Contacts of the helix formed by residues 339 - 344 (chain O) in PDB entry 1FQV
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 CYS 339 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311O LYS* 4.2 15.5 - - - +
314O LEU* 3.5 21.3 - - + +
335O LEU* 3.3 35.0 - - + -
336O LYS 3.0 31.2 + - - +
337O ASN 3.0 0.4 - - - -
338O ASP* 1.3 83.9 - - - +
340O PHE* 1.3 58.5 + - + +
341O GLN* 2.9 5.6 - - - -
342O GLU* 2.6 36.3 + - - +
343O PHE* 3.5 8.7 + - + -
360O ILE* 6.2 0.2 - - + -
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Residues in contact with PHE 340 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336O LYS 4.1 2.0 - - - -
337O ASN* 3.1 36.3 - - + +
339O CYS* 1.3 79.0 - - + +
341O GLN* 1.3 57.9 + - - +
342O GLU 3.0 0.7 - - - -
343O PHE* 3.3 16.0 + + - +
344O PHE* 2.9 50.1 + - + -
354O LEU* 4.3 6.5 - - + -
360O ILE* 3.5 43.1 - - + -
364O THR 3.3 23.6 - - - -
365O LEU* 4.3 7.0 - - + -
367O GLU* 3.8 22.4 - - + +
368O LEU* 3.6 29.2 - - + -
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Residues in contact with GLN 341 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311O LYS* 3.9 13.0 - - - +
337O ASN 4.6 0.2 + - - -
338O ASP* 3.1 36.5 + - - +
339O CYS 2.9 0.4 + - - -
340O PHE* 1.3 77.6 - - - +
342O GLU* 1.3 70.6 + - - +
344O PHE* 3.5 20.7 - - + +
345O GLN* 3.3 23.3 + - - +
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Residues in contact with GLU 342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311O LYS* 4.8 10.0 - - + -
314O LEU* 3.8 12.6 - - + +
315O SER* 2.7 43.7 + - - +
318O VAL* 3.2 49.3 - - + +
339O CYS* 2.6 20.4 + - - +
341O GLN* 1.3 88.1 - - - +
343O PHE* 1.3 57.9 + - - +
344O PHE 3.1 1.8 - - - -
345O GLN* 3.0 32.1 + - - +
346O LEU 3.8 0.5 + - - -
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Residues in contact with PHE 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314O LEU* 3.7 34.1 - - + -
327O LEU* 3.7 30.5 - - + -
329O LEU* 3.8 14.8 - - + -
335O LEU* 4.9 1.3 - - + -
339O CYS* 4.2 4.3 - - + -
340O PHE* 3.3 33.4 + + - +
342O GLU* 1.3 76.6 - - - +
344O PHE* 1.3 63.0 + - - +
346O LEU* 3.1 31.1 + - + +
349O LEU* 4.2 6.0 - - + +
352O LEU* 3.6 32.5 - - + -
354O LEU* 4.0 20.6 - - + -
360O ILE* 6.0 0.2 - - + -
368O LEU* 4.3 2.5 - - + -
371O ILE* 3.6 25.1 - - + +
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Residues in contact with PHE 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340O PHE* 2.9 40.8 + - + +
341O GLN* 3.5 19.1 - - + +
342O GLU 3.1 0.2 - - - -
343O PHE* 1.3 79.1 - - - +
345O GLN* 1.3 58.3 + - + +
346O LEU 3.1 9.1 + - - +
347O ASN* 3.9 9.9 - - - +
367O GLU* 3.5 18.6 - - + -
368O LEU* 4.4 2.2 - - - -
370O GLU* 3.2 43.3 - - + -
371O ILE* 3.4 30.3 - - + +
372O PRO* 6.0 2.1 - - - +
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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