Contacts of the helix formed by residues 220 - 236 (chain A) in PDB entry 2XGZ
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 THR 220 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.7 9.5 - - - +
218A ILE* 3.1 21.5 - - - +
219A GLN* 1.3 92.4 - - + +
221A ALA* 1.3 64.3 + - - +
222A GLU* 3.1 24.3 + - - +
223A GLU* 3.2 19.3 + - - +
224A ALA 3.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.6 14.9 - - + +
166A LEU* 4.0 19.3 - - + -
169A PHE* 4.4 5.2 - - + -
220A THR* 1.3 73.2 - - - +
222A GLU* 1.3 65.4 + - - +
224A ALA* 3.4 2.8 + - - +
225A LEU* 2.9 37.1 + - + +
281A LEU* 5.4 3.4 - - + -
285A LEU* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR* 3.1 27.6 + - - +
221A ALA* 1.3 79.0 + - - +
223A GLU* 1.3 59.1 + - - +
225A LEU* 4.4 0.4 - - - +
226A ASP* 2.9 40.7 + - - +
281A LEU* 5.2 8.1 - - - +
285A LEU* 3.5 24.3 - - + +
289A TYR* 3.5 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 2.7 38.6 + - - +
217A ASN 4.6 0.9 - - - +
218A ILE* 3.8 8.1 - - + +
219A GLN* 2.7 41.1 + - - +
220A THR* 3.2 19.8 + - - +
221A ALA 3.4 0.2 - - - -
222A GLU* 1.3 77.1 - - - +
224A ALA* 1.3 61.6 + - - +
226A ASP* 3.8 6.4 - - - +
227A LEU* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.9 27.8 - - + +
164A LEU* 3.9 5.6 - - + -
169A PHE* 3.9 19.5 - - + -
218A ILE* 3.8 14.0 - - + +
220A THR 3.3 10.8 + - - +
221A ALA 3.4 8.0 + - - +
223A GLU* 1.3 77.1 - - - +
225A LEU* 1.3 59.2 + - - +
227A LEU* 3.3 4.7 + - - +
228A ILE* 3.0 32.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
169A PHE* 3.9 26.0 - - + -
221A ALA 2.9 22.0 + - - +
222A GLU 4.0 0.2 - - - +
224A ALA* 1.3 73.4 - - - +
226A ASP* 1.3 60.0 + - - +
228A ILE* 3.3 6.5 + - + +
229A VAL* 3.0 32.7 + - - +
243A ILE* 3.8 36.8 - - + -
245A LEU* 4.3 3.1 - - + -
285A LEU* 3.9 23.8 - - + -
289A TYR* 3.6 44.9 - - + -
291A ILE* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 5.3 0.7 - - - +
222A GLU* 2.9 27.4 + - - +
223A GLU* 3.8 5.8 + - - +
225A LEU* 1.3 75.6 - - - +
227A LEU* 1.3 63.6 + - - +
229A VAL* 3.4 5.4 + - - +
230A ASP* 3.0 33.0 + - - +
289A TYR* 2.7 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.9 21.5 - - + -
193A LEU* 3.6 9.4 - - + +
196A LEU* 4.1 21.2 - - + +
197A THR* 3.7 20.2 - - - +
200A ARG* 3.4 39.9 - - - +
201A TYR* 3.9 24.5 - - + +
216A PRO* 4.8 1.1 - - + -
218A ILE* 4.2 7.9 - - + -
223A GLU 3.0 14.0 + - - +
224A ALA 3.4 8.1 - - - +
226A ASP* 1.3 77.2 - - - +
228A ILE* 1.3 57.0 + - - +
230A ASP* 3.4 5.4 + - - +
231A ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 4.0 17.7 - - + -
154A LEU* 4.3 8.7 - - + -
169A PHE* 3.5 40.2 - - + -
170A MET 5.4 0.2 - - - +
171A ILE* 3.7 28.9 - - + -
189A VAL* 5.4 1.8 - - + -
193A LEU* 4.3 15.0 - - + -
224A ALA 3.0 15.7 + - - +
225A LEU* 3.3 13.2 + - + +
227A LEU* 1.3 72.9 - - - +
229A VAL* 1.3 65.1 + - - +
231A ALA* 3.0 4.4 + - - +
232A ILE* 3.0 30.7 + - + +
243A ILE* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU 3.0 20.2 + - - +
226A ASP* 3.4 7.2 + - - +
228A ILE* 1.3 73.6 - - - +
230A ASP* 1.3 60.1 + - - +
232A ILE* 3.2 12.6 + - + +
233A LYS* 2.9 55.3 + - + +
243A ILE* 4.6 6.5 - - + -
289A TYR* 4.0 22.4 - - + -
290A PRO* 4.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.9 14.5 - - + +
200A ARG* 2.7 35.2 + - - +
226A ASP* 3.0 18.8 + - - +
227A LEU 3.4 10.1 - - - +
229A VAL* 1.3 80.2 - - - +
231A ALA* 1.3 55.5 + - - +
233A LYS* 3.6 10.4 + - - +
234A ALA* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 3.7 12.4 - - + +
192A ASN* 3.8 8.1 - - - +
193A LEU* 3.6 42.6 - - + +
196A LEU* 3.8 8.2 - - + +
227A LEU 3.1 10.9 + - - +
228A ILE* 3.0 10.1 + - + +
230A ASP* 1.3 72.5 - - - +
232A ILE* 1.3 60.9 + - - +
234A ALA 3.5 0.2 + - - -
235A ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 4.3 2.2 - - + -
189A VAL* 3.7 22.4 - - + -
228A ILE* 3.0 35.0 + - + +
229A VAL* 3.5 13.0 - - + +
231A ALA* 1.3 73.4 - - - +
233A LYS* 1.3 63.6 + - - +
235A ALA* 3.4 2.9 + - - +
236A GLY 3.0 4.2 + - - -
237A HIS* 2.9 34.8 + - - +
238A ASP* 3.6 26.5 - - + +
241A ILE* 3.8 41.1 - - + +
243A ILE* 4.7 10.1 - - + -
290A PRO* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 2.9 39.8 + - + +
230A ASP* 3.8 11.2 - - - +
232A ILE* 1.3 75.9 - - - +
234A ALA* 1.3 57.7 + - - +
236A GLY* 2.9 20.1 + - - -
238A ASP* 3.9 36.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
192A ASN* 3.6 24.6 + - + +
196A LEU* 4.7 9.4 - - + -
230A ASP 2.9 20.1 + - - +
231A ALA* 3.9 3.6 - - - +
232A ILE 3.3 0.2 - - - -
233A LYS* 1.3 76.2 - - - +
235A ALA* 1.3 61.1 + - - +
236A GLY 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 4.0 14.1 - - + +
189A VAL* 4.0 7.9 - - + +
192A ASN* 3.5 21.5 - - - +
231A ALA 3.0 17.3 + - - +
232A ILE 3.8 2.5 - - - +
234A ALA* 1.3 75.7 - - - +
236A GLY* 1.3 58.1 + - - +
237A HIS* 3.4 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE 3.0 0.4 + - - -
233A LYS 2.9 17.5 + - - -
234A ALA 3.1 1.0 - - - -
235A ALA* 1.3 79.5 - - - +
237A HIS* 1.3 65.1 + - - +
238A ASP* 3.5 10.5 + - - +
----------------------------------------------------------
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