Contacts of the helix formed by residues 222 - 226 (chain D) in PDB entry 4DAJ
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 ILE 222 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 3.9 18.6 - - + -
148D TYR* 3.8 35.4 - - + +
199D TRP* 4.5 4.7 - - + -
203D ILE* 3.9 29.2 - - + -
221D PHE* 1.3 83.3 - - - +
223D GLN* 1.3 70.4 + - - +
224D PHE* 3.3 34.3 - - + -
225D LEU* 3.0 48.3 + - + +
226D SER 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ILE 5.6 5.1 + - - +
206D TRP* 3.1 26.4 - - + +
207D GLN* 3.0 34.9 + - - +
210D VAL* 4.1 11.3 - - - +
212D LYS 2.9 25.7 + - - -
213D ARG* 4.4 0.7 - - - +
214D THR* 3.2 36.0 + - - +
215D VAL* 4.6 8.9 - - + +
221D PHE* 3.4 13.1 + - - -
222D ILE* 1.3 73.2 - - + +
224D PHE* 1.3 58.4 + - - +
225D LEU 2.8 5.5 + - - -
226D SER* 2.8 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D TRP* 4.3 22.2 - + - -
202D ALA* 3.8 27.6 - - + -
203D ILE* 4.0 9.2 - - + -
206D TRP* 3.2 54.9 - + + +
222D ILE* 3.3 22.7 - - + -
223D GLN* 1.3 77.8 - - - +
225D LEU* 1.3 76.9 + - + +
226D SER* 3.2 5.9 + - - -
227D GLU* 4.3 1.9 + - - +
230D ILE* 3.5 34.4 - - + +
234D THR* 5.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D TYR* 4.3 14.8 - - + +
199D TRP* 5.1 2.5 - - + -
221D PHE* 5.5 2.2 - - + -
222D ILE* 3.3 50.9 - - + +
223D GLN 2.8 2.0 + - - -
224D PHE* 1.3 98.9 - - + +
226D SER* 1.3 64.1 + - - +
227D GLU 3.0 6.2 + - - +
230D ILE* 4.6 3.1 - - + +
231D THR* 3.3 42.0 + - + +
234D THR* 5.0 4.9 - - + +
2000D 0HK 4.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ARG* 3.9 25.2 + - - -
214D THR* 4.2 16.7 - - - +
221D PHE* 4.2 16.2 - - - -
222D ILE 3.8 1.9 + - - -
223D GLN 2.8 19.2 + - - -
224D PHE 3.2 2.6 - - - -
225D LEU* 1.3 77.3 - - - +
227D GLU* 1.3 57.8 + - - +
228D PRO* 3.9 5.2 - - - +
----------------------------------------------------------
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