Contacts of the helix formed by residues 355 - 361 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175L THR* 4.6 2.0 - - - +
353L PHE* 3.5 29.9 + - + -
354L LEU* 1.3 73.2 - - - +
356L ALA* 1.3 64.4 + - - +
357L GLU* 4.0 17.5 - - + +
358L LEU* 3.2 36.3 + - + +
359L PHE* 3.2 21.5 + - - +
366L ALA* 3.3 11.8 + - - +
368L ASN* 3.3 24.7 - - + +
371L LEU* 5.3 2.4 - - - +
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Residues in contact with ALA 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L ASP* 5.1 13.4 - - + +
173L ARG 5.9 0.2 - - - +
175L THR* 4.2 19.3 - - + +
354L LEU 3.8 2.8 + - - -
355L GLU* 1.3 71.4 - - - +
357L GLU* 1.3 62.1 + - - +
359L PHE* 3.6 4.3 + - - +
360L TYR* 2.9 42.6 + - + -
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Residues in contact with GLU 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355L GLU* 3.1 19.2 - - + +
356L ALA* 1.3 76.6 - - - +
358L LEU* 1.3 68.5 + - + +
359L PHE 3.2 0.7 + - - -
360L TYR* 3.3 10.2 + - - -
361L LYS* 3.3 14.9 + - + +
379O GLN* 3.6 34.0 + - + +
383O SER* 4.0 17.7 + - - -
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Residues in contact with LEU 358 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355L GLU* 3.2 31.0 + - + +
356L ALA 3.5 0.2 - - - -
357L GLU* 1.3 83.2 - - + +
359L PHE* 1.3 63.3 + - - +
361L LYS* 3.0 29.3 + - + +
363L ILE* 3.2 47.2 + - + +
366L ALA* 4.0 13.9 - - + +
367L ILE 3.6 27.1 - - - +
368L ASN* 4.0 14.4 - - + +
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Residues in contact with PHE 359 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L GLN 4.8 7.9 - - - -
175L THR* 4.2 25.6 - - - +
176L GLY* 5.3 3.6 - - - -
355L GLU 3.2 16.2 + - - +
356L ALA* 3.7 8.3 - - - +
357L GLU 3.2 0.8 - - - -
358L LEU* 1.3 80.9 - - - +
360L TYR* 1.3 80.5 - + - +
362L GLY* 3.5 5.0 + - - -
363L ILE 3.7 6.5 - - - -
364L ARG* 3.1 69.8 + - + +
366L ALA* 3.7 10.0 - - + +
354O LYS* 3.6 28.7 - - - -
375O GLN* 5.8 0.2 - - - -
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Residues in contact with TYR 360 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L GLN 5.2 2.7 + - - -
356L ALA* 2.9 33.9 - - + -
357L GLU 3.3 3.1 + - - +
358L LEU 3.3 0.4 - - - -
359L PHE* 1.3 93.8 - + - +
361L LYS* 1.3 58.3 + - - +
362L GLY 3.1 5.4 - - - -
364L ARG* 4.7 3.4 - - - +
350O PRO 4.8 0.2 - - - -
351O LEU* 3.2 47.7 + - + -
352O ASP* 4.5 1.4 - - - -
353O SER 5.1 0.5 + - - -
354O LYS* 3.4 29.7 - - + +
372O SER 4.9 0.2 - - - +
375O GLN* 3.4 44.1 + - + +
376O GLU* 3.3 28.9 + - - +
379O GLN* 4.0 24.6 - - + +
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Residues in contact with LYS 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357L GLU* 3.3 14.5 + - + +
358L LEU* 3.0 28.7 + - + +
360L TYR* 1.3 77.8 - - - +
362L GLY* 1.3 57.6 + - - +
363L ILE* 3.5 12.8 + - + +
431L LYS* 4.7 4.2 + - - -
376O GLU* 3.3 18.9 - - - +
379O GLN* 4.8 9.4 - - + -
380O THR* 5.8 3.6 - - - +
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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