Contacts of the helix formed by residues 284 - 294 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38U ASP* 5.1 5.8 - - + +
282U GLN* 3.2 31.2 - - - +
286U LEU* 3.8 20.6 - - + -
274X ARG* 2.9 33.7 + - - +
282X GLN* 3.8 7.0 - - - +
283X PRO* 1.3 72.7 - - - +
285X LEU* 1.3 58.8 + - - +
287X THR* 3.5 12.1 - - - +
288X ASP* 2.8 37.1 + - - +
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Residues in contact with LEU 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278U VAL* 6.3 2.2 - - + -
281U ARG* 5.9 4.3 - - - +
262X THR* 3.7 25.5 - - + +
281X TYR* 3.7 32.8 - - + -
282X GLN* 3.4 18.6 - - + +
283X PRO 3.0 6.3 + - - +
284X THR* 1.3 75.0 - - - +
286X ALA* 1.3 72.1 + - + +
287X THR 3.2 1.1 - - - -
288X ASP* 3.6 2.4 + - - +
289X MET* 3.3 29.3 + - + +
320X PRO* 3.6 33.9 - - + +
321X ALA* 4.3 10.1 - - - +
324X THR* 4.1 13.7 - - - +
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Residues in contact with ALA 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238U ALA* 3.9 13.4 - - + +
245U GLN* 5.9 4.9 - - - +
275U LYS 6.2 0.2 - - - +
278U VAL* 4.2 24.5 - - + +
282U GLN* 5.2 0.9 + - - +
283X PRO 4.8 1.0 + - - -
285X LEU* 1.3 86.1 - - + +
287X THR* 1.3 64.8 + - + +
289X MET* 3.7 4.5 + - - +
290X GLY* 3.3 14.7 + - - -
324X THR* 4.4 21.2 - - + +
328X HIS* 4.8 1.9 + - - -
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Residues in contact with THR 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238U ALA 3.8 8.3 - - - +
239U SER 5.9 1.1 - - - -
240U GLU 4.9 2.5 - - - +
241U ALA* 5.7 0.2 - - - -
242U ALA* 4.2 17.5 - - + +
245U GLN* 4.3 17.0 - - - +
279U ALA* 6.1 1.8 - - - -
282U GLN* 3.2 36.8 + - - +
284X THR* 3.5 14.2 - - - +
285X LEU 4.2 0.2 - - - +
286X ALA* 1.3 78.3 - - + +
288X ASP* 1.3 65.9 + - - +
289X MET 3.0 4.7 - - - -
290X GLY* 2.8 18.2 + - - -
291X LEU* 2.9 24.0 + - - +
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Residues in contact with ASP 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261X PHE* 3.2 34.4 - - + -
274X ARG* 4.4 6.6 + - - -
282X GLN* 4.8 9.0 + - - +
284X THR* 2.8 44.5 + - - +
285X LEU* 3.6 2.2 + - - +
287X THR* 1.3 83.3 + - - +
289X MET* 1.3 58.3 + - - +
291X LEU* 3.9 15.8 + - - +
292X LEU* 3.8 11.4 + - - +
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Residues in contact with MET 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X ILE* 5.5 9.4 - - + +
259X PHE* 6.5 0.4 - - - -
261X PHE* 4.3 9.6 - - + -
262X THR* 3.8 22.9 - - - +
285X LEU* 3.3 24.5 + - + +
286X ALA* 3.9 5.4 - - - +
287X THR 3.0 0.6 - - - -
288X ASP* 1.3 77.4 - - - +
290X GLY* 1.3 53.1 + - - +
291X LEU 3.3 0.4 - - - -
292X LEU* 3.3 3.0 + - + +
293X GLN* 2.8 49.5 + - + +
321X ALA* 3.8 12.1 - - + +
324X THR* 4.4 6.7 - - - -
325X THR* 3.3 37.5 - - + +
328X HIS* 3.5 29.2 - - + +
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Residues in contact with GLY 290 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238U ALA* 3.3 24.2 - - - -
239U SER* 3.6 8.6 - - - -
286X ALA 3.3 5.5 + - - -
287X THR 2.8 4.0 + - - -
289X MET* 1.3 76.2 - - - +
291X LEU* 1.3 55.6 + - - +
292X LEU 3.0 9.5 + - - -
294X GLU* 3.2 30.6 + - - +
328X HIS* 3.9 15.0 + - - -
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Residues in contact with LEU 291 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239U SER* 3.5 34.1 - - - +
120X ASP* 5.7 2.7 - - - +
121X PRO* 4.8 10.3 - - + +
234X LEU* 5.0 2.3 - - - +
287X THR* 2.9 23.2 + - - +
288X ASP* 3.9 14.6 + - - +
289X MET 3.3 0.2 - - - -
290X GLY* 1.3 74.7 - - - +
292X LEU* 1.3 58.0 + - - +
295X ARG* 3.2 27.2 + - - -
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Residues in contact with LEU 292 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233X ALA* 3.8 22.2 - - + +
234X LEU* 3.4 31.9 - - + -
237X LEU* 3.5 24.7 - - + +
258X ILE* 4.5 13.9 - - + -
261X PHE* 3.7 44.4 - - + -
288X ASP 3.8 12.3 - - - +
289X MET* 3.3 4.2 + - - +
290X GLY 3.0 0.2 - - - -
291X LEU* 1.3 80.9 - - - +
293X GLN* 1.3 64.5 + - - +
294X GLU 3.5 0.7 - - - -
295X ARG* 3.8 5.2 + - - +
296X ILE* 3.2 25.2 - - + +
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Residues in contact with GLN 293 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152X LYS* 2.9 25.9 + - - +
258X ILE* 3.8 20.3 - - - +
289X MET* 2.8 24.5 + - - +
292X LEU* 1.3 76.8 - - - +
294X GLU* 1.3 60.3 + - - +
295X ARG 3.2 1.8 - - - -
296X ILE* 3.2 26.7 + - - +
308X GLN* 2.9 40.3 + - - +
325X THR* 3.8 23.4 - - - +
328X HIS* 3.2 39.7 - - + +
329X LEU* 5.4 0.6 - - - +
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Residues in contact with GLU 294 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211U LYS* 3.2 26.7 - - + +
212U ARG* 2.7 43.5 + - - +
213U SER* 4.3 5.2 + - - -
237U THR* 3.7 9.0 + - - -
238U ALA* 5.0 1.3 - - + -
239U SER* 3.7 17.9 - - - +
121X PRO* 3.9 15.9 - - + -
122X PRO* 3.8 10.1 - - - +
127X GLN* 5.0 3.5 + - - -
152X LYS* 4.4 3.8 + - - -
290X GLY* 3.2 23.0 + - - +
293X GLN* 1.3 73.9 - - - +
295X ARG* 1.3 59.0 + - - +
296X ILE 3.1 6.0 + - - -
297X THR* 3.4 23.9 - - - +
328X HIS* 5.0 3.8 - - + -
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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