Contacts of the strand formed by residues 182 - 189 (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 SER 182 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N LEU* 4.5 3.1 - - - +
171N ILE* 3.7 40.9 + - - +
174N ILE* 4.7 0.3 - - - +
180N GLY 4.7 1.4 + - - -
181N PHE* 1.3 77.2 - - - +
183N VAL* 1.3 67.0 + - - +
214N LYS 3.4 4.9 + - - -
215N VAL* 3.1 20.8 - - - +
216N ALA* 3.1 10.0 + - - +
251N VAL* 4.5 0.2 - - - -
252N LEU* 3.2 35.7 - - - +
254N PHE* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N LEU* 6.3 0.2 - - + -
182N SER* 1.3 79.5 - - - +
184N PHE* 1.3 61.1 + - - +
185N THR* 4.1 7.0 - - - +
216N ALA* 3.7 16.4 - - + +
218N VAL* 4.6 5.2 - - + -
236N GLY* 3.7 21.8 - - - +
239N ILE* 3.9 28.5 - - + -
240N ALA* 4.1 19.5 - - + +
243N PHE* 4.5 7.6 - - + -
251N VAL* 4.5 4.3 - - + -
252N LEU 2.6 12.5 + - - +
253N LEU* 3.2 20.3 - - + +
254N PHE* 3.1 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 184 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167N ILE* 3.6 36.8 - - + -
171N ILE* 5.5 0.2 - - + -
183N VAL* 1.3 71.5 - - - +
185N THR* 1.3 60.4 + - - +
186N GLY* 4.3 18.6 - - - -
189N GLU* 4.8 8.3 - - - -
197N LEU* 3.4 37.2 - - + -
201N MET* 4.7 5.6 - - + -
215N VAL* 3.6 10.4 - - + +
216N ALA 2.9 11.3 + - - +
217N LEU* 3.6 20.3 - - + -
218N VAL* 3.0 25.9 + - - +
219N PHE* 4.8 5.8 - + - -
254N PHE* 3.4 28.5 - + + -
256N ASP* 4.4 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N VAL* 3.8 1.7 + - - +
184N PHE* 1.3 78.6 + - - +
186N GLY* 1.3 61.1 + - - +
187N VAL* 3.3 14.1 + - + +
218N VAL* 3.5 16.2 - - + +
232N VAL* 3.3 31.2 - - + +
233N ALA* 4.2 4.9 - - - -
236N GLY* 3.8 12.1 - - - +
253N LEU* 3.4 22.2 - - - +
254N PHE 2.7 17.0 + - - +
255N ILE* 3.6 8.6 - - + -
256N ASP* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N PHE* 4.1 10.3 - - - -
185N THR* 1.3 69.4 - - - +
187N VAL* 1.3 61.9 + - - -
189N GLU* 3.5 27.5 - - - +
218N VAL 2.7 15.1 + - - -
219N PHE* 4.7 1.8 - - - -
220N GLY* 2.7 31.0 + - - -
256N ASP 3.4 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185N THR* 3.3 7.4 + - + +
186N GLY* 1.3 69.2 - - - -
188N GLY* 1.3 68.1 - - - +
189N GLU 3.1 0.2 - - - -
229N ARG* 3.4 25.4 - - + +
232N VAL* 3.9 10.3 - - + -
233N ALA* 3.9 19.7 - - + -
255N ILE* 3.7 27.6 - - + -
256N ASP 2.7 21.8 + - - +
257N ASN 2.9 21.8 + - - +
260N ARG* 3.2 9.3 + - - +
261N PHE* 3.8 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N VAL* 1.3 76.6 - - - +
189N GLU* 1.3 59.6 + - - +
190N ARG* 3.6 0.9 + - - +
220N GLY 2.9 16.1 + - - -
222N MET* 3.1 30.6 - - - +
229N ARG* 4.4 14.9 - - - +
260N ARG* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N PHE* 4.8 9.4 - - - -
186N GLY* 3.5 24.0 - - - +
187N VAL 3.1 1.5 - - - -
188N GLY* 1.3 76.9 - - - +
190N ARG* 1.3 76.8 + - - +
191N THR 3.4 0.7 + - - -
193N GLU* 3.7 32.1 - - - +
194N GLY* 4.3 1.3 - - - +
197N LEU* 4.9 3.5 - - - +
219N PHE* 3.7 30.5 - - + -
220N GLY 3.4 6.6 + - - +
221N GLN* 3.4 8.4 - - + +
222N MET* 3.3 18.7 + - - -
256N ASP* 3.6 25.9 - - - +
260N ARG* 5.0 4.3 + - - +
610N PO4 5.2 0.7 + - - -
----------------------------------------------------------
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