Contacts of the helix formed by residues 229 - 246 (chain S) in PDB entry 3EXG
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 ASP 229 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ILE* 4.9 6.3 - - - +
10S LYS 5.5 0.9 + - - -
70S ALA* 4.4 0.4 - - - -
226S ASP* 3.4 14.5 + - - +
227S GLY 3.3 0.8 - - - -
228S MET* 1.3 76.3 - - - +
230S ILE* 1.3 64.7 + - - +
231S LEU* 2.8 32.7 + - - +
232S CYS* 3.4 22.5 - - - -
233S VAL* 3.3 24.1 + - - +
290S LEU* 5.1 11.4 - - + +
294S ARG* 3.0 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S TYR* 4.2 27.8 - - + -
39S MET* 4.4 18.4 - - + -
70S ALA* 4.0 13.3 - - + +
73S VAL* 3.7 22.4 - - + +
74S GLY* 3.4 34.8 - - - +
77S ALA* 5.1 2.2 - - + -
228S MET 3.6 4.9 + - - -
229S ASP* 1.3 73.8 - - - +
231S LEU* 1.3 64.0 + - + +
233S VAL* 3.9 0.6 - - - +
234S ARG* 3.1 26.0 + - + +
287S PRO 4.8 3.6 - - - +
291S LEU* 3.9 35.7 - - + -
294S ARG* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S PHE* 3.9 30.7 - - + -
9S ILE* 3.8 12.1 - - + -
25S THR* 3.9 10.6 - - + +
27S LEU* 3.9 29.2 - - + -
35S TYR* 5.0 2.7 - - + -
229S ASP* 2.8 15.2 + - - +
230S ILE* 1.3 88.1 - - + +
232S CYS* 1.3 59.4 + - - +
234S ARG* 3.7 20.0 + - - +
235S GLU* 2.9 29.5 + - - +
291S LEU* 4.8 4.0 - - + -
294S ARG* 3.0 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 232 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ILE* 4.0 25.6 - - + +
10S LYS* 4.7 12.3 - - - +
12S CYS* 5.9 4.7 - - - -
225S VAL* 4.5 6.3 - - + -
226S ASP* 3.6 27.1 - - - +
229S ASP* 3.4 33.2 + - - -
231S LEU* 1.3 76.0 - - - +
233S VAL* 1.3 57.5 + - - +
235S GLU* 3.7 6.7 - - + -
236S ALA* 2.5 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S ALA 3.8 18.6 - - - +
71S CYS* 4.0 4.5 - - - +
74S GLY* 3.5 24.2 - - - -
75S LEU* 3.6 19.7 - - + +
225S VAL* 4.2 11.4 - - + -
226S ASP 3.6 15.7 - - - +
227S GLY* 4.1 13.0 - - - -
229S ASP 3.3 18.0 + - - +
230S ILE 3.9 2.0 - - - +
232S CYS* 1.3 77.0 - - - +
234S ARG* 1.3 51.5 + - - +
236S ALA* 3.7 1.2 - - - +
237S THR* 2.7 41.8 + - - +
253S MET* 4.9 1.1 - - + -
255S LEU* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S THR* 2.8 33.5 + - - +
26S VAL 3.2 19.7 + - - -
27S LEU* 3.9 17.0 - - - +
28S THR 5.2 0.2 - - - +
31S ASP* 4.6 6.3 + - - -
35S TYR* 3.4 41.1 + - - -
74S GLY 3.4 10.9 + - - +
77S ALA* 3.3 28.9 - - + -
78S GLY* 3.9 0.4 - - - +
230S ILE* 3.1 18.1 + - + +
231S LEU* 3.7 12.0 + - - +
233S VAL* 1.3 80.3 - - - +
235S GLU* 1.3 64.6 + - - +
237S THR* 3.5 1.8 - - - -
238S ARG* 3.0 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 235 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ILE* 3.5 24.0 - - + -
21S PRO* 4.6 6.3 - - + -
22S PRO* 3.1 30.4 - - - +
25S THR* 3.2 27.8 + - - -
231S LEU 2.9 18.8 + - - +
232S CYS* 3.0 11.6 + - + +
234S ARG* 1.3 76.0 + - - +
236S ALA* 1.3 59.0 + - - +
238S ARG* 2.9 42.7 + - - +
239S PHE* 2.9 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S CYS* 4.9 3.4 - - - -
21S PRO* 4.4 8.1 - - + +
223S LEU* 4.7 5.9 - - + +
225S VAL* 3.4 34.8 - - + -
232S CYS 2.5 19.7 + - - +
233S VAL* 3.7 3.4 - - - +
235S GLU* 1.3 72.4 - - - +
237S THR* 1.3 63.1 + - - +
239S PHE* 3.3 10.2 + - - +
240S ALA* 3.1 24.4 + - - +
253S MET* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S GLY 4.5 0.2 - - - -
75S LEU* 3.1 33.4 - - + +
78S GLY* 3.4 30.1 - - - +
