Contacts of the strand formed by residues 265 - 271 (chain S) 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 HIS 265 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146S GLU* 3.6 23.3 + - - -
163S ARG* 3.4 11.6 + - - +
197S GLU 4.2 4.9 + - - -
198S SER* 3.3 36.2 + - - -
200S LYS 3.7 15.0 + - - +
201S LEU* 3.4 13.0 - - + -
202S TYR* 3.0 26.7 + - - -
259S PHE* 4.8 2.0 - - - -
263S GLY 4.6 6.0 + - - -
264S LYS* 1.3 80.3 - - - +
266S ALA* 1.3 60.8 + - - +
320S SER* 3.2 26.9 - - - -
321S GLY* 3.9 4.9 - - - -
322S SER* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201S LEU* 3.2 12.8 - - - +
202S TYR 3.1 11.4 - - - +
204S VAL* 4.9 4.0 - - + -
256S GLY* 3.6 33.0 - - - +
259S PHE* 4.2 11.6 - - + +
265S HIS* 1.3 74.1 - - - +
267S LEU* 1.3 63.7 + - - +
322S SER 3.0 9.2 + - - +
323S LEU* 3.9 11.9 - - + -
324S THR* 3.3 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148S VAL* 4.4 6.3 - - + -
184S THR* 3.9 26.9 - - + -
185S ILE* 4.9 5.8 - - + -
188S GLN* 5.1 0.7 - - - +
201S LEU* 3.7 25.1 - - + -
202S TYR 2.8 13.0 + - - +
203S CYS* 3.4 18.3 - - + +
204S VAL* 2.8 22.5 + - - +
266S ALA* 1.3 79.0 - - - +
268S ILE* 1.3 60.5 + - - +
269S VAL* 3.9 8.4 + - + +
324S THR* 3.5 35.9 - - + +
326S LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204S VAL* 3.0 23.1 - - + +
206S VAL* 3.8 14.4 - - + -
252S ALA 3.2 33.7 - - - +
253S ALA* 4.0 2.2 - - - -
256S GLY* 5.9 0.7 - - - -
267S LEU* 1.3 73.6 - - - +
269S VAL* 1.3 61.1 + - - +
270S TYR* 3.4 50.8 + - + +
323S LEU* 3.7 21.3 - - + +
324S THR 2.9 19.4 + - - +
325S ALA* 3.5 3.6 - - + -
326S LEU* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181S ALA* 3.8 30.7 - - + +
185S ILE* 4.8 15.5 - - + -
204S VAL 2.9 11.0 + - - +
205S TYR* 4.4 15.5 - - + -
206S VAL* 3.0 26.3 + - - +
267S LEU* 4.6 11.2 - - + +
268S ILE* 1.3 74.4 - - - +
270S TYR* 1.3 59.4 + - - +
271S ASP* 3.1 20.9 + - + +
326S LEU* 3.7 34.1 - - + +
328S VAL* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206S VAL* 4.3 7.0 - - + -
208S VAL* 5.9 1.1 - - + -
249S PRO* 3.6 19.3 - - + -
253S ALA* 3.9 8.0 - - - +
268S ILE* 3.4 52.8 - - + +
269S VAL* 1.3 69.7 - - - +
271S ASP* 1.3 58.7 + - - +
272S ASP* 3.6 5.6 - - - -
273S LEU* 3.6 23.2 + - + -
307S LEU* 3.5 48.8 + - + +
308S LEU* 3.9 21.5 - - + -
311S ALA* 5.2 4.0 - - + +
323S LEU* 5.3 2.3 - - - +
325S ALA* 3.9 14.3 - - + +
326S LEU 3.9 3.6 + - - -
327S PRO* 3.5 11.3 - - + +
328S VAL* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 271 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177S LYS* 5.7 1.6 + - - -
178S THR* 2.9 37.7 + - - +
205S TYR* 3.8 8.2 - - + +
206S VAL* 2.8 15.8 + - - +
208S VAL* 2.8 22.5 + - - +
210S GLN* 2.7 39.0 + - - +
269S VAL* 3.1 15.5 + - + +
270S TYR* 1.3 74.3 - - - +
272S ASP* 1.3 67.4 + - - +
328S VAL* 4.2 14.8 - - + +
----------------------------------------------------------
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