.3 - - + +
383B ILE* 5.7 1.6 - - + -
386B LEU* 5.8 3.1 - - + -
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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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300A VAL* 3.5 35.5 - - + +
303A SER* 3.6 45.7 + - - -
304A MET* 3.8 8.5 - - + +
332B ASP* 2.7 54.1 + - - +
333B MET 3.8 2.7 - - - +
335B LEU* 1.3 79.0 - - + +
337B GLU* 1.3 61.9 + - - +
339B LEU* 3.1 18.1 + - + +
340B LEU* 3.1 26.4 + - + +
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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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259A GLN* 4.2 8.0 - - - +
297A LYS* 2.8 49.0 + - - +
300A VAL* 3.5 13.8 - - + +
301A LEU* 5.0 7.2 - - + +
333B MET* 2.9 25.6 + - + +
334B LEU* 4.0 6.1 - - - +
336B LYS* 1.3 75.9 - - - +
338B TYR* 1.3 59.9 + - - +
341B SER* 3.1 13.3 + - - -
342B GLY 2.9 19.9 + - - -
343B ASP 4.2 3.1 + - - +
346B GLU* 4.0 21.0 - - + +
347B ALA* 5.4 7.6 - - + +
350B CYS* 5.1 14.4 - - - -
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Residues in contact with TYR 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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334B LEU 3.5 11.5 + - - +
335B LEU* 3.2 6.1 + - - +
337B GLU* 1.3 80.0 - - - +
339B LEU* 1.3 63.1 + - - +
342B GLY* 3.1 23.8 - - - +
343B ASP 3.2 30.3 - - - -
344B ILE* 3.2 34.6 - - + +
347B ALA* 3.7 17.9 - - + -
382B MET* 3.3 48.9 - - + +
383B ILE* 5.5 6.7 - - + -
385B ASP* 4.2 5.7 + - + -
386B LEU* 3.5 49.2 + - + -
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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
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335B LEU 2.9 17.1 + - - +
336B LYS* 3.1 19.7 + - + +
338B TYR* 1.3 80.8 - - - +
340B LEU* 1.3 82.4 + - + +
341B SER 4.7 0.2 - - - -
342B GLY 4.6 0.2 + - - -
370B MET* 3.9 26.5 - - + -
382B MET* 4.3 13.4 - - + +
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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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296A ASP* 3.9 18.8 - - - +
299A THR* 5.5 10.5 - - + -
300A VAL* 3.3 36.3 - - + +
336B LYS* 3.1 7.4 + - + +
339B LEU* 1.3 98.6 - - + +
341B SER* 1.3 69.0 + - - +
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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