Contacts of the strand formed by residues 230 - 234 (chain F) in PDB entry 3HYW
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 LYS 230 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ILE* 3.8 0.9 - - - +
227F GLU* 2.9 66.6 + - + +
229F ASP* 1.3 96.1 + - - +
231F VAL* 1.3 67.1 + - - +
232F ILE* 4.1 13.0 - - + -
242F GLU* 3.5 39.4 + - + +
243F VAL 3.2 17.3 - - - +
244F PRO* 4.3 1.3 - - + -
245F ALA* 3.7 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F VAL* 3.9 15.3 - - + -
185F ILE* 4.3 13.7 - - + -
223F VAL* 4.0 14.6 - - + -
225F ALA 3.6 3.6 - - - +
226F ILE* 3.7 26.2 - - + -
230F LYS* 1.3 76.9 - - - +
232F ILE* 1.3 67.2 + - - +
233F TYR* 4.1 2.0 + - - +
241F HIS 4.0 0.2 - - - +
242F GLU* 3.2 3.5 - - - -
243F VAL* 2.8 43.8 + - + +
245F ALA* 4.0 3.4 - - + -
248F THR* 3.7 29.2 - - + -
250F PHE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F VAL* 3.7 1.9 - - - +
224F LYS* 2.8 35.5 + - + -
225F ALA* 2.9 29.8 + - + +
227F GLU* 3.3 33.7 - - + +
230F LYS* 4.1 15.0 - - + -
231F VAL* 1.3 78.0 - - - +
233F TYR* 1.3 62.5 + - - +
240F THR* 3.4 29.6 - - + -
241F HIS 3.4 5.2 - - - +
242F GLU* 4.0 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F ILE* 4.1 15.9 - - + -
218F ILE* 3.5 45.2 - - + +
221F VAL* 3.7 25.8 - - + -
222F ALA 3.2 15.0 - - - +
223F VAL* 3.9 15.5 - - + +
224F LYS* 4.1 4.3 - - - +
231F VAL* 4.4 6.1 - - + -
232F ILE* 1.3 77.2 - - - +
234F GLU* 1.3 63.5 + - - +
240F THR* 3.4 5.4 - - - +
241F HIS* 2.8 80.8 + + + +
242F GLU* 4.4 8.5 - - - -
243F VAL* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F VAL* 3.5 3.5 - - - -
222F ALA* 2.7 45.5 + - + +
224F LYS* 2.9 44.3 + - + +
233F TYR* 1.3 76.8 - - - +
235F ASP* 1.3 65.4 + - - +
238F GLY* 3.6 40.5 - - - +
239F ASN 3.2 5.6 - - - +
240F THR* 3.9 2.3 + - - +
306F ILE* 4.7 0.9 - - - +
----------------------------------------------------------
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