Contacts of the strand formed by residues 215 - 220 (chain W) 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 VAL 215 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92W LEU* 3.9 6.0 - - - +
93W GLY* 2.8 26.3 + - - -
171W ILE* 3.9 19.1 - - + -
182W SER* 3.2 26.9 - - - +
184W PHE* 3.9 13.5 - - + +
201W MET* 3.5 28.0 - - + -
206W VAL* 4.4 6.7 - - + +
207W ILE* 3.7 19.1 - - + +
213W SER 3.7 1.2 - - - -
214W LYS* 1.3 83.6 - - - +
216W ALA* 1.3 73.4 + - - +
217W LEU* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W THR* 3.6 41.5 - - - +
92W LEU* 3.9 5.5 - - + +
93W GLY 4.0 0.7 - - - +
94W ARG 4.8 0.4 - - - +
96W ILE* 5.9 0.7 - - + -
182W SER 2.9 12.2 + - - +
183W VAL* 3.5 14.7 - - + -
184W PHE* 2.9 26.3 + - - -
215W VAL* 1.3 77.9 - - - +
217W LEU* 1.3 63.3 + - - +
239W ILE* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94W ARG 3.3 8.5 + - - +
95W ILE* 3.6 26.5 - - + +
96W ILE* 2.8 34.2 + - - +
184W PHE* 3.5 34.3 - - + -
197W LEU* 4.7 1.1 - - + -
198W TYR* 3.6 24.5 - - + -
201W MET* 3.8 21.5 - - + -
207W ILE* 3.5 29.6 - - + -
215W VAL* 4.9 1.3 - - + +
216W ALA* 1.3 78.1 - - - +
218W VAL* 1.3 62.8 + - - +
219W PHE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96W ILE* 4.1 6.7 - - + -
97W ASN 4.8 7.4 - - - +
183W VAL* 4.5 4.9 - - + -
184W PHE 2.8 10.2 + - - +
185W THR* 3.7 25.6 - - + +
186W GLY 3.0 20.1 + - - -
217W LEU* 1.3 79.7 - - - +
219W PHE* 1.3 78.5 + - - +
232W VAL* 4.0 10.3 - - + +
235W THR* 4.0 22.4 - - + -
236W GLY* 3.6 21.8 - - - +
239W ILE* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 4.4 13.9 - - + -
95W ILE* 3.5 25.6 - - + -
96W ILE 3.5 11.5 + - - +
97W ASN* 3.9 12.8 - - - +
103W ILE* 4.7 5.1 - - + +
184W PHE* 4.4 11.4 - + - -
186W GLY* 4.1 11.2 - - - +
189W GLU* 4.3 16.4 - - + -
194W GLY* 3.6 36.1 - - - -
197W LEU* 4.3 18.2 - - + -
198W TYR* 5.8 1.1 - - + -
217W LEU* 4.0 26.5 - - + -
218W VAL* 1.3 93.9 - - - +
220W GLY* 1.3 59.2 + - - +
221W GLN* 3.5 15.3 - - + -
224W GLU* 3.8 13.2 - - - +
232W VAL* 3.9 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186W GLY 2.9 17.5 + - - -
188W GLY* 2.9 22.7 + - - -
219W PHE* 1.3 71.5 - - - +
221W GLN* 1.3 70.4 + - - +
224W GLU* 3.7 8.1 - - - -
229W ARG* 3.6 7.8 - - - +
232W VAL* 3.4 27.9 - - - +
----------------------------------------------------------
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