Contacts of the strand formed by residues 340 - 345 (chain B) in PDB entry 3K0J
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 ILE 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B HIS* 3.9 32.5 - - + +
334B PHE* 4.0 8.3 - - + -
335B SER* 3.9 25.8 - - - +
338B GLY 3.8 4.7 + - - +
339B GLN* 1.3 84.2 - - - +
341B LEU* 1.3 66.3 + - - +
342B ASP 3.5 22.2 - - - +
343B ILE* 3.9 14.1 - - + -
357B VAL* 4.7 4.9 - - + -
358B ILE 3.3 16.8 - - - +
359B PHE* 3.7 26.5 - - + -
162F U 4.1 5.8 - - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN* 4.3 16.4 - - - +
340B ILE* 1.3 77.5 - - - +
342B ASP* 1.3 64.8 + - - +
358B ILE* 2.7 25.2 + - + +
359B PHE 3.5 23.6 - - - +
360B LYS* 4.3 19.3 - - + +
393B ILE* 3.4 22.7 - - + +
394B ILE* 4.1 16.6 - - + -
397B MET* 5.3 6.7 - - - -
162F U 4.5 2.9 - - - +
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS* 5.3 3.2 + - - -
340B ILE* 3.5 6.8 - - - +
341B LEU* 1.3 83.3 - - - +
343B ILE* 1.3 77.0 + - - +
344B LEU* 3.5 22.4 - - + +
357B VAL* 3.6 0.2 - - - -
358B ILE* 2.8 33.1 + - + +
393B ILE* 4.0 20.0 - - + +
162F U 3.8 23.6 + - - -
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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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327B LYS* 3.1 50.8 + - + +
330B LEU* 4.2 8.1 - - + -
331B HIS* 3.4 44.2 - - + +
340B ILE* 3.9 7.4 - - + -
342B ASP* 1.3 83.1 + - - +
344B LEU* 1.3 62.9 + - - +
345B VAL* 4.2 9.9 - - + -
355B ALA* 5.4 0.4 - - + -
356B PHE 3.3 6.7 - - - +
357B VAL* 3.5 25.8 - - + -
162F U 3.3 25.3 + - + +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS* 4.9 1.8 - - - +
342B ASP* 3.5 26.5 - - + +
343B ILE* 1.3 73.0 - - - +
345B VAL* 1.3 61.3 + - - +
351B MET* 5.7 3.3 - - + +
355B ALA* 3.5 6.1 - - - -
356B PHE* 2.7 48.9 + - + +
358B ILE* 4.6 14.4 - - + -
391B SER* 5.5 0.2 - - - -
393B ILE* 6.4 1.6 - - + -
128F A 3.3 31.9 - - + +
129F C 4.2 16.4 - - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LYS* 3.7 37.0 - - + +
326B LEU* 4.2 26.5 - - + -
327B LYS* 3.8 31.0 - - + +
330B LEU* 4.9 0.2 - - + -
343B ILE* 3.7 7.7 + - + -
344B LEU* 1.3 80.5 - - - +
346B SER* 1.3 74.4 + - - +
347B ARG* 4.7 1.8 - - + -
351B MET* 5.8 0.9 - - - -
354B GLN 4.7 4.3 - - - +
355B ALA* 4.0 18.2 - - + +
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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