Contacts of the strand formed by residues 334 - 338 (chain B) in PDB entry 5V8V
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 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B VAL* 4.3 11.4 - - + -
275B SER 3.2 10.3 - - - +
276B VAL* 5.0 1.1 - - + -
308B LEU* 4.0 27.4 - - + -
312B LEU* 4.0 10.5 - - + -
332B PRO 4.2 0.4 - - - +
333B ASP* 1.3 77.4 - - - +
335B SER* 1.3 62.6 + - - +
336B PHE* 4.0 27.5 - - + -
343B TYR 3.8 0.9 - - - +
344B THR* 3.4 1.6 - - - -
345B LEU* 2.7 42.3 + - + +
350B TYR* 3.6 36.6 - - + +
366B ILE* 4.0 24.5 - - + -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY 3.8 0.7 - - - +
274B VAL* 3.2 8.5 - - - +
275B SER* 2.8 48.6 + - - -
277B GLY 5.1 4.7 + - - -
333B ASP* 5.0 1.9 - - - +
334B ILE* 1.3 72.5 - - - +
336B PHE* 1.3 63.1 + - - +
342B GLU* 3.7 20.1 - - - +
343B TYR 3.3 5.4 - - - -
344B THR* 2.8 33.7 + - - +
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Residues in contact with PHE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B MET* 3.6 28.9 - - + -
273B GLY 3.7 3.1 - - - -
274B VAL* 4.1 11.4 - - + -
298B ILE* 4.0 33.9 - - + -
308B LEU* 6.5 0.4 - - + -
334B ILE* 4.0 25.8 - - + -
335B SER* 1.3 74.0 - - - +
337B HIS* 1.3 59.1 + - - +
338B LEU* 3.4 19.8 + - + +
342B GLU* 3.6 2.2 - - - -
343B TYR* 2.7 46.9 + - - +
345B LEU* 4.5 9.2 - - + -
366B ILE* 6.3 1.6 - - + -
379B TRP* 4.0 28.9 - + - -
381B LEU* 4.3 11.9 - - + -
385B PHE* 4.1 17.5 - + + -
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B MET* 3.6 7.0 - - - +
272B LYS* 3.0 50.5 + - + +
273B GLY* 2.9 20.6 + - - +
336B PHE* 1.3 69.1 - - - +
338B LEU* 1.3 60.6 + - - +
339B GLY 4.5 0.6 + - - -
340B GLY* 3.3 42.4 + - - -
341B LYS 3.4 4.0 - - - -
342B GLU* 2.8 37.8 + - + +
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Residues in contact with LEU 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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257B HIS* 3.3 10.4 - - - -
259B ILE* 3.9 15.9 - - + -
269B ILE* 4.0 16.4 - - + -
270B GLN 4.0 6.7 - - - +
271B MET* 3.7 40.4 - - + -
289B ALA* 4.3 5.6 - - + -
336B PHE* 3.4 11.8 + - + +
337B HIS* 1.3 73.6 - - - +
339B GLY* 1.3 66.2 + - - +
340B GLY 3.2 1.3 - - - -
341B LYS 2.9 18.3 + - - +
343B TYR* 3.6 16.5 - - + -
381B LEU* 4.1 10.8 - - + -
385B PHE* 3.9 28.7 - - + -
402B PHE* 4.3 11.0 - - + -
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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