Contacts of the helix formed by residues 223 - 236 (chain A) in PDB entry 3G33
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 SER 223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.3 17.3 - - - +
221A GLY 4.1 0.9 - - - -
222A ASN* 1.3 85.5 + - - +
224A GLU* 1.3 66.1 + - - +
225A ALA* 3.5 12.2 + - - +
226A ASP* 3.7 10.5 + - - +
227A GLN* 3.2 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.9 14.8 - - + -
191A LEU* 3.7 34.1 - - + +
193A GLN* 4.6 14.1 + - - -
223A SER* 1.3 76.6 - - - +
225A ALA* 1.3 58.3 + - - +
227A GLN* 3.1 11.0 + - - +
228A LEU* 2.7 31.0 + - + +
249A LEU* 5.5 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A SER* 3.5 6.8 + - - +
224A GLU* 1.3 78.2 - - - +
226A ASP* 1.3 62.9 + - - +
228A LEU* 3.4 10.9 + - - +
229A GLY* 3.3 16.3 + - - -
249A LEU* 4.7 19.2 - - + +
254A PHE* 4.2 10.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
220A CYS 4.2 2.4 - - - +
221A GLY* 3.4 6.2 - - - -
222A ASN* 2.6 38.9 + - + +
223A SER* 3.6 14.3 + - - +
224A GLU 3.2 0.6 - - - -
225A ALA* 1.3 76.2 - - - +
227A GLN* 1.3 66.4 + - - +
229A GLY* 3.2 12.2 + - - +
230A LYS* 3.2 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 2.8 35.6 + - + +
184A TRP* 3.0 26.5 - - - +
186A ARG* 5.2 1.1 - - + +
191A LEU* 3.4 20.9 - - + -
219A PHE* 3.3 18.2 - - - +
221A GLY* 2.9 36.4 + - - +
223A SER 3.2 11.8 + - - +
224A GLU* 3.1 11.4 + - - +
226A ASP* 1.3 78.2 - - - +
228A LEU* 1.3 61.6 + - - +
230A LYS* 3.4 4.9 + - - +
231A ILE* 3.1 31.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
188A PRO* 4.3 20.0 - - + +
191A LEU* 3.4 39.7 - - + -
192A LEU* 4.7 13.2 - - + -
224A GLU 2.7 31.4 - - - +
225A ALA* 3.7 9.0 - - - +
226A ASP 3.3 0.2 - - - -
227A GLN* 1.3 73.0 - - - +
229A GLY* 1.3 66.3 + - - +
231A ILE* 2.9 10.0 + - + +
232A PHE* 2.9 59.0 + - + -
249A LEU* 4.6 9.6 - - + -
254A PHE* 3.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA 3.3 8.5 + - - -
226A ASP* 3.2 9.6 + - - -
228A LEU* 1.3 80.1 - - - +
230A LYS* 1.3 61.3 + - - +
231A ILE 3.4 0.2 + - - -
232A PHE* 3.7 2.7 + - - +
233A ASP* 3.0 32.0 + - - +
254A PHE* 4.0 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 3.6 30.2 - - + -
220A CYS* 3.4 34.5 - - - +
221A GLY 4.6 0.2 - - - +
226A ASP* 3.2 28.3 + - - +
227A GLN* 3.8 7.4 - - - +
228A LEU 3.2 0.2 - - - -
229A GLY* 1.3 75.9 - - - +
231A ILE* 1.3 61.0 + - - +
233A ASP* 3.8 13.8 + - - +
234A LEU* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG 4.6 1.8 - - - +
188A PRO* 4.5 11.0 - - + -
191A LEU* 4.5 9.4 - - + -
203A TRP* 3.4 50.7 - - + +
219A PHE* 3.7 25.0 - - + -
227A GLN* 3.1 32.3 - - + +
228A LEU* 2.9 13.9 + - + +
230A LYS* 1.3 75.1 - - - +
232A PHE* 1.3 71.6 + - + +
233A ASP 3.1 1.6 - - - -
234A LEU* 3.2 14.0 + - - +
235A ILE* 3.3 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 5.8 0.2 - - + -
192A LEU* 5.4 1.1 - - + -
228A LEU* 2.9 54.2 + - + +
229A GLY* 4.4 2.7 - - - +
231A ILE* 1.3 80.9 - - + +
233A ASP* 1.3 56.8 + - - +
234A LEU 3.1 1.1 + - - -
235A ILE* 4.3 7.4 - - + -
236A GLY* 3.1 31.2 + - - +
237A LEU* 4.3 10.5 - - + +
238A PRO* 3.7 36.1 - - + -
243A TRP* 3.8 19.5 - + - -
254A PHE* 3.7 41.3 - + + -
255A PRO 5.8 0.4 - - - +
257A ARG* 3.4 15.5 - - + +
283A PHE* 4.0 16.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLY* 3.0 20.5 + - - +
230A LYS* 4.0 9.4 - - - +
231A ILE 3.1 1.4 - - - -
232A PHE* 1.3 77.6 - - - +
234A LEU* 1.3 60.5 + - + +
236A GLY 4.8 0.2 - - - -
257A ARG* 3.2 38.0 + - - +
258A GLY 5.3 1.1 - - - +
260A ARG* 3.2 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.6 10.5 - - + +
219A PHE* 3.5 31.2 - - + -
230A LYS 4.0 7.6 - - - +
231A ILE 3.2 5.7 + - - +
232A PHE 3.1 0.2 - - - -
233A ASP* 1.3 90.9 - - + +
235A ILE* 1.3 65.5 + - + +
236A GLY 3.3 1.2 + - - -
258A GLY 4.9 0.2 - - - -
260A ARG* 3.1 50.1 + - - +
265A VAL* 3.7 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 4.0 13.5 - - + -
219A PHE* 5.3 2.7 - - + -
231A ILE* 3.3 34.7 + - + +
232A PHE* 4.3 6.3 - - + -
234A LEU* 1.3 80.7 - - + +
236A GLY* 1.3 72.5 + - - +
259A PRO* 3.7 20.4 - - - +
278A LEU* 6.5 1.1 - - + -
281A LEU* 3.7 37.9 - - + +
283A PHE* 4.3 22.7 - - + +
----------------------------------------------------------
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 PHE* 3.1 21.9 + - - -
234A LEU 3.3 2.2 - - - -
235A ILE* 1.3 95.3 - - - +
237A LEU* 1.3 66.1 + - - -
238A PRO* 3.4 7.1 - - - +
257A ARG 3.4 12.3 - - - -
258A GLY 3.7 14.4 - - - -
259A PRO* 4.1 1.3 - - - -
----------------------------------------------------------
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