Contacts of the helix formed by residues 463 - 473 (chain O) in PDB entry 3FKS
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 ILE 463 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413O PHE* 3.5 9.5 - - + -
436O ASP* 4.5 9.6 + - - +
440O SER* 3.1 37.1 + - - +
443O ALA* 5.5 0.2 - - + -
444O VAL* 4.4 8.7 - - + -
449O TYR* 3.4 51.4 - - + +
457O PHE* 4.2 12.6 - - + -
462O GLY* 1.3 72.5 - - - -
464O GLU* 1.3 69.0 + - + +
466O VAL* 3.0 31.2 + - + +
467O VAL* 3.7 7.3 + - + +
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Residues in contact with GLU 464 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436O ASP* 5.3 6.4 + - - +
462O GLY* 3.1 1.5 - - - -
463O ILE* 1.3 86.0 - - + +
465O ASP* 1.3 56.8 + - - +
466O VAL 3.2 0.9 - - - -
467O VAL* 3.2 26.0 - - + +
468O ALA* 3.7 9.4 + - - +
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Residues in contact with ASP 465 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430O LYS* 3.0 38.9 - - - +
460O VAL* 4.0 11.6 - - + +
461O GLY* 3.2 21.6 + - - +
462O GLY 3.1 14.9 + - - +
464O GLU* 1.3 76.5 - - - +
466O VAL* 1.3 64.2 + - - +
468O ALA* 4.2 10.9 - - - +
469O LYS* 3.5 18.5 + - - +
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Residues in contact with VAL 466 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413O PHE* 3.5 35.4 - - + -
452O ILE* 4.3 9.6 - - + -
456O ALA* 3.5 34.9 - - + +
457O PHE* 3.9 25.1 - - + -
460O VAL* 4.0 8.1 - - + -
462O GLY 3.6 2.2 - - - +
463O ILE* 3.0 22.3 + - + +
465O ASP* 1.3 78.0 - - - +
467O VAL* 1.3 55.6 + - + +
469O LYS* 3.0 6.1 + - - +
470O ALA* 2.8 32.1 + - - +
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Residues in contact with VAL 467 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449O TYR* 4.2 24.9 - - + +
452O ILE* 4.3 12.3 - - + -
463O ILE 4.1 5.4 - - - +
464O GLU* 3.2 24.5 - - + +
466O VAL* 1.3 76.8 - - + +
468O ALA* 1.3 61.1 + - - +
470O ALA* 3.0 10.8 + - + +
471O GLU* 2.9 35.8 + - + +
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Residues in contact with ALA 468 (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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464O GLU 3.7 13.4 + - - +
465O ASP* 4.2 11.0 - - - +
466O VAL 3.2 0.4 - - - -
467O VAL* 1.3 83.5 - - + +
469O LYS* 1.3 58.9 + - - +
471O GLU* 3.5 8.7 + - - +
472O LYS* 3.2 35.7 + - - +
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Residues in contact with LYS 469 (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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455O HIS* 3.5 34.6 + - - +
456O ALA* 4.0 10.3 - - - +
458O TYR* 2.9 26.9 + - - -
459O MET* 4.2 5.7 + - - +
460O VAL* 3.5 20.4 - - + +
465O ASP* 3.5 13.7 + - - +
466O VAL 3.0 8.2 + - - +
468O ALA* 1.3 77.4 - - - +
470O ALA* 1.3 60.0 + - - +
471O GLU 3.3 0.4 - - - -
472O LYS* 3.8 14.3 - - + +
473O LEU* 3.1 40.2 + - + +
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Residues in contact with ALA 470 (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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452O ILE* 4.5 14.6 - - + -
453O PRO* 5.3 5.4 - - + -
456O ALA* 4.4 16.1 - - + +
466O VAL 2.8 12.3 + - - +
467O VAL* 3.0 17.0 + - + +
469O LYS* 1.3 78.6 - - - +
471O GLU* 1.3 57.8 + - + +
473O LEU* 3.5 5.4 + - - +
474O ALA* 2.8 27.8 + - - +
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Residues in contact with GLU 471 (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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467O VAL* 2.9 21.2 + - + +
468O ALA* 3.7 10.3 - - - +
470O ALA* 1.3 77.4 - - + +
472O LYS* 1.3 64.5 + - + +
473O LEU 3.1 0.2 - - - -
474O ALA* 3.1 26.0 + - - +
475O ALA* 3.4 9.9 + - - +
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Residues in contact with LYS 472 (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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468O ALA* 3.2 22.8 + - - +
469O LYS* 3.8 16.6 - - + +
470O ALA 3.4 0.2 - - - -
471O GLU* 1.3 79.0 - - + +
473O LEU* 1.3 64.3 + - + +
475O ALA* 3.8 16.0 + - - +
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Residues in contact with LEU 473 (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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453O PRO* 6.0 7.4 - - + -
455O HIS* 4.2 37.0 - - + +
456O ALA* 4.6 5.8 - - + +
469O LYS* 3.1 36.3 + - + +
470O ALA* 3.5 5.8 + - - +
472O LYS* 1.3 79.7 - - + +
474O ALA* 1.3 62.2 + - - +
475O ALA 3.3 7.3 - - - +
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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