Contacts of the helix formed by residues 564 - 573 (chain B) in PDB entry 4EGA
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 ASP 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B CAS 4.0 11.4 - - - +
562B VAL* 4.0 13.6 + - + +
563B PHE* 1.3 75.2 - - - +
565B PRO* 1.3 70.7 - - - +
566B VAL* 3.3 10.8 + - - +
567B GLU* 3.2 39.0 + - + +
568B LYS* 3.2 27.4 + - - +
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Residues in contact with PRO 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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256B HIS* 5.4 0.2 - - - -
257B ILE* 4.1 30.3 - - + +
260B VAL* 3.8 26.2 - - + -
318B CAS 3.8 22.0 - - + -
322B MET* 4.3 8.0 - - - +
563B PHE* 3.5 16.1 - - + +
564B ASP* 1.3 89.4 - - - +
566B VAL* 1.3 58.2 + - + +
568B LYS* 4.7 0.4 - - + -
569B ALA* 3.0 25.6 + - - +
577B LEU* 3.2 24.4 - - + +
581B LEU* 5.9 0.2 - - + -
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Residues in contact with VAL 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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318B CAS 3.5 44.2 - - + -
321B GLN* 4.3 18.4 - - + +
322B MET* 5.0 8.3 - - + -
564B ASP* 3.3 8.4 + - - +
565B PRO* 1.3 73.7 - - + +
567B GLU* 1.3 67.7 + - - +
569B ALA* 3.8 4.2 - - - +
570B GLU* 3.0 36.0 + - + +
574B TYR* 3.6 20.6 - - + +
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Residues in contact with GLU 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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564B ASP* 3.2 34.1 + - - +
566B VAL* 1.3 78.7 - - - +
568B LYS* 1.3 88.0 + - + +
570B GLU* 3.2 8.9 + - - +
571B GLU* 3.2 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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550B LYS* 3.3 30.2 - - - +
562B VAL 5.7 0.7 - - - -
563B PHE* 4.1 17.3 - - + +
564B ASP 3.2 18.6 + - - +
565B PRO 4.2 2.9 - - - +
567B GLU* 1.3 94.3 + - - +
569B ALA* 1.3 61.9 + - - +
571B GLU* 3.1 8.7 + - - +
572B PHE* 2.8 43.9 + - + +
577B LEU* 4.2 19.3 - - + -
593B TYR* 3.5 20.4 - - - +
595B ASP* 3.0 28.6 + - - +
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Residues in contact with ALA 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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322B MET* 5.3 0.7 - - - -
565B PRO 3.0 19.1 + - - +
566B VAL 3.8 0.9 - - - +
568B LYS* 1.3 76.6 - - - +
570B GLU* 1.3 58.2 + - - +
573B GLY* 2.7 40.3 + - - -
574B TYR* 3.3 48.1 + - + -
577B LEU* 3.8 12.0 - - + +
811B DMS 5.0 0.9 - - - +
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Residues in contact with GLU 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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321B GLN* 4.0 7.6 + - - +
566B VAL* 3.0 28.4 + - + +
567B GLU* 3.7 7.0 - - - +
568B LYS 3.2 0.4 - - - -
569B ALA* 1.3 76.0 - - - +
571B GLU* 1.3 58.9 + - - +
574B TYR* 3.0 29.9 + - - +
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Residues in contact with GLU 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 GLU* 3.2 14.7 + - + +
568B LYS* 3.1 17.2 + - - +
570B GLU* 1.3 80.1 - - - +
572B PHE* 1.3 100.3 + - + +
595B ASP* 5.0 1.2 - - - +
765B ARG* 3.6 30.3 + - - +
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Residues in contact with PHE 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 32.3 + - + +
571B GLU* 1.3 109.3 - - - +
573B GLY* 1.3 59.9 + - - +
576B ALA* 3.4 13.6 - - - +
577B LEU* 5.9 0.2 - - + -
593B TYR* 3.6 24.5 - - - -
595B ASP* 3.6 18.2 - - - -
598B MET* 3.3 31.6 - - + -
599B ILE* 3.6 35.0 - - + -
602B LEU* 4.2 17.3 - - + +
765B ARG* 3.5 27.7 + - - +
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Residues in contact with GLY 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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569B ALA* 2.7 24.9 + - - -
570B GLU 4.7 0.2 - - - -
571B GLU 3.7 0.6 - - - -
572B PHE* 1.3 75.7 - - - +
574B TYR* 1.3 60.1 + - - -
575B ASP 3.6 1.3 - - - -
576B ALA* 3.9 4.9 - - - -
577B LEU* 2.9 29.6 + - - +
811B DMS 4.0 17.3 - - - -
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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