79S ILE* 3.7 16.4 - - + -
162S LEU* 5.1 3.8 - - + -
190S ILE* 5.1 2.9 - - + +
192S ILE* 6.3 0.2 - - + -
233S VAL 2.7 28.4 + - - -
234S ARG* 3.5 5.4 - - - -
236S ALA* 1.3 74.1 - - - +
238S ARG* 1.3 52.0 + - - +
240S ALA* 3.3 1.9 + - - +
241S ALA* 2.7 33.7 + - + +
253S MET* 3.7 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S TYR* 5.2 1.4 + - - -
77S ALA 3.1 22.6 + - - -
78S GLY* 3.5 22.7 - - - +
234S ARG* 3.0 54.1 + - - +
235S GLU* 2.9 22.3 + - - +
237S THR* 1.3 74.6 - - - +
239S PHE* 1.3 57.5 - - - +
241S ALA* 3.8 2.3 - - - +
242S ALA* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 239 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17S LEU* 4.2 22.9 - - + -
19S GLU* 3.6 11.9 - - + -
20S GLY* 3.5 27.6 - - - -
21S PRO* 3.6 26.9 - - + -
22S PRO* 5.4 3.6 - - + -
223S LEU* 3.6 34.8 - - + -
235S GLU 2.9 11.8 + - - +
236S ALA 3.5 6.5 - - - +
238S ARG* 1.3 78.7 - - - +
240S ALA* 1.3 59.4 + - - +
242S ALA* 4.2 3.1 - - - +
243S TYR* 3.2 28.6 + + - +
251S ILE* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190S ILE* 4.1 18.2 - - + -
223S LEU* 5.2 2.5 - - + -
236S ALA 3.1 15.9 + - - +
237S THR* 3.9 2.0 - - - +
239S PHE* 1.3 76.6 - - + +
241S ALA* 1.3 69.3 + - - +
242S ALA 3.1 1.1 - - - -
243S TYR* 2.8 19.1 + - - +
244S CYS* 2.8 16.3 + - - +
251S ILE* 4.0 26.0 - - + -
253S MET* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S GLY 3.8 14.8 - - - +
79S ILE* 4.7 2.5 - - + -
160S VAL* 3.6 10.1 - - + +
190S ILE* 3.8 14.8 - - + +
237S THR* 2.7 24.5 + - + +
238S ARG* 3.8 3.4 - - - +
240S ALA* 1.3 74.6 - - - +
242S ALA* 1.3 59.9 + - - +
244S CYS* 3.3 2.4 + - - +
245S ARG* 3.0 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238S ARG 2.8 22.0 + - - +
239S PHE* 4.3 3.6 - - - +
241S ALA* 1.3 70.5 - - - +
243S TYR* 1.3 67.6 + - - +
245S ARG* 3.5 14.0 + - - +
246S SER* 3.3 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17S LEU* 4.0 26.4 - - + +
221S PRO* 3.3 24.1 - - + +
239S PHE* 3.2 25.5 + + + +
240S ALA* 2.8 14.0 + - - +
242S ALA* 1.3 75.3 - - - +
244S CYS* 1.3 62.7 + - - +
246S SER* 3.0 24.3 + - - -
248S LYS* 3.4 57.0 + - + +
249S GLY 3.7 12.1 - - - -
250S PRO 3.7 18.0 + - - -
251S ILE* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160S VAL* 3.7 16.2 - - + -
188S PRO* 4.1 20.3 - - + +
189S CYS 3.6 13.0 - - - -
190S ILE* 3.5 29.8 - - - -
240S ALA 2.8 8.9 + - - +
241S ALA 3.6 8.3 - - - +
243S TYR* 1.3 73.7 - - - +
245S ARG* 1.3 66.2 + - - +
246S SER 3.0 2.7 + - - -
247S GLY* 3.1 13.7 + - - -
248S LYS 4.2 0.5 + - - -
249S GLY 3.5 26.1 + - - +
251S ILE* 3.8 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S GLY 4.6 1.4 + - - -
79S ILE* 4.6 2.6 - - - +
80S ASN* 4.0 18.9 + - - +
83S ASP* 3.1 36.5 + - - -
158S ASP* 2.9 61.6 + - - +
159S GLU* 4.3 0.2 - - - +
160S VAL* 3.7 11.2 - - + +
188S PRO* 5.8 1.1 - - - -
241S ALA* 3.0 37.7 + - - +
242S ALA* 3.9 11.9 - - - +
243S TYR 3.5 0.2 - - - -
244S CYS* 1.3 76.6 - - - +
246S SER* 1.3 55.8 + - - +
247S GLY* 3.1 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242S ALA 3.3 11.8 + - - -
243S TYR* 3.0 14.7 + - - -
244S CYS 3.0 2.2 + - - -
245S ARG* 1.3 76.0 - - - +
247S GLY* 1.3 58.1 + - - +
248S LYS* 3.4 20.1 + - - +
----------------------------------------------------------
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