Contacts of the helix formed by residues 355 - 362 (chain S) 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 GLU 355 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175S THR* 4.7 1.5 - - - +
353S PHE* 3.5 28.7 + - + -
354S LEU* 1.3 70.1 - - - +
356S ALA* 1.3 63.9 + - - +
357S GLU* 4.2 11.6 - - + +
358S LEU* 3.2 37.4 + - + +
359S PHE* 3.2 1.7 + - - +
366S ALA* 3.2 27.5 + - - +
368S ASN* 3.4 25.3 + - + -
400S ARG* 3.2 19.2 + - - -
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Residues in contact with ALA 356 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172S ASP* 4.1 21.2 + - + +
173S ARG 5.7 0.4 - - - +
175S THR* 4.2 17.3 - - + -
354S LEU 3.5 4.6 + - - -
355S GLU* 1.3 72.1 - - - +
357S GLU* 1.3 67.0 + - + +
359S PHE* 3.0 15.0 + - - +
360S TYR* 3.2 39.5 + - + +
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Residues in contact with GLU 357 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355S GLU* 3.2 13.9 - - + +
356S ALA* 1.3 82.3 - - + +
358S LEU* 1.3 61.4 + - + +
360S TYR* 3.9 11.0 + - - +
361S LYS* 3.5 26.3 + - - +
379V GLN* 2.9 36.3 + - - +
383V SER* 5.4 2.6 - - - -
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Residues in contact with LEU 358 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355S GLU* 3.2 35.5 + - + +
356S ALA 3.1 0.4 - - - -
357S GLU* 1.3 77.3 - - + +
359S PHE* 1.3 65.5 + - - +
360S TYR 3.4 0.2 - - - -
361S LYS* 3.6 13.1 + - + +
362S GLY 3.4 3.8 + - - -
363S ILE* 3.1 50.0 + - + +
366S ALA* 3.5 16.6 - - + -
367S ILE 3.8 25.6 - - - +
368S ASN 3.9 0.7 - - - +
400S ARG* 3.5 29.6 - - - +
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Residues in contact with PHE 359 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174S GLN* 4.1 20.4 - - + +
175S THR* 3.4 31.9 - - - +
176S GLY* 4.7 2.9 - - - -
355S GLU 3.2 11.1 + - - +
356S ALA* 3.0 14.7 + - - +
358S LEU* 1.3 77.3 - - - +
360S TYR* 1.3 77.4 + + + +
362S GLY* 3.4 12.3 + - - -
363S ILE 3.9 1.8 - - - -
364S ARG* 3.9 45.1 + - + -
365S PRO* 5.9 0.9 - - + -
366S ALA* 3.5 11.4 - - + +
354V LYS* 6.2 3.1 - - + -
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Residues in contact with TYR 360 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174S GLN 5.6 3.5 + - - -
356S ALA* 3.2 38.8 + - + +
357S GLU* 4.3 10.1 - - - +
359S PHE* 1.3 86.3 - + - +
361S LYS* 1.3 67.1 + - - +
362S GLY* 3.0 5.0 + - - -
364S ARG* 5.1 0.2 + - - -
351V LEU* 3.9 31.6 - - + -
352V ASP* 3.6 30.7 + - + +
354V LYS* 3.6 37.2 - - + +
375V GLN* 3.6 34.2 - - + +
376V GLU* 4.6 1.4 + - - +
379V GLN* 4.2 14.4 - - + +
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Residues in contact with LYS 361 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357S GLU* 3.5 18.1 + - - +
358S LEU* 3.9 11.0 - - + +
359S PHE 3.4 0.4 - - - -
360S TYR* 1.3 78.3 - - - +
362S GLY* 1.3 57.9 + - - +
363S ILE* 3.7 24.2 - - + +
431S LYS* 4.7 3.6 + - - -
375V GLN 4.7 2.2 - - - -
376V GLU* 3.3 27.4 - - + +
379V GLN* 4.2 33.8 - - + +
380V THR* 5.4 8.1 - - - +
383V SER* 4.9 11.9 + - - -
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Residues in contact with GLY 362 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358S LEU 4.0 0.2 - - - -
359S PHE 3.4 9.6 + - - -
360S TYR 3.0 5.9 - - - -
361S LYS* 1.3 80.2 - - - +
363S ILE* 1.3 63.6 + - - +
364S ARG* 3.2 28.7 + - - -
431S LYS* 3.3 25.3 + - - +
376V GLU* 4.7 7.9 - - - -
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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