Contacts of the strand formed by residues 181 - 187 (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 PHE 181 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89X ARG* 4.2 28.5 - - - -
92X LEU* 3.7 32.1 - - + -
178X HIS* 4.0 2.0 - - - -
180X GLY* 1.3 79.7 - - - -
182X SER* 1.3 65.8 + - - +
213X SER 4.7 4.9 - - - -
214X LYS* 3.4 17.0 - - + +
243X PHE* 3.4 39.5 - + + -
247X GLU* 4.2 8.3 - - + -
249X GLN* 3.8 33.0 - - + -
250X ASP 3.1 7.8 + - - +
251X VAL* 3.4 8.8 - - + -
252X LEU 3.1 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X LEU* 4.5 2.3 - - - +
175X ALA* 4.3 19.3 + - - +
178X HIS* 4.7 4.5 - - - +
180X GLY 5.3 0.3 + - - -
181X PHE* 1.3 76.5 + - - +
183X VAL* 1.3 67.8 + - - +
214X LYS* 2.7 15.5 + - - +
215X VAL* 3.1 36.4 - - - -
216X ALA 3.1 4.5 + - - -
252X LEU* 3.2 29.3 - - - +
254X PHE* 5.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X LEU* 6.1 0.2 - - + -
181X PHE 5.5 0.4 - - - -
182X SER* 1.3 82.1 - - - +
184X PHE* 1.3 65.5 + - - +
185X THR* 4.5 0.4 - - - +
215X VAL* 4.7 0.7 - - - -
216X ALA* 3.7 12.6 - - + +
218X VAL* 5.1 1.6 - - + -
236X GLY* 3.5 28.0 - - - +
239X ILE* 3.8 29.2 - - + -
240X ALA* 3.9 20.4 - - + -
243X PHE* 4.5 8.5 - - + -
251X VAL* 4.5 6.3 - - + -
252X LEU 2.7 10.1 + - - +
253X LEU* 3.0 33.1 - - + +
254X PHE* 3.1 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 184 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167X ILE* 4.7 9.0 - - + -
171X ILE* 4.2 20.6 - - + -
182X SER 4.3 0.2 - - - -
183X VAL* 1.3 72.8 - - - +
185X THR* 1.3 64.0 + - - +
186X GLY* 4.0 15.5 - - - -
197X LEU* 3.6 27.8 - - + -
215X VAL* 4.3 6.7 - - + +
216X ALA 3.2 8.4 + - - +
217X LEU* 4.0 17.7 - - + -
218X VAL* 3.1 28.4 + - - +
219X PHE* 3.9 26.5 - + - -
254X PHE* 3.3 37.9 - + + -
256X ASP* 4.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183X VAL* 4.5 0.3 - - - +
184X PHE* 1.3 80.0 + - - +
186X GLY* 1.3 58.8 + - - +
187X VAL* 3.3 23.3 + - + +
218X VAL* 3.5 9.6 - - + +
232X VAL* 3.4 27.1 - - + +
233X ALA* 4.2 5.8 - - - +
236X GLY* 3.9 22.4 - - - -
237X LEU 4.7 0.2 + - - -
253X LEU* 3.5 19.9 - - - +
254X PHE 2.9 12.7 + - - +
255X ILE* 4.8 6.7 - - + +
256X ASP 3.3 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184X PHE* 4.0 10.8 - - - -
185X THR* 1.3 68.4 - - - +
187X VAL* 1.3 62.2 + - - +
189X GLU* 5.6 0.2 - - - -
218X VAL 2.8 14.2 + - - +
219X PHE* 3.8 19.7 - - - -
220X GLY* 3.1 29.8 + - - +
221X GLN* 3.9 8.6 - - - +
232X VAL* 4.5 1.9 - - - +
256X ASP 3.4 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185X THR* 3.8 22.0 - - + +
186X GLY* 1.3 73.2 - - - -
188X GLY* 1.3 69.1 + - - +
189X GLU 2.9 1.7 + - - -
220X GLY 4.1 1.8 - - - -
229X ARG 3.9 19.5 - - - +
232X VAL* 3.9 18.2 - - + -
233X ALA* 4.1 15.9 - - + -
255X ILE* 4.4 10.1 - - + -
256X ASP 2.8 9.3 + - - -
257X ASN 2.8 44.0 + - - +
258X ILE* 5.1 0.7 - - - -
260X ARG* 3.3 20.1 - - + +
261X PHE* 4.3 5.4 - - + +
----------------------------------------------------------
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