Contacts of the strand formed by residues 202 - 208 (chain L) 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 TYR 202 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L LEU* 3.5 39.5 - - + -
192L ASN* 5.3 1.6 - - - -
197L GLU* 2.7 35.2 + - - -
200L LYS* 3.8 27.0 + - + +
201L LEU* 1.3 72.8 - - - +
203L CYS* 1.3 61.7 + - - +
204L VAL* 5.3 0.4 - - - -
229L LYS 5.7 0.2 - - - -
230L TYR* 3.8 22.2 - - + +
259L PHE* 3.6 37.0 - + + -
264L LYS* 4.5 8.3 - - + -
265L HIS 3.1 16.8 + - - +
266L ALA* 3.1 9.2 - - - +
267L LEU 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L ILE* 3.6 52.5 - - + -
188L GLN* 4.1 9.0 - - - -
201L LEU 3.7 14.4 - - - -
202L TYR* 1.3 73.6 - - - +
204L VAL* 1.3 64.9 + - - +
205L TYR 4.0 0.9 - - - +
230L TYR* 3.3 16.5 + - - +
231L SER* 3.3 11.6 - - - +
232L ILE* 2.8 26.0 + - - +
267L LEU* 3.3 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L ILE* 5.8 0.7 - - - -
202L TYR 4.9 3.4 - - - +
203L CYS* 1.3 78.2 - - - +
205L TYR* 1.3 59.4 + - - +
206L VAL* 4.6 1.8 - - + -
232L ILE* 3.3 33.9 - - + +
234L VAL* 4.7 3.6 - - + -
252L ALA* 3.7 31.2 - - + +
255L ILE* 4.5 4.7 - - + -
256L GLY* 4.1 23.1 - - - +
259L PHE* 4.7 4.7 - - + -
266L ALA* 5.3 1.3 - - + -
267L LEU* 2.7 12.2 + - - +
268L ILE* 3.1 21.5 - - + +
269L VAL* 3.0 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178L THR* 3.7 18.8 - - + +
181L ALA* 5.3 3.8 - - + -
182L LEU* 5.9 3.8 - - + -
185L ILE* 4.2 22.2 - - + -
203L CYS* 4.0 2.0 - - + +
204L VAL* 1.3 72.2 - - - +
206L VAL* 1.3 77.9 + - - +
207L ALA* 4.1 13.0 - - + -
210L GLN* 3.0 26.2 + - - -
215L VAL* 5.6 1.1 - - + -
218L LEU* 3.4 34.3 - - + +
222L LEU* 5.7 1.8 - - + -
231L SER* 6.2 1.1 - - - -
232L ILE 2.9 7.1 + - - +
233L ILE* 3.2 24.2 - - + +
234L VAL 3.0 24.6 + - - +
269L VAL* 3.9 34.3 - - + +
271L ASP* 3.2 12.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204L VAL* 4.3 1.1 - - + +
205L TYR* 1.3 88.6 - - - +
207L ALA* 1.3 62.7 + - - +
208L VAL* 3.7 24.2 - - + -
234L VAL* 3.5 11.0 - - + +
248L ALA* 4.2 6.7 - - + +
249L PRO* 4.2 16.6 - - + -
252L ALA* 3.4 26.7 - - + -
268L ILE* 3.4 27.4 - - + -
269L VAL 2.9 11.9 + - - +
270L TYR* 4.3 9.4 - - + -
271L ASP* 2.8 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205L TYR* 4.1 9.9 - - + -
206L VAL* 1.3 74.4 - - - +
208L VAL* 1.3 63.0 + - - +
210L GLN* 4.0 10.9 + - - +
215L VAL* 3.5 35.2 - - + -
233L ILE* 5.1 0.2 - - + -
234L VAL 3.0 9.6 + - - +
235L ALA* 4.0 12.3 - - + -
236L ALA 2.8 28.8 + - - -
237L THR* 4.0 1.9 + - - -
271L ASP 3.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L VAL* 3.7 18.4 - - + -
207L ALA* 1.3 71.1 - - - +
209L GLY* 1.3 62.7 + - - +
210L GLN* 3.0 11.9 + - - +
236L ALA 3.8 2.7 - - - -
245L GLN* 3.7 28.3 - - + +
248L ALA* 3.8 7.4 - - + -
249L PRO* 3.7 31.4 - - + -
271L ASP 2.7 11.7 + - - +
272L ASP 3.2 25.5 + - - +
273L LEU* 6.2 0.2 - - + -
275L LYS* 3.5 11.3 - - - +
276L GLN* 4.0 26.5 - - + +
----------------------------------------------------------
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