Contacts of the helix formed by residues 226 - 238 (chain A) in PDB entry 3GSB
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 GLY 226 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.5 4.1 - - - +
224A ASP 3.2 1.0 + - - -
225A ALA* 1.3 69.5 - - - +
227A PHE* 1.3 55.1 + - - +
229A GLU* 2.9 29.4 + - - +
230A GLY* 2.8 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 3.7 28.5 - + - -
189A TYR* 4.1 9.6 - + - -
190A ASN* 3.3 64.2 - - - +
191A ASP 3.7 4.5 - - - -
192A LEU* 4.1 26.8 - - + +
211A LEU* 4.1 12.6 - - + -
223A PRO* 4.1 12.3 - - + -
224A ASP* 3.1 21.9 + - + +
225A ALA 3.1 3.4 + - - -
226A GLY* 1.3 76.9 - - - +
228A LEU* 1.3 64.9 + - + +
230A GLY* 3.7 1.0 + - - -
231A LEU* 3.2 40.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
211A LEU* 3.9 27.6 - - + -
213A PRO* 4.2 7.6 - - + +
223A PRO* 3.8 34.3 - - + -
224A ASP 4.5 0.8 + - - -
226A GLY 3.3 0.4 - - - -
227A PHE* 1.3 79.4 - - + +
229A GLU* 1.3 74.7 + - - +
231A LEU* 2.8 20.2 + - + +
232A ARG* 3.0 11.3 + - - +
242A LEU* 5.3 0.5 - - - +
244A PHE* 4.5 21.9 - - + -
258A VAL* 4.5 11.4 - - + +
259A GLN* 6.5 0.4 - - - -
262A PHE* 4.2 22.9 - - + -
264A VAL* 4.2 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLY* 2.9 34.8 + - - +
228A LEU* 1.3 76.0 + - - +
230A GLY* 1.3 65.2 + - - +
232A ARG* 2.8 18.1 + - - +
233A GLU* 2.8 15.7 + - - +
262A PHE* 4.5 8.5 - - - +
264A VAL* 4.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.9 20.6 - - - -
226A GLY 2.8 20.4 + - - -
229A GLU* 1.3 71.9 - - - +
231A LEU* 1.3 57.4 + - - +
233A GLU* 3.1 9.3 + - - +
234A ILE* 2.9 39.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
146A PHE* 4.1 20.4 - - + -
192A LEU* 4.3 6.0 - - + +
195A VAL* 4.3 25.6 - - + -
209A VAL* 4.4 9.6 - - + -
211A LEU* 3.5 39.5 - - + -
227A PHE* 3.2 32.8 + - + +
228A LEU* 2.8 14.4 + - + +
230A GLY* 1.3 76.4 - - - +
232A ARG* 1.3 55.8 + - - +
234A ILE* 4.0 6.7 - - + -
235A THR* 2.8 32.6 + - - +
242A LEU* 4.0 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU 3.0 4.6 + - - +
229A GLU* 2.8 14.5 + - - +
231A LEU* 1.3 71.9 - - - +
233A GLU* 1.3 64.8 + - - +
235A THR* 2.8 33.7 + - - -
236A LEU* 3.2 44.3 + - - +
240A ALA 4.9 1.6 + - - -
242A LEU* 3.5 26.2 - - + +
264A VAL* 3.6 24.0 - - + -
265A THR 3.3 18.2 + - - +
267A ASP* 2.6 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 2.8 12.3 + - - +
230A GLY* 3.4 12.9 - - - +
232A ARG* 1.3 78.5 - - - +
234A ILE* 1.3 64.9 + - + +
236A LEU* 3.5 7.6 + - - +
237A GLU* 3.4 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.5 6.1 - - + -
195A VAL* 4.2 20.4 - - + -
196A LYS* 4.3 30.1 - - + -
199A PHE* 4.2 20.4 - - + -
230A GLY* 2.9 24.4 + - - +
231A LEU* 3.6 15.0 - - + +
233A GLU* 1.3 74.0 - - + +
235A THR* 1.3 97.4 + - + +
237A GLU* 3.2 13.2 + - - +
238A HIS* 3.0 34.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
199A PHE* 4.5 7.9 - - + -
209A VAL* 3.9 27.8 - - + -
231A LEU* 2.8 20.9 + - - +
232A ARG* 2.8 30.0 + - - -
234A ILE* 1.3 91.0 - - + +
236A LEU* 1.3 59.3 + - - +
238A HIS 3.3 3.3 + - - -
240A ALA* 2.8 50.2 + - + +
241A LEU 4.6 4.9 - - - +
242A LEU* 3.8 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.2 51.3 + - - +
233A GLU* 3.6 8.1 - - - +
234A ILE 3.2 0.2 - - - -
235A THR* 1.3 81.1 + - - +
237A GLU* 1.3 61.8 + - - +
238A HIS 3.2 1.2 + - - -
239A ASP* 3.3 18.5 + - - +
240A ALA 4.8 2.5 - - - +
267A ASP* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU* 3.4 16.1 + - - +
234A ILE* 3.2 16.1 + - - +
236A LEU* 1.3 79.5 - - - +
238A HIS* 1.3 80.2 + - - +
239A ASP* 3.6 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 2.9 22.6 + - - +
199A PHE* 3.9 52.1 - + + +
200A ALA* 5.4 1.2 + - - -
203A PRO* 6.4 1.8 - - + -
234A ILE* 3.0 27.5 + - + +
235A THR 3.3 3.7 + - - +
236A LEU 3.1 0.6 - - - -
237A GLU* 1.3 107.6 + - + +
239A ASP* 1.3 70.2 + - - +
240A ALA* 3.2 1.5 + - - -
----------------------------------------------------------
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