Contacts of the helix formed by residues 284 - 294 (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 THR 284 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L ASP* 5.0 7.0 - - + +
282L GLN* 3.6 13.9 - - - +
286L LEU* 3.8 34.8 - - + -
274O ARG* 3.3 23.9 + - - +
282O GLN* 3.0 1.8 - - - +
283O PRO* 1.3 81.0 - - + +
285O LEU* 1.3 63.6 + - - +
286O ALA 3.2 3.5 + - - -
287O THR* 3.3 7.3 + - - +
288O ASP* 2.9 49.7 + - - +
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Residues in contact with LEU 285 (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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262O THR* 3.6 16.4 - - + +
281O TYR* 3.4 42.6 - - + -
282O GLN* 3.1 26.9 + - + +
283O PRO 3.4 2.4 + - - -
284O THR* 1.3 75.2 - - - +
286O ALA* 1.3 64.3 + - - +
288O ASP* 3.8 2.0 + - - +
289O MET* 3.4 37.5 + - + +
320O PRO* 3.8 34.8 - - + +
321O ALA* 4.2 0.4 - - - +
324O THR* 3.9 13.2 - - - +
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Residues in contact with ALA 286 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238L ALA* 4.4 3.7 - - - +
245L GLN* 5.4 9.6 - - - +
278L VAL* 4.5 21.3 - - + -
279L ALA* 6.0 2.2 - - - +
282L GLN* 4.3 10.0 + - - +
283O PRO 5.1 0.4 + - - -
284O THR 3.2 0.6 - - - -
285O LEU* 1.3 84.2 - - + +
287O THR* 1.3 60.4 + - + +
289O MET* 3.2 5.4 + - - +
290O GLY* 3.0 24.1 + - - -
324O THR* 4.7 14.2 - - + +
328O HIS* 5.3 1.7 + - - -
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Residues in contact with THR 287 (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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238L ALA 4.4 6.7 - - - -
239L SER 5.8 0.9 - - - -
240L GLU 4.2 11.4 - - - +
241L ALA* 4.8 1.8 - - - -
242L ALA* 4.1 19.7 - - + +
245L GLN* 4.6 8.1 - - - +
282L GLN* 3.2 36.0 + - - +
284O THR* 3.3 8.8 + - - +
286O ALA* 1.3 74.1 - - + +
288O ASP* 1.3 69.8 + - - +
290O GLY 4.3 0.7 - - - +
291O LEU* 2.9 45.4 + - - +
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Residues in contact with ASP 288 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261O PHE* 3.2 31.8 - - + -
262O THR* 6.4 0.2 - - + -
265O GLY* 5.9 1.0 - - - -
274O ARG* 4.3 6.9 + - - -
282O GLN* 4.2 15.9 + - - +
284O THR* 2.9 43.7 + - - +
285O LEU* 4.0 5.8 - - - +
287O THR* 1.3 81.3 + - - +
289O MET* 1.3 59.7 + - - +
291O LEU* 4.0 10.2 + - - +
292O LEU* 4.0 6.8 + - - +
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Residues in contact with MET 289 (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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258O ILE* 6.3 2.2 - - + -
261O PHE* 4.2 11.6 - - + -
262O THR* 3.6 23.6 - - + +
285O LEU* 3.4 27.9 + - + +
286O ALA* 3.2 5.3 + - - +
287O THR 3.1 0.6 - - - -
288O ASP* 1.3 79.0 - - - +
290O GLY* 1.3 53.7 + - - +
291O LEU 3.3 0.2 - - - -
292O LEU* 3.0 4.9 + - + +
293O GLN* 2.7 49.5 + - - +
321O ALA* 4.0 11.7 - - + +
324O THR* 3.8 19.5 - - + -
325O THR* 3.9 34.3 - - - +
328O HIS* 4.1 14.1 - - + +
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Residues in contact with GLY 290 (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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238L ALA 3.3 28.9 - - - -
239L SER* 4.1 2.2 - - - -
286O ALA 3.0 11.0 + - - -
287O THR 3.2 0.4 + - - -
289O MET* 1.3 73.5 - - - +
291O LEU* 1.3 55.2 + - - +
292O LEU 2.9 9.4 + - - -
294O GLU* 3.1 32.6 + - - +
328O HIS* 4.2 14.8 - - - -
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Residues in contact with LEU 291 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239L SER* 3.7 29.2 - - - +
120O ASP* 5.5 4.9 - - - +
121O PRO* 4.8 12.6 - - + +
234O LEU* 4.3 6.8 - - - +
287O THR* 2.9 31.4 + - - +
288O ASP* 4.4 9.4 - - - +
289O MET 3.3 0.4 - - - -
290O GLY* 1.3 73.6 - - - +
292O LEU* 1.3 57.8 + - - +
295O ARG* 3.3 24.2 + - - +
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Residues in contact with LEU 292 (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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233O ALA* 4.0 11.7 - - + -
234O LEU* 3.7 32.5 - - + +
237O LEU* 3.8 17.5 - - + -
258O ILE* 3.9 19.5 - - + -
261O PHE* 3.5 40.2 - - + -
288O ASP 4.0 9.0 - - - +
289O MET* 3.0 7.6 + - + +
290O GLY 2.9 0.2 - - - -
291O LEU* 1.3 81.1 - - - +
293O GLN* 1.3 70.9 + - - +
294O GLU 3.3 1.1 - - - -
295O ARG* 3.5 10.1 + - - +
296O ILE* 3.3 21.7 + - + +
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Residues in contact with GLN 293 (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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152O LYS* 3.0 32.5 + - - +
258O ILE* 4.4 12.6 - - - +
289O MET* 2.7 30.8 + - + +
292O LEU* 1.3 74.6 - - - +
294O GLU* 1.3 61.4 + - - +
295O ARG 3.1 0.4 - - - -
296O ILE* 2.9 36.8 + - - +
297O THR* 5.0 0.2 - - - -
308O GLN* 3.0 36.7 + - - +
325O THR* 3.9 23.0 - - - +
328O HIS* 3.5 35.2 - - + +
329O LEU* 4.9 1.4 - - - +
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Residues in contact with GLU 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211L LYS* 3.5 19.9 - - - +
212L ARG* 2.7 51.3 + - - +
213L SER* 4.6 2.3 + - - -
237L THR* 3.8 7.8 + - - -
238L ALA* 4.3 4.0 + - + -
239L SER* 3.4 20.3 + - - +
121O PRO* 3.6 23.5 - - + +
122O PRO* 3.8 3.8 - - - +
127O GLN* 5.3 3.6 + - - -
152O LYS* 5.1 2.1 + - - -
290O GLY* 3.1 23.8 + - - +
293O GLN* 1.3 78.2 - - - +
295O ARG* 1.3 59.6 + - - +
297O THR* 3.4 21.2 - - - +
328O HIS* 5.3 3.1 + - + -
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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