Contacts of the helix formed by residues 222 - 228 (chain A) in PDB entry 2OMZ
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 4.0 9.9 - - + -
214A ILE* 4.1 3.8 - - + -
219A VAL* 3.6 24.7 - - + -
220A SER 3.5 1.0 + - - +
221A ASP* 1.3 70.9 - - - +
223A SER* 1.4 63.5 + - - +
224A VAL* 3.2 3.6 - - - +
225A LEU* 3.0 34.6 + - + +
234A LEU* 5.4 0.9 - - + -
236A ALA* 5.8 0.2 - - + -
241A ILE* 3.8 34.1 - - + -
243A ASP 3.6 24.6 + - - +
244A ILE* 4.3 7.2 - - + -
246A PRO* 3.3 15.6 - - + +
247A LEU* 4.1 31.4 - - + -
258A LEU* 5.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASP* 2.8 27.5 + - - -
222A ILE* 1.4 76.4 - - - +
224A VAL* 1.3 63.6 + - - +
225A LEU 3.3 0.7 + - - -
226A ALA* 3.3 21.1 + - - +
227A LYS* 4.7 6.0 + - - -
246A PRO* 3.5 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 3.3 46.0 - - + +
201A LYS* 3.9 10.1 - - + +
203A LEU* 4.1 6.3 - - + -
204A ALA* 3.5 42.0 - - + +
221A ASP 5.3 0.4 + - - +
222A ILE* 3.2 0.9 + - - +
223A SER* 1.3 81.4 + - - +
225A LEU* 1.3 78.2 + - + +
227A LYS* 3.1 29.1 + - + +
228A LEU* 4.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 4.4 6.1 - - + -
203A LEU* 4.2 4.9 - - + -
212A LEU* 3.7 26.7 - - + -
214A ILE* 4.5 3.8 - - + -
222A ILE* 3.0 44.8 + - + +
224A VAL* 1.3 88.7 - - + +
226A ALA* 1.3 60.1 + - - +
227A LYS 3.1 0.2 - - - -
228A LEU* 3.0 28.9 + - + +
231A LEU* 4.9 1.3 - - + -
234A LEU* 3.6 37.2 - - + -
236A ALA* 6.0 0.2 - - + -
246A PRO* 4.5 0.4 - - + -
247A LEU* 4.4 4.5 - - + -
250A LEU* 3.4 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A SER 3.3 15.9 + - - +
224A VAL 3.1 0.8 - - - -
225A LEU* 1.3 76.1 - - - +
227A LYS* 1.3 64.4 + - + +
228A LEU 3.3 0.2 - - - -
229A THR* 3.5 18.9 - - - +
246A PRO* 3.3 31.4 + - + +
249A ILE* 3.5 18.3 - - + +
250A LEU* 3.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 3.6 41.7 - - + +
207A THR* 3.6 20.0 - - + +
223A SER 4.8 10.1 + - - -
224A VAL* 3.1 19.7 + - + +
226A ALA* 1.3 78.6 - - + +
228A LEU* 1.3 59.0 + - + +
229A THR* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.4 30.1 - - + +
204A ALA 4.4 4.3 - - - +
206A LEU 3.4 30.5 - - - +
207A THR* 4.3 6.1 - - - +
209A LEU* 4.0 21.8 - - + +
212A LEU* 4.1 9.9 - - + -
224A VAL 4.1 6.5 - - - +
225A LEU* 3.0 37.7 + - + +
227A LYS* 1.3 77.4 - - + +
229A THR* 1.3 57.8 + - - +
230A ASN 3.2 3.4 - - - -
231A LEU* 3.2 38.1 + - + +
250A LEU* 3.5 10.8 - - - +
----------------------------------------------------------
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