Contacts of the helix formed by residues 227 - 232 (chain B) in PDB entry 1JEQ
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 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 4.5 3.4 - - + -
30B PRO* 3.8 17.0 - - + -
33B GLN* 3.2 41.5 + - + +
34B ALA* 4.0 15.9 - - + -
37B VAL* 3.5 21.9 - - + +
135B PHE* 3.6 22.4 - + + -
136B THR 4.0 7.4 - - - -
164B PHE* 2.9 44.2 - - + -
165B LEU* 2.8 28.6 + - - -
166B PRO* 3.7 17.7 - - + +
226B SER* 1.3 70.9 - - - +
228B SER* 1.3 62.7 + - - +
230B SER* 3.1 17.1 + - - -
231B LEU* 3.3 10.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.9 2.7 + - - -
183B PHE* 4.3 16.4 - - - -
184B ARG 3.7 6.6 + - - -
185B LEU* 3.7 20.7 - - - -
186B GLY* 2.7 42.8 + - - +
187B GLY 3.9 4.9 + - - -
226B SER* 3.2 7.5 + - - -
227B PHE* 1.3 79.5 - - - +
229B GLU* 1.3 62.3 + - - +
231B LEU* 3.1 12.4 + - - +
232B ARG* 3.8 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 3.5 17.8 + - - -
224B ILE 4.4 1.9 - - - +
225B TYR* 3.4 21.0 - - + -
226B SER* 2.8 50.5 + - - +
228B SER* 1.3 76.7 - - - +
230B SER* 1.3 60.5 + - - +
231B LEU 3.2 0.2 - - - -
232B ARG* 3.4 34.6 + - - +
233B LYS* 3.1 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.0 14.8 - - - -
40B MET* 3.7 10.6 - - - +
164B PHE* 3.0 39.7 - - - -
225B TYR* 3.6 7.3 - - - +
226B SER 3.0 11.7 + - - -
227B PHE 3.1 12.9 + - - -
229B GLU* 1.3 77.6 - - - +
231B LEU* 1.3 62.9 + - - +
232B ARG 3.2 0.2 - - - -
233B LYS 3.3 16.5 - - - +
235B CYS* 3.6 12.4 - - - -
236B VAL* 4.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 5.7 1.1 - - + +
36B LYS* 4.3 11.2 - - + +
37B VAL* 4.1 27.6 - - + +
40B MET* 3.7 18.2 - - + +
185B LEU* 3.5 40.6 - - + -
186B GLY* 4.5 5.2 - - - +
227B PHE* 3.3 11.4 + - + +
228B SER 3.1 8.6 + - - +
230B SER* 1.3 80.7 - - - +
232B ARG* 1.3 55.9 + - - +
233B LYS 3.4 2.4 + - - -
483B PRO* 4.4 1.0 - - - +
488B GLN* 3.4 21.3 + - - +
511B HIS* 3.7 40.6 + - + +
515B MET* 3.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 3.1 24.4 - - - +
187B GLY 2.8 19.7 + - - -
188B HIS* 3.7 33.6 + - + +
228B SER 4.0 1.6 - - - +
229B GLU* 3.4 27.5 + - - +
231B LEU* 1.3 77.7 - - - +
233B LYS* 1.3 96.6 + - - +
478B PRO* 6.2 1.2 - - - +
481B LYS* 2.9 19.4 - - - +
482B ILE* 3.5 6.6 - - + +
483B PRO* 3.4 10.0 - - - +
515B MET* 3.7 28.7 - - + -
----------------------------------------------------------
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