Contacts of the helix formed by residues 338 - 348 (chain J) 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 338 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J ARG* 4.1 7.9 - - - +
294J GLU* 4.2 9.6 - - - +
332J GLN 6.3 0.2 - - - +
335J ASP* 3.4 29.9 + - + +
336J VAL 3.2 0.8 - - - -
337J SER* 1.3 77.7 - - - +
339J TYR* 1.3 63.7 + - - +
340J ILE 3.6 0.4 - - - +
341J PRO* 3.7 15.5 - - + -
342J THR* 2.6 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J ARG* 3.6 46.8 - - + +
294J GLU* 3.6 25.3 + - + +
296J TYR* 4.6 11.7 - + + -
297J PRO 5.0 3.4 + - - -
298J GLY* 5.0 2.3 + - - -
300J VAL* 3.4 30.7 - - + +
301J PHE* 4.8 0.2 - - - +
337J SER 3.7 0.6 + - - -
338J ALA* 1.3 74.8 - - - +
340J ILE* 1.3 77.2 + - + +
342J THR* 3.4 4.5 - - + -
343J ASN* 3.0 46.4 + - - +
263N GLN* 4.3 16.7 + - + +
267N GLU* 4.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J SER* 4.7 9.6 - - - +
277J ALA* 3.9 14.6 - - + -
294J GLU* 4.6 2.8 + - - +
296J TYR* 3.7 50.5 - - + +
300J VAL* 4.2 11.0 - - + -
304J HIS* 4.2 21.5 - - + +
329J ILE* 4.3 17.9 - - + -
339J TYR* 1.3 84.0 - - + +
341J PRO* 1.3 73.9 - - + +
343J ASN* 3.0 18.2 + - - +
344J VAL* 3.2 13.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170J ILE* 4.0 14.1 - - + -
329J ILE* 4.0 28.7 - - + -
330J GLU 5.0 3.8 - - - +
331J THR* 4.2 12.3 - - + -
335J ASP 4.2 1.8 - - - +
336J VAL* 3.9 17.3 - - - +
338J ALA* 3.5 26.5 - - + +
340J ILE* 1.3 96.8 - - + +
342J THR* 1.3 61.2 + - - +
344J VAL* 3.4 2.7 + - + +
345J ILE* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J ARG* 5.7 1.8 - - - +
336J VAL 3.0 12.8 + - - -
337J SER* 2.9 17.0 + - - +
338J ALA 2.6 26.7 + - - -
339J TYR* 3.4 7.0 - - + +
341J PRO* 1.3 76.4 - - - +
343J ASN* 1.3 63.9 + - - +
345J ILE* 4.3 4.5 - - - +
346J SER* 3.4 23.6 + - - -
259N PHE* 5.4 11.7 - - + -
263N GLN* 5.7 3.4 - - - +
311N TYR* 4.5 21.0 + - + +
313N PRO* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 343 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300J VAL* 4.2 3.2 + - - +
301J PHE* 3.3 38.5 - - + +
304J HIS* 5.2 6.1 + - + +
339J TYR* 3.0 44.4 + - - +
340J ILE* 3.0 15.9 + - - +
342J THR* 1.3 79.5 - - - +
344J VAL* 1.3 66.4 + - + +
346J SER* 3.0 21.0 + - - -
347J ILE* 3.1 18.5 + - + +
263N GLN* 3.1 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J LEU* 3.6 32.1 - - + -
273J LEU* 4.4 9.4 - - + -
304J HIS* 4.1 25.6 - - + +
308J LEU* 4.1 10.3 - - + -
327J PRO* 4.5 1.1 - - + -
329J ILE* 3.7 25.1 - - + -
340J ILE 3.2 14.5 + - - +
341J PRO 3.4 1.5 + - - +
343J ASN* 1.3 74.0 - - - +
345J ILE* 1.3 57.2 + - - +
347J ILE* 3.3 5.1 + - - -
348J THR* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J LEU* 3.8 17.5 - - + -
170J ILE* 3.8 21.5 - - + -
336J VAL* 4.2 22.7 - - + +
341J PRO 3.1 19.1 + - - +
342J THR* 4.3 4.0 - - - +
344J VAL* 1.3 78.0 - - - +
346J SER* 1.3 63.9 + - - +
347J ILE 3.1 1.1 + - - -
348J THR* 3.5 11.3 + - - +
351J GLN* 3.1 44.1 + - + +
190N ARG* 4.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 346 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J PHE* 3.7 17.7 - - - -
342J THR* 3.4 14.5 + - - -
343J ASN 3.0 15.6 + - - -
345J ILE* 1.3 79.5 - - - +
347J ILE* 1.3 56.0 + - - +
190N ARG* 2.7 28.5 + - - +
222N MET* 4.3 6.6 - - - +
260N ARG* 4.3 22.1 + - - -
263N GLN* 5.2 2.8 + - - -
311N TYR* 5.8 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J ARG* 2.8 22.4 + - - +
301J PHE* 3.5 40.6 - - + +
304J HIS* 4.2 5.6 - - + -
305J SER* 3.9 26.5 - - - +
308J LEU* 3.5 29.2 - - + -
309J GLU* 3.7 18.4 - - + +
343J ASN* 3.1 21.7 + - + +
344J VAL 3.7 3.1 - - - +
345J ILE 3.1 0.6 - - - -
346J SER* 1.3 77.7 - - - +
348J THR* 1.3 62.3 + - - +
190N ARG* 3.1 15.1 + - - +
222N MET* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 348 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J ARG* 3.3 19.7 - - + +
168J LEU* 3.7 13.3 - - + +
308J LEU* 3.8 21.3 - - + -
327J PRO* 4.3 6.3 - - + -
344J VAL* 2.9 39.3 + - + +
345J ILE* 3.5 8.3 + - - +
347J ILE* 1.3 81.0 - - - +
349J ASP* 1.3 63.6 + - - +
350J GLY 3.2 17.0 + - - -
351J GLN* 3.4 10.6 + - - -
375J ARG* 4.4 1.0 - - - -
190N ARG* 3.4 12.1 + - - -
----------------------------------------------------------
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