Contacts of the strand formed by residues 339 - 346 (chain A) in PDB entry 4FOV
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 THR 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A LEU* 4.0 25.9 - - + +
258A LEU* 3.6 29.6 - - + -
330A ILE* 3.9 9.6 - - + -
331A VAL 3.7 10.8 - - - +
332A GLU* 4.3 6.8 + - - +
337A GLY 3.7 2.4 + - - -
338A LYS* 1.3 74.6 - - - +
340A ILE* 1.3 62.0 + - - +
463A THR* 3.2 7.8 - - - -
464A SER* 2.9 38.8 + - - -
467A ARG* 4.0 10.4 - - - +
471A TRP* 3.6 16.2 - - + -
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ILE* 3.4 4.7 - - - +
331A VAL* 2.8 44.2 + - + +
333A ASP* 4.5 10.3 - - + -
338A LYS* 4.6 8.5 - - + +
339A THR* 1.3 79.6 - - - +
341A LEU* 1.3 62.8 + - - +
342A LEU* 3.6 24.7 - - + -
461A MET* 4.0 18.4 - - + -
462A THR 3.6 3.1 - - - +
463A THR* 4.0 14.1 - - + -
471A TRP* 4.6 0.9 - - - -
504A LEU* 3.8 29.2 - - + -
506A PHE* 3.8 10.7 - - + -
522A SER* 3.8 20.6 - - - +
523A GLY* 4.3 1.8 - - - -
526A TRP* 4.9 2.0 - - + -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER* 3.8 15.0 - - - -
277A ILE* 4.1 17.7 - - + -
279A THR* 3.7 20.2 - - + -
295A ALA* 3.7 25.4 - - + -
296A MET* 3.6 17.9 - - + +
328A SER* 4.1 3.6 - - - -
329A SER 3.4 10.8 - - - +
330A ILE* 4.2 7.6 - - + -
340A ILE* 1.3 73.9 - - - +
342A LEU* 1.3 79.0 + - - +
461A MET* 3.3 1.9 - - - -
462A THR* 2.7 40.6 + - + -
471A TRP* 3.8 23.0 - - + -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A SER* 3.1 5.5 - - - -
329A SER 2.8 32.1 + - - +
340A ILE* 3.6 20.0 - - + -
341A LEU* 1.3 79.3 - - - +
343A ALA* 1.3 60.8 + - - +
459A ILE* 4.2 4.0 - - + -
460A ALA 3.1 15.0 - - - +
461A MET* 3.5 26.2 - - + -
477A LEU* 3.9 22.0 - - + -
490A LEU* 3.1 24.0 - - + +
506A PHE* 3.7 36.1 - - + -
517A LEU* 4.8 3.6 - - + -
526A TRP* 4.7 4.5 - - + -
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ILE* 3.9 28.7 - - + -
296A MET* 4.0 13.0 - - - +
325A PHE* 4.8 0.2 - - + -
326A ILE 4.0 2.5 - - - +
327A ASP 3.2 15.5 - - - +
328A SER* 3.9 3.8 - - - -
341A LEU* 4.6 0.4 - - + -
342A LEU* 1.3 75.6 - - - +
344A ASP* 1.3 71.3 + - - +
345A VAL* 4.0 1.3 - - - +
459A ILE* 3.6 3.4 - - - +
460A ALA* 3.0 30.2 + - - +
490A LEU* 3.6 4.0 - - - -
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A PHE* 3.3 7.8 - - - +
326A ILE* 2.9 51.9 + - + +
327A ASP* 3.5 17.1 + - - +
343A ALA* 1.3 74.8 - - - +
345A VAL* 1.3 60.9 + - - +
346A MET* 4.5 8.7 - - + -
457A ASN* 5.7 1.1 - - + -
458A TYR 3.4 9.2 - - - +
459A ILE* 4.1 7.2 - - - +
488A THR 5.1 0.7 - - - -
489A TYR* 3.9 11.8 - - - +
490A LEU* 3.0 36.0 + - - +
701A CXS 3.9 15.4 - - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PHE* 3.9 13.7 - - + -
324A SER 3.8 2.0 - - - -
325A PHE* 3.8 22.7 - - + -
343A ALA 4.0 0.2 - - - +
344A ASP* 1.3 78.8 - - - +
346A MET* 1.3 65.2 + - - +
347A PRO* 4.3 0.4 - - - -
445A PHE* 3.6 26.2 - - + -
457A ASN* 3.6 6.4 - - - +
458A TYR* 2.9 39.1 + - + +
459A ILE 4.0 3.6 - - - -
460A ALA* 3.3 40.8 - - + +
474A PHE* 5.0 1.8 - - + -
476A LEU* 4.1 6.5 - - + -
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Residues in contact with MET 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A SER* 3.8 14.4 - - - +
298A PHE* 4.2 1.4 - - - -
323A ALA* 3.3 4.2 - - - +
324A SER* 2.8 47.4 + - - +
326A ILE* 4.2 11.2 - - + -
344A ASP* 4.5 7.2 - - + -
345A VAL* 1.3 74.9 - - - +
347A PRO* 1.3 67.6 - - + +
350A ILE* 3.3 25.4 - - - +
351A GLY* 3.9 17.3 - - - -
352A ASN* 4.1 12.3 - - - +
445A PHE* 4.4 3.4 - - - -
457A ASN* 3.8 32.5 - - + -
489A TYR* 4.8 1.3 - - + -
701A CXS 3.7 34.8 - - + -
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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