Contacts of the helix formed by residues 397 - 405 (chain V) 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 SER 397 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406S ALA* 3.6 27.6 + - - +
410S SER* 4.4 15.7 - - - -
395V GLU 3.5 2.8 + - - -
396V LEU* 1.3 72.2 - - - +
398V GLU* 1.3 61.8 + - - +
399V GLN* 3.7 9.1 + - - +
400V ASP* 3.6 19.5 + - - +
401V LYS* 2.9 33.8 + - - +
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Residues in contact with GLU 398 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397V SER* 1.3 76.6 - - - +
399V GLN* 1.3 70.7 + - + +
401V LYS* 4.0 21.5 + - - +
402V LEU* 4.2 11.8 + - - +
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Residues in contact with GLN 399 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420S LEU* 6.6 0.2 - - + -
424S GLU* 5.2 7.7 - - - +
397V SER* 3.3 7.5 + - - +
398V GLU* 1.3 88.3 - - + +
400V ASP* 1.3 59.2 + - + +
401V LYS 3.7 0.3 + - - -
402V LEU* 4.1 4.3 + - - +
403V THR* 3.0 17.3 + - - -
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Residues in contact with ASP 400 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406S ALA* 6.3 0.2 - - + -
407S GLN* 3.1 36.0 + - + +
380V THR* 4.2 13.0 - - - +
384V LEU* 4.0 5.7 - - - +
396V LEU* 3.2 27.5 - - + +
397V SER* 3.5 16.7 + - - +
399V GLN* 1.3 78.1 - - + +
401V LYS* 1.3 63.6 + - - +
402V LEU 3.4 1.1 - - - -
403V THR* 3.8 9.7 - - - -
404V VAL* 3.3 30.0 + - - +
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Residues in contact with LYS 401 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393V MET* 5.7 3.3 - - + +
394V ASP 5.8 1.8 - - - -
396V LEU* 3.8 28.9 + - + -
397V SER 2.9 22.4 + - - +
398V GLU* 4.3 20.0 + - - +
399V GLN 3.4 0.4 - - - -
400V ASP* 1.3 78.2 - - - +
402V LEU* 1.3 57.6 + - - +
403V THR 3.2 6.0 + - - -
404V VAL* 3.6 13.2 - - + +
405V GLU* 4.7 7.1 + - - +
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Residues in contact with LEU 402 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398V GLU* 4.2 11.9 + - - +
399V GLN 4.1 4.0 + - - +
400V ASP 3.4 0.4 - - - -
401V LYS* 1.3 75.9 - - - +
403V THR* 1.3 63.8 + - - +
406V ARG* 3.5 46.6 + - - +
450V ASP* 4.7 5.4 - - + +
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Residues in contact with THR 403 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377V THR* 4.3 19.3 - - + +
380V THR* 4.8 22.9 - - + +
399V GLN 3.0 18.9 + - - -
400V ASP* 3.8 13.1 - - - -
401V LYS 3.2 2.2 + - - -
402V LEU* 1.3 82.4 + - - +
404V VAL* 1.3 68.4 + - - +
405V GLU 3.2 3.4 - - - +
406V ARG* 3.0 9.9 + - + +
407V ALA* 3.0 23.8 + - + +
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Residues in contact with VAL 404 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380V THR* 6.1 1.1 - - + +
381V TYR* 3.2 44.4 - - + -
384V LEU* 5.6 3.1 - - + +
388V ILE* 4.6 11.9 - - + -
393V MET* 3.5 30.3 - - + -
396V LEU* 3.7 20.2 - - + -
400V ASP* 3.3 32.3 - - - +
401V LYS* 3.6 14.1 - - + +
403V THR* 1.3 74.8 - - - +
405V GLU* 1.3 63.0 + - + +
406V ARG 3.6 0.2 + - - -
407V ALA* 3.8 2.6 + - - -
408V ARG* 3.9 4.0 + - - +
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Residues in contact with GLU 405 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393V MET* 3.1 40.8 - - + +
401V LYS 5.1 5.2 - - - +
403V THR* 3.2 1.8 - - - +
404V VAL* 1.3 78.8 - - + +
406V ARG* 1.3 59.6 + - - +
407V ALA 3.4 1.3 + - - -
408V ARG* 2.7 38.8 + - - +
409V LYS* 3.3 38.2 + - - +
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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