Contacts of the strand formed by residues 472 - 478 (chain A) in PDB entry 4JWE
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 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A GLN 3.8 0.2 - - - +
425A VAL* 4.0 1.8 - - - +
426A PHE* 2.8 49.2 + - - +
427A SER* 4.7 3.6 - - - -
428A THR* 5.3 0.4 - - + +
436A VAL* 4.5 7.0 - - + -
459A LEU* 3.8 20.6 - - + -
462A ILE* 3.8 23.1 - - + -
470A PRO* 4.2 13.5 - - + -
471A GLN* 1.3 70.5 - - - +
473A GLU* 1.3 61.8 + - - +
474A VAL* 3.4 4.9 + - + +
488A ALA* 4.2 15.7 - - + -
489A LYS 3.4 3.8 - - - +
490A ASP* 3.2 37.0 - - + +
10D LEU* 4.3 22.7 - - + -
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Residues in contact with GLU 473 (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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423A SER* 3.4 26.9 + - - -
424A GLN 3.7 6.3 - - - +
425A VAL* 4.3 12.1 - - + +
471A GLN 3.7 2.8 + - - -
472A ILE* 1.3 70.1 - - - +
474A VAL* 1.3 62.1 + - - +
475A THR* 4.1 12.4 + - - +
487A SER* 3.8 1.4 + - - +
488A ALA* 3.3 2.6 - - - -
489A LYS* 2.8 44.3 + - + +
491A LYS* 3.6 31.2 + - + +
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE* 4.1 16.6 - - + -
411A LEU* 3.5 8.0 - - + +
423A SER* 3.2 2.6 - - - -
424A GLN 2.9 32.8 + - - -
426A PHE* 3.5 29.4 - - + -
438A ILE* 4.1 26.5 - - + -
472A ILE* 4.0 8.1 - - + +
473A GLU* 1.3 74.9 - - - +
475A THR* 1.3 62.3 + - - +
476A PHE* 3.9 26.7 - - + -
486A VAL* 4.5 5.2 - - + -
487A SER 3.3 8.7 - - - +
488A ALA* 4.2 6.1 - - + -
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Residues in contact with THR 475 (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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421A LYS* 3.5 34.5 + - + +
422A HIS 3.5 6.1 - - - +
423A SER* 2.7 26.0 + - - +
473A GLU* 4.1 11.3 + - - +
474A VAL* 1.3 73.0 - - - +
476A PHE* 1.3 69.2 + - - +
477A ASP* 4.7 4.3 - - + +
485A HIS 3.6 1.0 - - - +
486A VAL* 3.3 6.2 - - - -
487A SER* 2.9 47.0 + - - +
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Residues in contact with PHE 476 (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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399A LEU* 3.8 18.6 - - + -
400A GLY* 3.5 40.6 - - - -
401A ILE* 3.6 19.3 - - + -
411A LEU* 3.9 22.7 - - + -
412A ILE* 3.6 20.7 - - + +
421A LYS* 3.3 3.5 - - - +
422A HIS 2.9 35.9 + - - +
440A VAL* 3.7 22.9 - - + -
474A VAL* 3.9 6.3 - - + -
475A THR* 1.3 79.3 - - - +
477A ASP* 1.3 60.7 + - - +
478A ILE 4.2 0.4 - - - -
484A LEU* 3.9 13.5 - - + -
485A HIS 3.5 3.8 - - - -
486A VAL* 3.6 22.2 - - + -
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Residues in contact with ASP 477 (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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420A THR 3.5 6.5 - - - -
421A LYS* 3.3 31.4 - - + +
475A THR* 4.8 4.5 - - + -
476A PHE* 1.3 73.5 - - - +
478A ILE* 1.3 71.9 + - - +
479A ASP* 4.0 6.2 + - - +
483A ILE 3.5 2.6 - - - +
484A LEU* 3.6 1.0 - - - +
485A HIS* 2.9 53.8 + - + +
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Residues in contact with ILE 478 (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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395A THR* 3.7 23.3 - - + +
399A LEU* 3.4 30.7 - - + -
412A ILE* 3.8 16.2 - - + -
418A ILE* 3.9 19.7 - - + -
419A PRO* 3.2 5.9 - - - +
420A THR* 2.8 33.1 + - + +
477A ASP* 1.3 77.8 - - - +
479A ASP* 1.3 70.3 + - - +
482A GLY* 3.7 27.6 - - - +
483A ILE 3.3 3.8 - - - +
484A LEU* 3.8 17.5 - - + +
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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