Contacts of the helix formed by residues 284 - 292 (chain F) 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 THR 284 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ASP* 4.9 9.4 - - + +
282C GLN* 3.3 30.1 - - - +
286C LEU* 3.7 25.1 - - + -
274F ARG* 3.3 27.3 + - - +
282F GLN* 3.0 4.4 - - - +
283F PRO* 1.3 76.5 - - + +
285F LEU* 1.3 60.1 + - - +
286F ALA 3.5 2.2 - - - -
287F THR* 3.6 10.5 - - - +
288F ASP* 3.0 35.7 + - - +
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Residues in contact with LEU 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ARG* 6.2 2.2 - - - +
262F THR* 3.7 15.4 + - + +
281F TYR* 3.5 42.6 - - + -
282F GLN* 3.2 23.8 + - + +
283F PRO 3.3 3.4 + - - -
284F THR* 1.3 77.3 - - - +
286F ALA* 1.3 64.7 + - + +
288F ASP* 4.0 2.5 - - - +
289F MET* 3.3 29.2 + - + +
320F PRO* 3.5 28.3 - - + +
321F ALA 4.3 0.4 - - - +
324F THR* 3.4 30.3 - - - +
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Residues in contact with ALA 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ALA* 4.8 9.5 - - + +
245C GLN* 6.1 2.2 - - - +
278C VAL* 4.3 24.2 - - + +
282C GLN* 5.2 3.0 + - - +
284F THR 3.5 0.2 - - - -
285F LEU* 1.3 82.9 - - + +
287F THR* 1.3 63.6 + - + +
289F MET* 3.3 5.6 + - - +
290F GLY* 3.1 22.0 + - - -
324F THR* 4.1 23.0 - - + +
328F HIS* 5.1 1.0 + - - -
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Residues in contact with THR 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ALA 4.4 10.7 - - - +
239C SER 5.4 1.6 - - - +
240C GLU 4.7 3.4 - - - +
241C ALA* 5.2 1.1 - - - -
242C ALA* 4.6 11.4 - - + +
245C GLN* 4.5 18.4 - - - +
279C ALA* 6.5 0.2 - - + -
282C GLN* 3.1 39.0 + - - +
284F THR* 3.4 12.1 + - - +
286F ALA* 1.3 74.9 - - + +
288F ASP* 1.3 68.3 + - - +
290F GLY* 2.8 14.6 + - - +
291F LEU* 2.9 25.3 + - - +
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Residues in contact with ASP 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PHE* 3.6 25.1 - - + -
262F THR* 6.2 0.4 - - + -
265F GLY* 5.9 1.0 - - - -
274F ARG* 4.9 3.8 + - - -
282F GLN* 4.3 14.5 + - - +
284F THR* 3.0 34.4 + - - +
285F LEU* 4.0 3.8 - - - +
286F ALA 3.4 0.2 - - - -
287F THR* 1.3 77.2 + - - +
289F MET* 1.3 57.7 + - - +
290F GLY 2.9 9.6 + - - -
291F LEU* 3.6 12.8 + - - +
292F LEU* 3.4 24.1 + - - +
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Residues in contact with MET 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F ILE* 5.4 8.3 - - + -
261F PHE* 4.1 6.7 - - + -
262F THR* 3.4 26.7 - - - +
285F LEU* 3.3 27.4 + - + +
286F ALA* 3.3 9.8 + - - +
287F THR 3.2 0.4 - - - -
288F ASP* 1.3 77.1 - - - +
290F GLY* 1.3 56.3 + - - +
292F LEU* 5.0 2.5 - - - -
293F GLN* 3.1 34.2 - - - +
321F ALA* 3.5 22.4 - - + +
324F THR* 3.9 11.2 - - + -
325F THR* 3.3 39.5 - - - +
328F HIS* 3.3 12.4 + - + +
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Residues in contact with GLY 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ALA* 4.4 12.8 - - - -
239C SER* 4.4 7.6 - - - -
286F ALA 3.1 7.5 + - - -
287F THR 2.8 10.2 + - - -
288F ASP 2.9 0.6 - - - -
289F MET* 1.3 80.3 - - - +
291F LEU* 1.3 64.0 + - - -
292F LEU 3.0 1.3 - - - -
294F GLU* 2.9 32.2 + - - +
328F HIS* 4.3 10.3 - - - -
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Residues in contact with LEU 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C SER* 3.9 29.1 - - - +
119F ALA 4.7 0.2 - - - +
120F ASP* 5.5 5.2 - - - +
121F PRO* 4.4 14.1 - - + +
234F LEU* 5.6 2.5 - - + -
287F THR* 2.9 27.5 + - - +
288F ASP* 4.3 11.9 - - - +
290F GLY* 1.3 72.0 - - - +
292F LEU* 1.3 56.4 + - - +
295F ARG* 3.1 30.9 + - - +
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Residues in contact with LEU 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F ALA* 4.3 19.5 - - + +
234F LEU* 3.5 32.3 - - + +
237F LEU* 3.5 31.3 - - + +
255F ILE* 6.1 1.6 - - + -
258F ILE* 4.2 19.1 - - + -
261F PHE* 3.6 41.7 - - + -
288F ASP 3.4 13.7 + - - +
289F MET* 5.0 1.8 - - - -
290F GLY 3.0 0.2 - - - -
291F LEU* 1.3 79.6 - - - +
293F GLN* 1.3 68.7 + - - +
294F GLU 3.3 0.2 - - - -
295F ARG* 3.4 11.3 + - - +
296F ILE* 3.6 9.0 - - + +
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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