Contacts of the helix formed by residues 286 - 294 (chain N) 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 ALA 286 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238K ALA* 4.2 6.1 - - - +
245K GLN* 5.7 7.0 - - - +
275K LYS 6.2 0.2 - - - +
278K VAL* 4.3 25.0 - - + +
279K ALA* 6.0 1.6 - - - +
282K GLN* 5.0 3.3 + - - +
283N PRO 5.0 0.4 + - - -
284N THR 3.4 0.2 - - - -
285N LEU* 1.3 78.7 - - - +
287N THR* 1.3 63.2 + - + +
289N MET* 3.3 4.7 + - - +
290N GLY* 3.0 22.7 + - - -
324N THR* 4.3 14.5 - - + +
328N HIS* 5.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238K ALA 4.2 7.1 - - - +
239K SER 5.6 0.7 - - - -
240K GLU 4.0 12.8 - - - +
241K ALA* 4.7 1.1 - - - -
242K ALA* 4.1 10.5 - - - +
245K GLN* 3.9 20.6 - - - +
279K ALA* 6.4 0.9 - - + -
282K GLN* 3.3 39.5 + - - +
284N THR* 3.6 4.5 - - - +
286N ALA* 1.3 74.4 - - + +
288N ASP* 1.3 70.2 + - - +
289N MET 3.0 1.8 - - - -
290N GLY* 2.9 1.4 + - - -
291N LEU* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261N PHE* 3.8 25.4 - - + -
265N GLY* 4.9 8.0 - - - +
274N ARG* 5.3 2.0 + - - -
282N GLN* 3.9 16.4 + - - +
284N THR* 2.9 37.9 + - - +
285N LEU 4.5 0.4 - - - +
286N ALA 3.4 0.4 - - - -
287N THR* 1.3 82.4 + - - +
289N MET* 1.3 60.0 + - - +
291N LEU* 3.9 20.6 + - - +
292N LEU* 4.2 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 289 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258N ILE* 4.9 2.9 - - + -
261N PHE* 4.3 18.2 - - + -
262N THR* 3.4 33.0 - - + +
285N LEU* 3.3 19.4 + - + +
286N ALA 3.3 5.3 + - - +
287N THR 3.0 0.8 - - - -
288N ASP* 1.3 77.4 - - - +
290N GLY* 1.3 58.7 + - - +
291N LEU 3.4 0.2 - - - -
292N LEU* 3.8 2.1 + - - +
293N GLN* 3.1 61.7 + - + +
321N ALA 5.1 0.7 - - - +
324N THR* 4.0 20.4 - - + +
325N THR* 3.8 26.5 - - + +
328N HIS* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 290 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238K ALA* 3.6 20.6 - - - -
239K SER* 3.9 7.9 + - - -
121N PRO* 4.3 0.2 - - - +
286N ALA 3.0 6.9 + - - -
287N THR 2.9 7.5 + - - -
289N MET* 1.3 76.0 - - - +
291N LEU* 1.3 55.1 + - - +
292N LEU 3.0 10.1 + - - -
293N GLN 4.6 0.2 - - - -
294N GLU* 3.2 34.8 + - - +
328N HIS* 4.5 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K SER* 3.5 32.5 - - - +
119N ALA 5.1 1.2 - - - +
120N ASP* 5.8 2.9 - - - +
121N PRO* 4.9 8.1 - - + -
234N LEU* 4.1 11.1 - - + +
287N THR* 2.9 25.7 + - - +
288N ASP* 4.2 16.8 - - - +
289N MET 3.4 0.6 - - - -
290N GLY* 1.3 76.1 - - - +
292N LEU* 1.3 57.9 + - - +
295N ARG* 3.4 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233N ALA* 3.7 26.9 - - + +
234N LEU* 3.6 21.1 - - + -
237N LEU* 3.5 24.4 - - + +
253N LEU* 6.2 1.1 - - + -
255N ILE* 5.6 4.0 - - + -
258N ILE* 4.1 11.4 - - + -
261N PHE* 4.0 26.5 - - + -
288N ASP 4.4 8.3 - - - +
289N MET* 3.8 6.6 + - - +
290N GLY 3.0 0.4 - - - -
291N LEU* 1.3 79.8 - - - +
293N GLN* 1.3 85.8 - - - +
294N GLU 3.2 1.3 - - - -
295N ARG* 3.2 17.9 + - - +
296N ILE* 3.6 14.1 - - + +
308N GLN* 4.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152N LYS* 2.8 49.4 + - - +
258N ILE* 3.9 5.3 - - - +
289N MET* 3.1 35.7 + - - +
292N LEU* 1.3 94.6 - - - +
294N GLU* 1.3 58.7 + - - +
296N ILE* 3.2 17.2 + - - +
308N GLN* 3.6 32.1 + - - +
325N THR* 4.5 5.5 - - - +
328N HIS* 3.2 39.6 - - + +
329N LEU* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210K GLN 3.6 5.9 - - - +
211K LYS* 3.2 21.9 - - - +
212K ARG* 2.7 42.9 + - + +
213K SER* 4.7 2.6 + - - -
237K THR* 4.0 5.4 - - - -
238K ALA* 4.0 5.5 + - + +
239K SER* 3.7 18.4 - - - +
121N PRO* 3.3 26.6 - - + +
122N PRO* 3.8 7.6 - - - +
127N GLN* 4.8 2.4 + - - -
152N LYS* 4.6 3.1 + - - -
290N GLY* 3.2 23.8 + - - +
292N LEU 3.2 0.8 - - - -
293N GLN* 1.3 77.0 - - - +
295N ARG* 1.3 58.1 + - - +
296N ILE 3.1 6.0 + - - -
297N THR* 4.1 14.0 - - - +
328N HIS* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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