Contacts of the helix formed by residues 475 - 479 (chain u) in PDB entry 6FF7
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 PHE 475 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3999 LEU* 5.3 2.2 - - - -
471u ASP* 3.2 24.7 + - + +
472u ILE* 4.6 2.5 - - - +
474u TYR* 1.3 76.0 - - + +
476u ASP* 1.3 61.7 + - - +
477u LYS 3.2 3.9 + - - +
478u LEU* 4.0 12.8 + - + +
479u LEU* 4.8 2.3 + - - +
498u MET* 5.6 7.0 - - + +
502u LEU* 5.2 14.4 - - + -
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Residues in contact with ASP 476 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3939 PRO 5.3 0.3 - - - -
3959 TRP* 3.2 24.9 + - + +
3969 LEU 3.3 3.1 + - - -
472u ILE* 3.3 27.1 - - - +
473u GLN* 3.4 14.2 + - - +
474u TYR 3.3 2.8 + - - -
475u PHE* 1.3 76.6 - - - +
477u LYS* 1.3 59.8 - - - +
478u LEU 3.3 0.2 - - - -
479u LEU* 3.3 24.0 - - - +
480u VAL 4.9 0.2 + - - -
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Residues in contact with LYS 477 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3959 TRP 1.7 28.4 + - - +
3969 LEU* 0.5 289.3 - - - +
3999 LEU* 2.6 21.0 - - + +
475u PHE 3.2 1.8 - - - -
476u ASP* 1.3 68.6 - - - +
478u LEU* 1.3 37.7 - - - +
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Residues in contact with LEU 478 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3969 LEU* 2.0 8.0 - - - +
3999 LEU* 5.2 0.6 - - - +
460u PRO* 3.3 22.0 - - + +
461u SER* 5.2 4.3 - - - -
475u PHE* 4.0 9.9 + - + +
476u ASP 3.3 1.2 - - - -
477u LYS* 1.3 71.6 - - - +
479u LEU* 1.3 61.7 + - - +
480u VAL 3.2 10.1 + - - +
481u ASP* 5.4 0.2 - - - -
498u MET* 6.4 2.2 - - + -
499u LYS* 6.0 8.7 - - + +
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Residues in contact with LEU 479 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3929 ILE* 4.9 0.8 - - - +
3939 PRO* 3.5 1.1 - - + -
3949 TYR 5.9 0.2 - - - +
3969 LEU* 3.2 1.0 - - - +
457u ASN* 3.9 34.4 - - - +
458u ASP 5.4 4.3 - - - +
460u PRO* 3.8 18.6 - - + +
461u SER* 5.6 2.3 + - - -
475u PHE 4.8 1.5 + - - +
476u ASP* 3.3 19.2 + - - +
478u LEU* 1.3 77.1 - - - +
480u VAL* 1.3 54.9 + - - +
481u ASP 4.3 0.3 + - - -
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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