Contacts of the helix formed by residues 284 - 294 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282T GLN* 3.4 36.6 - - + +
286T LEU* 3.7 18.2 - - + -
269W SER* 5.2 0.3 - - - -
274W ARG* 3.6 24.2 + - - +
282W GLN* 3.1 11.4 - - - +
283W PRO* 1.3 79.5 - - + +
285W LEU* 1.3 63.7 + - - +
286W ALA 3.4 2.0 - - - -
287W THR* 3.4 6.8 + - - +
288W ASP* 3.0 42.5 + - - -
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Residues in contact with LEU 285 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281T ARG* 4.9 14.6 - - - +
262W THR* 3.8 29.4 - - + -
281W TYR* 4.4 8.5 - - + -
282W GLN* 3.4 33.0 + - + +
283W PRO 3.3 3.2 + - - -
284W THR* 1.3 77.9 - - - +
286W ALA* 1.3 66.0 + - - +
288W ASP* 3.6 1.4 - - + +
289W MET* 3.2 23.5 + - + +
320W PRO* 3.5 31.4 - - + +
324W THR* 3.3 31.6 - - + +
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Residues in contact with ALA 286 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238T ALA* 5.0 3.8 - - - +
245T GLN* 6.0 2.2 - - - +
278T VAL* 3.9 28.6 - - + +
279T ALA* 5.9 1.3 - - - +
282T GLN* 5.3 3.8 - - - +
283W PRO 5.2 0.4 + - - -
284W THR 3.4 0.8 - - - -
285W LEU* 1.3 81.3 - - - +
287W THR* 1.3 62.3 + - + +
289W MET* 3.3 5.4 + - - +
290W GLY* 3.0 21.1 + - - -
324W THR* 4.2 14.1 - - + +
328W HIS* 5.1 1.9 + - - -
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Residues in contact with THR 287 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238T ALA 3.9 11.9 - - - +
239T SER 5.2 1.1 - - - +
240T GLU 3.7 22.9 - - - +
241T ALA* 4.9 1.6 - - - -
242T ALA* 4.5 12.3 - - - +
245T GLN* 4.6 6.1 - - - +
282T GLN* 3.1 30.9 + - - +
284W THR* 3.4 9.5 + - - -
286W ALA* 1.3 78.2 - - + +
288W ASP* 1.3 64.6 + - - +
290W GLY 2.8 16.0 + - - +
291W LEU* 3.0 25.9 + - - +
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Residues in contact with ASP 288 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261W PHE* 3.9 24.2 - - + -
265W GLY* 4.4 6.9 - - - +
269W SER* 6.0 0.2 - - - -
274W ARG* 5.5 2.5 + - - -
282W GLN* 3.2 27.3 + - - +
284W THR* 3.0 41.0 + - - +
285W LEU* 3.6 4.5 - - + +
287W THR* 1.3 76.4 + - - +
289W MET* 1.3 61.6 + - - +
291W LEU* 4.1 6.1 + - - +
292W LEU* 4.0 10.0 + - - +
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Residues in contact with MET 289 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258W ILE* 4.2 13.7 - - + -
261W PHE* 4.5 13.9 - - + -
262W THR* 3.7 23.6 - - + +
285W LEU* 3.2 11.9 + - + +
286W ALA 3.5 8.3 - - - +
287W THR 3.1 0.4 - - - -
288W ASP* 1.3 78.1 - - - +
290W GLY* 1.3 64.3 + - - +
292W LEU* 3.6 3.1 + - - +
293W GLN* 3.1 45.0 + - + +
321W ALA 4.9 0.9 - - - +
324W THR* 3.7 20.4 - - + +
325W THR* 3.6 28.3 - - - +
328W HIS* 3.7 23.1 - - + +
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Residues in contact with GLY 290 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238T ALA* 4.2 25.1 - - - -
239T SER* 4.5 1.8 - - - -
286W ALA 3.0 11.1 + - - -
287W THR 2.8 8.7 + - - -
289W MET* 1.3 74.8 - - - +
291W LEU* 1.3 57.8 + - - -
292W LEU 3.0 0.5 + - - -
293W GLN 3.1 0.9 + - - -
294W GLU* 2.7 40.3 + - - +
328W HIS* 4.2 6.9 + - - -
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Residues in contact with LEU 291 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239T SER* 3.1 41.5 - - - +
118W HIS* 6.3 1.1 - - - +
119W ALA 5.3 2.4 - - - +
121W PRO* 4.4 13.0 - - + +
234W LEU* 5.4 4.3 - - + -
287W THR* 3.0 24.2 + - - +
288W ASP* 4.7 5.6 - - - +
290W GLY* 1.3 70.3 - - - +
292W LEU* 1.3 58.3 + - - +
294W GLU 4.2 0.2 - - - -
295W ARG* 3.2 30.5 + - - +
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Residues in contact with LEU 292 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233W ALA* 4.1 25.4 - - + +
234W LEU* 3.8 22.4 - - + +
237W LEU* 3.6 36.9 - - + +
253W LEU* 5.9 1.8 - - + -
255W ILE* 6.0 7.0 - - + -
258W ILE* 5.0 7.4 - - + -
261W PHE* 3.7 35.9 - - + -
288W ASP 4.0 10.3 + - - +
289W MET* 3.6 7.5 + - - +
290W GLY 3.1 0.6 - - - -
291W LEU* 1.3 79.5 - - - +
293W GLN* 1.3 78.5 + - + +
295W ARG* 3.5 10.1 + - - +
296W ILE* 3.8 10.2 - - + +
308W GLN* 6.2 0.4 - - - +
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Residues in contact with GLN 293 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152W LYS* 2.9 44.5 + - - +
258W ILE* 4.3 5.9 - - - +
289W MET* 3.1 37.8 + - - +
290W GLY 3.1 1.6 + - - -
292W LEU* 1.3 78.5 - - + +
294W GLU* 1.3 57.1 - - - +
295W ARG 3.1 5.8 - - - -
296W ILE* 3.0 28.0 + - - +
308W GLN* 2.8 45.7 + - - +
325W THR* 5.0 4.4 + - - +
328W HIS* 3.5 27.7 - - + +
329W LEU* 5.7 0.6 - - - +
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Residues in contact with GLU 294 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211T LYS* 3.7 15.1 - - - +
212T ARG* 2.9 46.3 + - + +
213T SER 4.8 0.7 + - - -
237T THR* 3.5 15.8 + - - -
238T ALA* 3.8 10.0 + - + -
239T SER* 3.7 31.6 - - - +
121W PRO* 3.6 20.5 - - + +
122W PRO* 3.8 6.6 - - - +
127W GLN* 4.6 4.5 + - - -
152W LYS* 5.0 1.7 + - - -
290W GLY* 2.7 25.7 + - - +
291W LEU 4.6 0.2 - - - +
293W GLN* 1.3 72.6 - - - +
295W ARG* 1.3 58.7 + - - +
296W ILE 3.4 1.3 - - - -
297W THR* 4.1 10.1 - - - +
328W HIS* 4.7 4.1 + - + -
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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
------------------------------------------------------------
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