Contacts of the helix formed by residues 229 - 239 (chain A) in PDB entry 3MIZ
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 TYR 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.3 47.3 - - + +
218A GLY 2.9 9.6 + - - -
219A MSE 3.7 9.4 + - - -
220A ASP* 2.6 31.2 + - - -
227A ASN* 3.6 35.4 - - - +
228A ASN* 1.3 74.2 - - - +
230A VAL* 1.3 58.6 + - - +
231A PHE* 3.4 3.1 - - - -
232A ALA* 3.4 15.5 + - + +
233A ALA* 2.9 28.5 + - + +
257A GLN* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ILE* 4.4 5.8 - - + +
218A GLY* 3.3 19.3 + - - +
219A MSE 4.2 0.9 - - + -
228A ASN* 3.2 23.3 + - - +
229A TYR* 1.3 75.3 - - - +
231A PHE* 1.3 57.7 + - - +
233A ALA* 3.2 3.0 + - - +
234A ALA* 2.8 30.0 + - - +
254A MSE 3.6 57.7 - - + +
257A GLN* 3.5 19.7 - - + +
258A ILE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR 3.4 0.4 - - - -
230A VAL* 1.3 74.9 - - - +
232A ALA* 1.3 64.4 + - + +
234A ALA* 3.4 2.2 + - - +
235A THR* 2.9 48.9 + - + -
257A GLN* 2.9 45.3 + - + +
260A ILE* 3.9 19.1 - - + -
261A ALA* 3.4 27.6 - - + -
264A ALA* 4.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR* 3.4 19.1 + - + +
230A VAL 3.3 0.6 - - - -
231A PHE* 1.3 86.1 - - + +
233A ALA* 1.3 63.2 + - - +
235A THR* 3.5 5.3 + - - -
236A GLU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ILE* 4.5 9.9 - - + -
216A SER* 4.7 11.3 + - - -
217A LEU 3.7 22.9 - - - +
229A TYR* 2.9 22.5 + - + +
230A VAL* 3.7 5.4 - - - +
232A ALA* 1.3 75.9 - - - +
234A ALA* 1.3 58.8 + - - +
236A GLU* 3.4 6.4 + - - +
237A MSE 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ILE* 3.6 23.1 - - + +
230A VAL 2.8 17.0 + - - +
231A PHE 3.8 0.4 - - - +
233A ALA* 1.3 74.8 - - - +
235A THR* 1.3 60.8 + - - +
237A MSE 3.6 4.5 - - - +
238A LEU* 3.0 37.4 + - + +
247A ILE* 5.4 0.9 - - + -
258A ILE* 4.1 19.5 - - + -
261A ALA* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 2.9 40.5 + - + -
232A ALA* 3.7 7.0 - - - -
233A ALA 3.2 0.2 - - - -
234A ALA* 1.3 75.5 - - - +
236A GLU* 1.3 64.5 + - - +
238A LEU* 3.3 5.7 + - - +
239A LYS* 3.0 56.0 + - + +
261A ALA* 3.7 15.9 + - - +
265A LEU* 4.3 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA 3.1 14.3 + - - +
233A ALA* 3.7 7.2 - - - +
235A THR* 1.3 77.9 - - - +
237A MSE 1.3 63.8 + - - +
239A LYS* 3.2 28.6 + - - +
240A GLN* 3.4 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 4.0 18.2 - - - -
182A TYR 4.0 2.0 - - - +
183A ILE* 3.7 30.5 - - + -
214A SER* 3.2 27.1 - - - +
216A SER* 3.3 28.9 - - - +
233A ALA 3.0 16.0 + - - +
234A ALA* 3.6 5.2 - - - +
236A GLU* 1.3 77.6 - - - +
238A LEU* 1.3 58.4 + - + +
240A GLN* 2.9 41.8 - - - +
243A ARG* 4.5 0.2 - - - -
244A PRO* 3.6 18.7 - - + +
247A ILE* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 3.0 25.8 + - + +
235A THR 3.3 0.2 + - - -
237A MSE 1.3 75.4 - - - +
239A LYS* 1.3 62.4 + - - +
240A GLN 3.3 1.7 - - - +
243A ARG* 3.2 39.4 + - + +
244A PRO* 4.7 2.5 - - + +
247A ILE* 3.6 29.4 - - + -
258A ILE* 4.7 3.4 - - + +
261A ALA* 4.3 6.1 - - + -
262A ALA* 3.7 38.1 - - + +
265A LEU* 3.7 18.6 - - + +
267A LEU* 4.0 17.0 - - + +
273A VAL* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 3.0 40.9 + - + +
236A GLU* 3.2 21.5 + - - +
238A LEU* 1.3 77.1 - - - +
240A GLN* 1.3 67.8 + - - +
241A ASP* 3.6 3.5 + - - +
265A LEU* 4.0 24.2 - - + -
----------------------------------------------------------
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