Contacts of the helix formed by residues 286 - 297 (chain Y) 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 Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Y ARG* 3.0 37.1 + - - -
260Y TYR* 3.1 19.6 + - - +
281Y VAL 4.0 1.2 + - - -
282Y ARG* 3.2 27.5 + - + +
285Y SER* 1.3 74.8 - - - +
287Y PRO* 1.3 71.1 - - - +
288Y ILE* 3.0 13.0 + - - +
289Y MET* 2.9 36.7 + - + +
290Y LEU* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 287 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Y MET* 3.8 8.1 - - - +
43Y ARG* 4.0 3.8 - - - +
67Y GLY 4.1 7.9 - - - +
69Y GLU* 3.5 23.6 - - + +
70Y ALA* 3.6 26.7 - - + +
228Y MET* 3.3 36.9 - - + +
230Y ILE* 4.8 2.3 - - - +
260Y TYR* 3.8 6.7 - - - +
285Y SER 3.2 3.8 - - - +
286Y ASP* 1.3 95.1 - - - +
288Y ILE* 1.3 61.1 + - - +
290Y LEU* 3.6 2.4 + - + +
291Y LEU* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Y TYR* 3.4 30.6 - - + +
39Y MET* 3.6 37.2 - - + +
40Y GLN* 3.3 33.0 - - + +
43Y ARG* 3.6 37.0 - - + +
69Y GLU* 4.8 1.6 - - + -
286Y ASP* 3.0 9.0 + - - +
287Y PRO* 1.3 75.7 - - + +
289Y MET* 1.3 60.0 + - - +
291Y LEU* 3.4 3.8 + - - +
292Y LYS* 2.9 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 289 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Y ARG 4.2 9.0 - - - +
283Y SER* 3.4 20.9 - - - +
284Y LYS 3.6 16.6 - - - +
285Y SER* 4.1 1.3 - - - -
286Y ASP* 2.9 19.5 + - + +
288Y ILE* 1.3 74.0 - - - +
290Y LEU* 1.3 105.8 + - + +
292Y LYS* 3.0 17.0 + - + +
293Y ASP* 2.8 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226Y ASP* 5.6 1.8 - - - +
228Y MET* 3.5 29.6 - - + +
229Y ASP* 4.6 10.3 - - + +
230Y ILE* 6.4 0.9 - - + -
284Y LYS 3.9 4.0 - - - +
285Y SER* 3.7 28.0 - - - +
286Y ASP 3.0 20.2 + - - +
287Y PRO 4.1 2.9 - - - +
289Y MET* 1.3 102.4 - - + +
291Y LEU* 1.3 63.2 + - - +
293Y ASP* 3.5 5.6 + - - +
294Y ARG* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Y LEU* 5.0 11.7 - - + -
32Y GLY* 3.8 11.4 - - - +
35Y TYR* 4.0 9.2 - - + -
36Y TYR* 3.6 30.7 - - + +
39Y MET* 3.3 35.7 - - + -
230Y ILE* 4.0 19.4 - - + +
231Y LEU* 5.2 7.4 - - + -
287Y PRO 3.3 6.2 + - - +
288Y ILE 3.8 2.0 - - - +
289Y MET 3.1 0.8 - - - -
290Y LEU* 1.3 77.5 - - - +
292Y LYS* 1.3 68.1 + - - +
294Y ARG* 3.0 18.0 + - + +
295Y MET* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Y TYR* 4.1 16.1 - - + +
288Y ILE* 2.9 16.4 + - + +
289Y MET* 3.3 18.3 - - - +
291Y LEU* 1.3 78.0 - - - +
293Y ASP* 1.3 68.6 + - - +
295Y MET* 3.0 6.1 + - - +
296Y VAL* 2.9 34.0 + - + +
303Y VAL* 4.6 21.1 - - - +
306Y LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289Y MET* 2.8 39.1 + - - +
290Y LEU* 3.7 7.2 - - - +
292Y LYS* 1.3 82.4 + - - +
294Y ARG* 1.3 60.7 + - + +
296Y VAL* 4.5 4.7 - - - +
297Y ASN* 2.8 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y PHE* 3.4 43.8 - - + +
8Y GLU 3.2 25.1 + - - -
9Y ILE* 3.7 8.9 - - - +
27Y LEU* 6.2 0.9 - - + -
229Y ASP* 2.8 44.3 + - - -
230Y ILE* 5.0 3.0 - - - +
231Y LEU* 3.3 26.3 - - - +
290Y LEU* 3.2 17.4 + - - +
291Y LEU* 3.0 17.1 + - + +
293Y ASP* 1.3 80.2 - - - +
295Y MET* 1.3 60.3 + - + +
297Y ASN* 3.8 3.1 + - - -
298Y SER* 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Y LEU* 4.0 13.7 - - + -
29Y ARG 4.8 1.6 - - - +
32Y GLY* 3.0 45.3 - - - +
33Y LEU* 3.4 27.6 - - + -
36Y TYR* 4.3 5.6 - - + -
291Y LEU* 2.9 26.3 + - + +
292Y LYS* 3.2 9.4 - - - +
294Y ARG* 1.3 77.5 - - + +
296Y VAL* 1.3 61.3 + - - +
298Y SER* 3.5 0.2 + - - -
299Y ASN 3.3 2.6 + - - -
300Y LEU* 2.9 44.5 + - - -
301Y ALA* 3.3 14.7 + - + -
306Y LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292Y LYS* 2.9 29.4 + - + +
293Y ASP* 4.0 5.2 - - - +
295Y MET* 1.3 71.4 - - - +
297Y ASN* 1.3 71.8 + - - +
298Y SER 2.9 10.1 + - - -
299Y ASN* 3.3 10.2 + - - -
301Y ALA 3.4 18.2 - - - +
302Y SER* 4.2 1.3 - - - -
303Y VAL* 3.9 31.2 - - + +
306Y LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 297 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y PHE* 6.3 0.4 - - + -
293Y ASP* 2.8 36.1 + - - +
294Y ARG* 4.5 2.9 - - - +
296Y VAL* 1.3 81.9 - - - +
298Y SER* 1.3 59.5 + - - +
299Y ASN 3.6 0.2 - - - -
----------------------------------------------------------
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