Contacts of the helix formed by residues 563 - 575 (chain B) in PDB entry 3F7F
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 GLU 563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519B THR* 5.8 1.1 + - - -
562B PHE* 1.3 81.2 - - - +
564B ILE* 1.3 65.5 + - - +
565B THR* 3.4 23.0 - - + +
566B ASN* 2.9 34.7 + - - +
567B LEU 3.4 7.3 + - - -
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Residues in contact with ILE 564 (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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562B PHE* 3.5 15.7 + - + +
563B GLU* 1.3 71.2 - - - +
565B THR* 1.3 67.9 + - - +
567B LEU* 3.2 28.1 + - + -
568B LYS* 3.3 8.8 + - - +
202C ASN* 4.0 20.4 - - + +
203C SER* 5.6 1.1 - - - -
205C LEU* 3.6 49.3 - - + +
206C LYS* 3.9 25.4 - - + +
208C LEU* 5.6 0.2 - - + -
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Residues in contact with THR 565 (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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563B GLU* 3.4 23.8 - - + +
564B ILE* 1.3 84.1 - - - +
566B ASN* 1.3 79.5 + - - +
568B LYS* 3.1 23.3 + - - +
569B ILE* 3.2 16.7 + - - +
205C LEU* 5.5 3.8 - - - -
193D HIS* 5.8 3.4 - - + -
195D GLU* 4.5 28.2 + - - +
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Residues in contact with ASN 566 (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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516B PHE* 3.7 21.2 - - + +
519B THR* 3.9 29.6 + - + +
563B GLU* 2.9 36.4 + - - +
565B THR* 1.3 84.8 - - - +
567B LEU* 1.3 59.2 + - - +
569B ILE* 3.3 22.8 + - - +
570B LEU* 2.9 27.9 + - - +
193D HIS* 4.6 9.7 + - - -
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Residues in contact with LEU 567 (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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516B PHE* 4.0 9.1 - - + -
562B PHE* 3.8 24.0 - - + -
563B GLU 3.4 2.8 + - - -
564B ILE* 3.2 29.5 + - + +
566B ASN* 1.3 77.7 - - - +
568B LYS* 1.3 54.1 + - - +
570B LEU* 3.3 3.4 + - + +
571B PHE* 2.6 33.3 + - - +
639B LEU* 3.9 26.7 - - + -
640B PHE* 3.4 33.4 - - + -
205C LEU 4.3 7.0 - - - +
208C LEU* 4.3 9.6 - - + -
209C THR* 3.6 23.3 - - - +
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Residues in contact with LYS 568 (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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564B ILE 3.3 7.4 + - - +
565B THR* 3.1 12.5 + - - +
567B LEU* 1.3 77.2 - - - +
569B ILE* 1.3 63.2 + - + +
571B PHE* 3.1 6.6 + - - +
572B ASP* 2.8 69.9 + - - +
205C LEU* 4.3 29.2 - - + +
208C LEU* 4.0 23.9 - - + +
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Residues in contact with ILE 569 (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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565B THR* 3.5 17.5 - - - +
566B ASN* 3.3 28.7 + - - +
568B LYS* 1.3 77.6 - - + +
570B LEU* 1.3 63.7 + - - +
572B ASP* 3.4 6.6 + - - +
573B GLU* 3.1 50.4 + - + +
193D HIS* 4.1 24.2 - - + +
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Residues in contact with LEU 570 (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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512B THR* 3.9 23.1 - - - +
513B LEU* 4.4 8.5 - - + +
516B PHE* 3.3 43.5 - - + -
566B ASN 2.9 17.0 + - - +
567B LEU* 3.5 4.9 - - + +
569B ILE* 1.3 79.0 - - - +
571B PHE* 1.3 63.9 - - - +
572B ASP 3.2 0.2 + - - -
573B GLU* 3.4 5.7 + - - +
574B LEU* 2.9 49.5 + - + +
636B THR* 4.7 8.5 - - + -
639B LEU* 4.7 2.7 - - + -
640B PHE* 3.7 26.7 - - + -
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Residues in contact with PHE 571 (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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567B LEU 2.6 21.8 + - - +
568B LYS* 3.6 6.5 - - - +
570B LEU* 1.3 73.7 - - - +
572B ASP* 1.3 68.9 + - - +
574B LEU* 3.5 7.2 + - + +
575B ASN* 2.4 56.7 + - - +
640B PHE* 3.9 32.8 - + + -
208C LEU* 3.5 48.9 - - + -
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Residues in contact with ASP 572 (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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568B LYS* 2.8 66.6 + - - +
569B ILE* 3.6 6.3 - - - +
571B PHE* 1.3 76.5 - - - +
573B GLU* 1.3 68.6 + - + +
575B ASN* 2.9 23.8 + - - +
576B SER* 3.9 2.8 + - - -
154D ASN 5.8 0.3 - - - +
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Residues in contact with GLU 573 (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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512B THR* 3.3 46.4 - - + +
515B GLY* 6.0 0.2 - - - -
569B ILE* 3.1 36.3 + - + +
570B LEU* 4.0 4.1 - - - +
572B ASP* 1.3 76.9 - - + +
574B LEU* 1.3 61.1 + - - +
576B SER* 2.7 28.7 + - - +
577B PHE* 3.2 9.7 - - + -
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Residues in contact with LEU 574 (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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509B TYR* 3.9 16.8 - - + -
512B THR* 4.3 6.1 - - - +
513B LEU* 3.7 27.4 - - + -
570B LEU* 2.9 26.9 + - + +
571B PHE* 3.5 8.1 - - + +
573B GLU* 1.3 76.7 - - - +
575B ASN* 1.3 62.5 + - - +
576B SER 3.0 1.7 + - - -
577B PHE* 3.0 24.0 + - + +
579B ILE* 4.4 22.9 - - + +
636B THR* 4.6 10.1 - - - -
640B PHE* 3.6 38.6 - - + -
642B LEU* 6.3 1.6 - - + -
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Residues in contact with ASN 575 (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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571B PHE* 2.4 57.5 - - - +
572B ASP* 2.9 12.4 + - - +
574B LEU* 1.3 75.5 - - - +
576B SER* 1.3 55.3 + - - +
577B PHE 3.2 8.3 + - - +
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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