Contacts of the strand formed by residues 228 - 232 (chain B) in PDB entry 2JG1
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 ALA 228 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 4.7 11.2 - - + -
221B VAL 3.3 13.0 - - - +
222B SER* 4.4 4.7 - - - -
223B LEU* 3.7 9.6 - - - +
227B GLY* 1.3 75.9 - - - +
229B PHE* 1.3 63.3 + - - +
230B ALA 4.3 0.2 - - - -
238B ARG* 3.3 8.1 - - - -
239B VAL* 2.9 40.9 + - + -
274B LEU* 5.4 1.3 - - + -
278B ASN* 3.7 23.1 + - - +
1312B ANP 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 3.9 24.0 - - + -
204B LEU* 3.8 35.2 - - + -
205B LYS* 3.8 24.0 - - + -
208B VAL* 3.8 24.9 - - + -
221B VAL* 2.8 51.0 + - + +
223B LEU* 3.8 7.7 - - + +
228B ALA* 1.3 74.3 - - - +
230B ALA* 1.3 64.2 + - - +
236B PHE* 3.6 33.9 - + + -
237B TYR 3.6 17.5 - - - -
238B ARG* 4.4 3.6 - - - +
310B VAL* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 4.1 13.5 - - + -
219B ILE 3.2 9.0 - - - +
220B ILE* 4.2 7.6 - - + -
228B ALA* 4.3 0.8 - - + -
229B PHE* 1.3 81.7 - - - +
231B LYS* 1.3 60.3 + - - +
232B HIS 4.2 0.2 - - - -
235B THR 4.1 0.2 - - - +
236B PHE* 3.3 5.0 - - - +
237B TYR* 2.8 40.2 + - + +
239B VAL* 5.5 1.5 - - + +
274B LEU* 3.9 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.0 32.9 + - + +
209B SER* 4.4 11.0 - - - +
213B PHE 5.2 4.8 + - - -
214B GLU* 6.2 0.8 - - - +
216B ILE 4.8 7.7 + - - +
217B GLU 3.6 1.0 - - - +
218B TRP* 3.4 7.8 - - - -
219B ILE* 2.8 54.1 + - + +
229B PHE* 4.8 0.4 - - - -
230B ALA* 1.3 73.8 - - - +
232B HIS* 1.3 61.0 + - - +
233B ASN* 2.9 25.2 + - - +
234B HIS* 4.9 3.8 - - - +
235B THR 3.4 6.7 - - - +
236B PHE* 3.6 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 2.8 49.1 + - + +
218B TRP* 3.5 38.0 + + + -
230B ALA 4.2 0.4 - - - -
231B LYS* 1.3 72.3 - - - +
233B ASN* 1.3 83.4 + - - +
234B HIS 3.0 0.7 + - - -
235B THR* 2.8 34.0 + - + +
237B TYR* 4.2 6.4 - - + -
270B ASP* 2.8 36.3 + - - +
----------------------------------------------------------
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