Contacts of the helix formed by residues 504 - 510 (chain F) in PDB entry 1W1W
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 504 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1218B LEU* 4.0 24.5 - - + -
1223B TYR* 4.8 4.5 - - - -
488F MET* 4.9 3.8 - - + -
502F VAL 3.9 0.2 + - - -
503F ILE* 1.3 72.9 - - - +
505F THR* 1.3 69.0 + - - +
507F VAL* 3.0 16.9 + - + +
508F LEU* 3.1 46.7 + - + +
524F ALA 3.8 4.7 - - - -
527F GLY* 3.9 4.7 - - - -
528F PHE* 3.7 31.0 - + - -
531F ILE* 2.9 35.2 - - + -
551F ILE* 3.0 43.8 + - + +
553F ILE* 4.0 9.8 - - + +
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Residues in contact with THR 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223B TYR* 4.2 19.6 + - + +
503F ILE* 3.2 13.6 - - - +
504F PHE* 1.3 84.4 - - - +
506F ASP* 1.3 59.3 + - - +
508F LEU* 3.4 10.5 + - + +
509F LYS* 3.0 24.9 + - - +
550F ASN* 4.1 13.9 + - - -
551F ILE 5.8 0.3 + - - -
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Residues in contact with ASP 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F GLU* 5.1 4.0 - - - +
502F VAL* 5.0 4.9 - - + -
503F ILE* 3.2 35.4 + - - +
504F PHE 3.1 0.8 - - - -
505F THR* 1.3 75.8 - - - +
507F VAL* 1.3 67.4 + - - +
508F LEU 3.1 1.6 - - - -
509F LYS* 2.8 35.7 + - + +
510F SER* 3.1 8.4 + - - -
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Residues in contact with VAL 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488F MET* 3.8 34.3 - - + -
491F ILE* 4.1 17.0 - - + -
492F LEU* 3.5 21.1 - - + -
495F GLU* 4.0 4.7 - - - +
502F VAL* 3.4 22.9 - - + -
503F ILE 3.3 14.8 - - - +
504F PHE* 3.0 9.8 + - + +
506F ASP* 1.3 76.8 - - - +
508F LEU* 1.3 63.1 + - - +
510F SER* 3.1 23.3 + - - +
511F GLN* 4.0 7.1 - - - +
553F ILE* 4.2 8.7 - - + -
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Residues in contact with LEU 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223B TYR* 3.8 31.6 - - + +
488F MET* 5.1 3.6 - - + -
504F PHE* 3.1 52.9 + - + +
505F THR* 3.5 9.9 - - + +
506F ASP 3.1 0.2 - - - -
507F VAL* 1.3 77.3 - - - +
509F LYS* 1.3 67.1 + - - +
510F SER 3.0 1.0 + - - -
511F GLN* 3.3 33.0 + - - +
512F ALA* 5.8 0.2 - - - +
523F GLU* 4.0 22.2 - - + +
524F ALA* 3.9 10.8 - - - +
527F GLY* 4.4 7.2 - - - -
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Residues in contact with LYS 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F THR 3.0 14.7 + - - +
506F ASP* 2.8 26.2 + - + +
508F LEU* 1.3 74.8 - - - +
510F SER* 1.3 58.3 + - - +
511F GLN 2.9 8.0 + - - -
512F ALA 3.6 16.8 + - - -
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Residues in contact with SER 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491F ILE* 3.4 18.3 - - - +
495F GLU* 3.2 23.8 + - - -
506F ASP 3.1 5.3 + - - -
507F VAL 3.1 11.0 + - - -
508F LEU 3.0 0.4 + - - -
509F LYS* 1.3 79.1 - - - +
511F GLN* 1.3 72.3 + - - +
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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