Contacts of the strand formed by residues 474 - 480 (chain A) in PDB entry 4PO2
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 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A ILE* 3.5 2.9 - - - +
428A PHE* 2.8 51.9 + - + +
429A THR* 5.0 2.9 - - - -
430A THR* 5.4 0.2 - - + -
438A VAL* 4.1 22.2 - - + -
461A LEU* 3.8 23.3 - - + -
464A ILE* 4.0 27.8 - - + -
472A PRO* 4.7 7.6 - - + +
473A GLN* 1.3 85.3 - - - +
475A GLU* 1.3 63.6 + - - +
476A VAL* 3.5 9.5 + - + -
490A ALA* 4.3 8.1 - - + -
491A THR 3.5 7.4 - - - +
492A ASP* 4.0 24.0 - - - -
5C LEU* 4.9 2.0 - - + -
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Residues in contact with GLU 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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425A THR* 3.5 27.5 - - + +
426A GLN 4.0 3.1 - - - -
427A ILE* 4.4 15.7 - - + +
473A GLN 4.1 1.4 - - - -
474A ILE* 1.3 69.0 - - - +
476A VAL* 1.3 59.7 + - - +
477A THR* 4.1 7.0 + - - +
489A THR 3.6 1.4 - - - +
490A ALA* 3.4 2.6 - - - -
491A THR* 2.9 53.8 + - - +
493A LYS* 3.7 36.8 + - + +
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Residues in contact with VAL 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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403A LEU* 4.3 13.2 - - + -
413A LEU* 3.5 7.6 - - + +
425A THR* 3.3 2.5 - - - +
426A GLN 2.9 38.8 + - - +
428A PHE* 3.6 24.9 - - + -
440A ILE* 4.2 22.9 - - + -
474A ILE* 4.1 12.3 - - + +
475A GLU* 1.3 76.3 - - - +
477A THR* 1.3 64.4 + - - +
478A PHE* 3.7 28.0 - - + -
488A VAL* 4.4 5.6 - - + -
489A THR 3.3 7.6 - - - +
490A ALA* 4.4 3.4 - - + -
5C LEU* 4.4 1.3 - - + -
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Residues in contact with THR 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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423A LYS* 3.6 31.9 - - + +
424A GLN 3.4 2.9 - - - +
425A THR* 2.7 31.7 + - - +
475A GLU* 4.4 8.5 + - - +
476A VAL* 1.3 72.1 - - - +
478A PHE* 1.3 68.8 + - - +
479A ASP* 4.5 4.5 - - + +
487A ASN 3.5 1.6 - - - +
488A VAL* 3.3 5.9 - - - +
489A THR* 2.9 45.8 + - - +
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Residues in contact with PHE 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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401A LEU* 4.0 18.4 - - + -
402A GLY* 3.4 43.7 - - - -
403A LEU* 4.1 7.9 - - + -
413A LEU* 3.5 26.7 - - + -
414A ILE* 3.7 23.9 - - + +
423A LYS* 3.3 3.1 - - - +
424A GLN 2.9 37.2 + - - +
442A VAL* 4.0 10.8 - - + -
476A VAL* 3.7 15.0 - - + -
477A THR* 1.3 76.2 - - - +
479A ASP* 1.3 59.7 + - - +
486A LEU* 4.0 10.3 - - + -
487A ASN 3.8 3.4 - - - -
488A VAL* 3.6 36.3 - - + -
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Residues in contact with ASP 479 (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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422A THR 3.5 6.1 - - - -
423A LYS* 3.2 33.1 + - + +
477A THR* 4.6 4.7 - - + -
478A PHE* 1.3 74.1 - - - +
480A ILE* 1.3 72.9 + - - +
481A ASP* 3.9 6.6 + - - +
485A ILE 3.4 1.6 - - - +
486A LEU* 3.3 4.7 - - - +
487A ASN* 2.8 53.3 + - + +
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Residues in contact with ILE 480 (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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397A ALA* 4.5 4.9 - - + -
401A LEU* 3.5 28.3 - - + -
414A ILE* 3.6 27.1 - - + -
420A ILE* 3.9 29.8 - - + -
421A PRO* 3.1 5.9 - - - +
422A THR* 2.9 38.5 + - + +
479A ASP* 1.3 79.0 - - - +
481A ASP* 1.3 71.7 + - - +
484A GLY* 3.7 26.2 - - - +
485A ILE 3.3 2.2 - - - +
486A LEU* 3.8 14.1 - - + -
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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