Contacts of the strand formed by residues 330 - 334 (chain F) in PDB entry 3KHU
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 LYS 330 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328F ASP 3.8 3.0 + - - +
329F LYS* 1.3 72.0 - - - +
331F ILE* 1.3 65.1 + - - +
363F HIS* 3.3 9.4 - - + +
365F HIS* 3.5 42.4 - - + +
403F GLU 3.1 16.4 + - - -
404F ALA 3.2 22.0 - - - +
406F ASP* 2.7 31.5 + - - +
407F GLY* 3.8 15.9 - - - +
408F ALA* 3.4 7.5 - - + +
409F HIS* 2.9 34.6 + - + -
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Residues in contact with ILE 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F ILE* 4.6 3.6 - - + -
322F LEU* 3.9 19.5 - - + -
326F VAL* 3.5 30.5 - - + -
329F LYS* 4.1 6.1 - - + +
330F LYS* 1.3 83.9 - - - +
332F ALA* 1.3 67.0 + - - +
333F ILE* 3.7 8.6 + - + -
357F LEU* 4.3 15.5 - - + -
362F ALA* 4.1 7.0 - - + -
363F HIS 2.9 7.1 + - - -
364F LEU* 3.4 13.8 - - + +
365F HIS 2.9 24.4 + - - -
408F ALA* 4.6 0.2 - - - -
409F HIS* 5.1 0.7 - - + -
410F ALA* 3.6 18.2 - - + +
412F VAL* 3.7 25.4 - - + -
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Residues in contact with ALA 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F ILE* 1.3 72.3 - - - +
333F ILE* 1.3 61.3 + - - +
334F LEU* 3.9 3.1 - - + -
365F HIS 3.3 5.4 - - - -
404F ALA* 3.4 34.2 + - + +
405F CYS* 4.0 20.4 - - - -
408F ALA* 4.3 1.2 - - + +
410F ALA 3.0 12.8 + - - +
411F VAL* 4.3 6.9 - - + +
412F VAL* 2.8 31.5 + - - +
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Residues in contact with ILE 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F ILE* 4.2 5.4 - - + +
332F ALA* 1.3 76.9 - - - +
334F LEU* 1.3 63.0 + - - +
335F GLY 3.8 17.9 + - - +
336F PHE* 4.9 0.2 - - + -
350F SER* 4.9 3.8 - - - -
353F ILE* 4.9 4.7 - - + -
354F SER* 4.1 22.4 - - - +
357F LEU* 4.0 23.3 - - + -
364F LEU* 4.2 17.0 - - + -
365F HIS 2.9 7.7 + - - +
366F ILE* 3.4 24.7 - - + +
367F TYR 2.9 26.9 + - - +
412F VAL* 3.6 20.0 - - + -
414F CYS* 4.2 13.9 - - - -
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Residues in contact with LEU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F ALA* 4.6 4.3 - - + -
333F ILE* 1.3 75.5 - - - +
335F GLY* 1.3 59.5 + - - +
367F TYR* 3.6 21.8 - - + -
401F PRO* 4.2 15.3 - - + +
404F ALA* 4.4 12.3 - - + -
405F CYS* 4.7 5.2 - - - -
411F VAL* 3.6 29.6 - - + -
412F VAL 2.9 13.9 + - - +
413F ILE* 3.5 11.7 - - + -
414F CYS 3.0 25.1 + - - -
415F THR 3.7 0.2 + - - -
420F PHE* 3.4 29.3 - - + -
423F LEU* 3.9 27.1 - - + -
425F TYR* 5.1 1.3 - - + +
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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