Contacts of the strand formed by residues 229 - 233 (chain A) in PDB entry 4HXG
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 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A HIS* 3.5 32.8 - - + +
184A VAL* 3.6 30.3 - - + -
202A ILE* 6.4 0.2 - - + -
204A LEU* 4.9 1.8 - - + -
213A LEU* 4.6 12.6 - - + -
221A ALA* 3.8 28.5 - - + -
223A ASP 3.7 8.7 - - - +
224A SER* 4.9 0.4 - - - -
228A ARG* 1.3 73.4 - - - +
230A LEU* 1.3 63.0 + - - +
231A LEU* 3.8 13.2 + - + -
247A TYR 3.4 2.6 - - - +
248A ILE* 3.7 2.0 - - - -
249A TYR* 2.9 56.2 + - + +
269A ILE* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 3.5 3.6 - - - -
222A ILE* 3.0 41.2 + - + +
223A ASP* 3.0 21.3 + - + +
228A ARG 4.1 0.8 + - - -
229A ILE* 1.3 71.1 - - - +
231A LEU* 1.3 62.2 + - - +
246A ILE* 4.1 9.9 - - + -
247A TYR 3.4 27.1 - - - +
248A ILE* 4.5 6.1 - - + +
256A ILE* 4.9 0.4 - - + -
267A ALA* 3.8 28.5 - - + -
268A LYS* 4.0 24.5 - - - +
269A ILE* 4.0 14.8 - - + +
274A VAL* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 4.3 12.1 - - + -
214A PHE* 4.1 19.7 - - + -
219A PHE* 3.5 46.7 - - + -
220A TYR 3.5 5.8 - - - -
221A ALA* 3.8 24.5 - - + +
229A ILE* 3.9 18.6 - - + +
230A LEU* 1.3 74.5 - - - +
232A TYR* 1.3 60.9 + - - +
233A GLY 4.1 0.2 - - - -
245A LYS 3.7 0.2 - - - +
246A ILE* 3.1 9.4 - - - +
247A TYR* 2.7 49.2 + - + +
249A TYR* 4.2 12.8 - - + -
253A VAL* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER 4.4 0.2 - - - +
219A PHE* 3.3 3.5 - - - -
220A TYR* 2.8 54.0 + + + +
222A ILE* 3.4 39.3 - - + -
230A LEU 4.1 0.2 + - - -
231A LEU* 1.3 72.7 - - - +
233A GLY* 1.3 59.4 + - - +
244A ASP* 3.4 37.0 + - + +
245A LYS 3.5 3.8 - - - -
246A ILE* 4.2 11.7 - - + -
263A GLU* 4.5 2.9 + - - +
264A VAL* 2.7 40.0 + - + -
265A ALA* 4.3 11.0 + - - -
266A GLN* 5.0 1.3 - - - -
267A ALA* 5.2 1.6 - - + -
279A PHE* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER 3.6 7.2 - - - -
219A PHE* 3.4 9.5 - - - +
231A LEU 4.1 0.6 - - - -
232A TYR* 1.3 75.9 - - - +
234A LYS* 1.3 63.1 + - - +
244A ASP* 3.9 19.1 - - - -
245A LYS* 2.8 25.0 + - - +
247A TYR* 2.9 17.7 - - - -
----------------------------------------------------------
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