Contacts of the helix formed by residues 286 - 298 (chain O) 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 286 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O ARG* 3.1 27.0 + - - -
228O MET* 4.8 1.8 - - - -
282O ARG* 3.4 38.3 + - + +
285O SER* 1.3 78.2 - - - +
287O PRO* 1.3 97.3 - - + +
288O ILE* 2.4 21.5 + - - +
289O MET* 3.7 17.9 + - + +
290O LEU* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 287 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O MET* 3.7 11.3 - - - +
43O ARG* 3.9 6.5 - - - +
67O GLY* 3.7 26.2 - - - +
69O GLU* 3.8 22.7 - - + +
70O ALA* 3.9 17.0 - - + +
228O MET* 3.4 32.7 - - + +
230O ILE* 4.6 2.8 - - - +
285O SER 3.8 2.2 - - - +
286O ASP* 1.3 95.7 - - + +
288O ILE* 1.3 60.6 + - - +
290O LEU* 3.4 6.5 - - + +
291O LEU* 3.3 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O TYR* 3.5 30.5 - - + +
39O MET* 3.5 50.7 - - + +
40O GLN* 3.5 31.6 - - + +
43O ARG* 3.8 27.8 - - + +
69O GLU* 4.9 0.4 - - + -
286O ASP* 2.4 25.8 + - - +
287O PRO* 1.3 66.4 - - + +
289O MET* 1.3 66.0 + - - +
291O LEU* 3.2 5.2 + - - +
292O LYS* 3.0 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 289 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282O ARG 4.3 3.8 - - - +
283O SER 4.1 15.9 - - - +
284O LYS 4.6 3.4 - - - +
285O SER* 3.7 16.8 - - - +
286O ASP* 3.4 25.5 + - + +
288O ILE* 1.3 80.3 - - - +
290O LEU* 1.3 94.4 + - + +
292O LYS* 3.8 15.7 - - + -
293O ASP* 2.8 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226O ASP* 5.7 1.3 - - - +
228O MET* 4.5 17.7 - - + +
229O ASP* 4.7 17.5 - - + +
230O ILE* 5.8 2.2 - - + -
285O SER* 4.3 18.6 - - - +
286O ASP 3.2 17.7 + - - +
287O PRO* 3.4 10.1 - - + +
288O ILE 3.2 0.4 - - - -
289O MET* 1.3 101.2 - - + +
291O LEU* 1.3 60.6 + - - +
293O ASP* 4.2 5.8 - - + +
294O ARG* 3.3 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU* 4.3 20.4 - - + -
32O GLY* 4.2 5.2 - - - +
35O TYR* 3.8 29.8 - - + -
36O TYR* 4.0 13.7 - - + +
39O MET* 4.0 21.3 - - + -
230O ILE* 4.0 28.2 - - + +
231O LEU* 5.0 5.4 - - + -
287O PRO 3.3 1.8 + - - -
288O ILE 3.2 8.6 + - - +
290O LEU* 1.3 74.1 - - - +
292O LYS* 1.3 56.4 + - - +
294O ARG* 3.8 15.5 - - + +
295O MET* 2.8 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O TYR* 3.9 26.6 - - + +
288O ILE* 3.0 14.5 + - + +
289O MET* 3.3 20.2 - - + +
291O LEU* 1.3 73.8 - - - +
293O ASP* 1.3 71.3 + - - +
294O ARG 3.1 0.9 - - - -
295O MET* 3.1 3.7 + - - +
296O VAL* 2.9 29.8 + - + +
303O VAL* 3.5 30.5 + - + +
306O LEU* 3.5 33.2 - - + +
307O LYS* 4.9 10.7 - - - +
310O ASP* 4.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O MET* 2.8 50.4 + - - +
290O LEU* 4.2 7.0 - - + +
292O LYS* 1.3 79.3 - - - +
294O ARG* 1.3 56.5 + - - +
296O VAL* 4.9 1.6 - - - -
297O ASN* 3.1 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O PHE* 3.6 39.6 - - + +
8O GLU 3.3 24.0 + - - -
9O ILE* 4.3 0.6 - - - +
27O LEU* 6.1 0.2 - - + -
229O ASP* 3.0 31.6 + - - -
230O ILE* 5.1 3.6 - - - +
231O LEU* 2.2 46.5 - - - +
290O LEU* 3.3 27.6 + - + +
291O LEU* 3.6 14.6 - - + +
292O LYS 3.1 0.6 - - - -
293O ASP* 1.3 75.1 - - - +
295O MET* 1.3 67.5 + - - +
296O VAL 3.1 1.0 + - - -
297O ASN* 4.1 1.7 - - - +
298O SER* 3.2 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU* 4.3 12.6 - - + -
29O ARG 4.6 2.2 - - - +
32O GLY* 3.0 44.0 - - - +
33O LEU* 3.6 26.7 - - + +
36O TYR* 4.8 3.8 - - + -
291O LEU* 2.8 41.0 + - + +
292O LYS* 3.1 5.6 + - - +
294O ARG* 1.3 74.0 - - + +
296O VAL* 1.3 57.6 + - - +
299O ASN 3.6 0.2 + - - -
300O LEU* 2.7 48.6 + - - +
301O ALA* 3.0 25.5 + - + +
306O LEU* 4.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292O LYS* 2.9 21.2 + - + +
293O ASP* 4.9 1.1 - - - -
295O MET* 1.3 73.6 - - - +
297O ASN* 1.3 71.2 + - - +
298O SER 2.7 16.5 + - - -
299O ASN* 2.7 16.3 + - - -
301O ALA 3.5 11.0 - - - +
302O SER* 4.0 2.0 - - - -
303O VAL* 3.5 42.6 - - + +
306O LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 297 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O ASP* 3.1 30.8 + - - +
294O ARG* 4.5 0.9 - - - +
296O VAL* 1.3 88.5 - - - +
298O SER* 1.3 56.7 + - - +
299O ASN 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O ALA* 4.5 4.3 - - - +
5O ALA* 3.5 25.5 - - - +
7O PHE* 3.6 19.4 - - - -
294O ARG 3.2 16.7 + - - -
296O VAL 2.7 3.8 + - - -
297O ASN* 1.3 76.1 - - - +
299O ASN* 1.3 68.9 + - - +
300O LEU* 3.2 11.2 + - - +
----------------------------------------------------------
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