Contacts of the helix formed by residues 282 - 292 (chain A) in PDB entry 2ETK
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 282 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA* 3.7 12.8 - - - +
281A ASP* 1.3 81.2 - - - +
283A LEU* 1.3 67.0 + - - +
284A VAL* 3.4 23.8 - - - +
285A GLY* 3.2 13.5 + - - -
286A THR* 3.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PRO* 3.9 36.7 - - + +
239A ASP* 5.9 2.7 - - - +
282A SER* 1.3 76.0 - - - +
284A VAL* 1.3 64.4 + - + +
285A GLY 3.3 1.0 + - - -
286A THR* 3.3 24.0 + - - +
287A TYR* 3.6 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER* 3.4 21.3 - - - +
283A LEU* 1.3 79.8 - - + +
285A GLY* 1.3 61.3 + - - +
287A TYR* 3.3 21.8 - - + +
288A SER* 3.5 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA* 3.5 18.8 - - - -
282A SER* 3.2 8.1 + - - -
283A LEU 3.2 0.8 - - - -
284A VAL* 1.3 79.9 - - - +
286A THR* 1.3 63.4 + - - +
287A TYR 3.1 2.1 + - - -
288A SER* 3.3 7.1 + - - -
289A LYS* 3.1 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PRO* 3.5 31.2 - - + +
239A ASP* 3.8 19.8 + - - +
278A PHE* 3.2 28.5 + - + +
279A TYR* 5.6 0.7 - - - -
280A ALA* 3.4 16.1 + - - +
282A SER 4.0 4.7 + - - -
283A LEU* 3.3 16.6 + - - +
285A GLY* 1.3 73.7 - - - +
287A TYR* 1.3 56.4 + - - +
289A LYS* 3.4 2.9 + - - +
290A ILE* 2.9 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 4.5 15.6 - - + +
283A LEU 3.6 3.2 + - - +
284A VAL* 3.3 20.8 + - + +
285A GLY 3.1 0.4 - - - -
286A THR* 1.3 77.7 - - - +
288A SER* 1.3 64.2 + - - +
290A ILE* 3.3 7.3 + - - +
291A MET* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL 3.5 8.4 + - - -
285A GLY* 3.3 9.7 + - - -
287A TYR* 1.3 78.0 - - - +
289A LYS* 1.3 59.2 + - - +
291A MET* 3.6 6.5 + - - +
292A ASN* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PRO 5.7 0.2 - - - +
278A PHE* 3.3 21.1 - - + +
279A TYR 2.8 29.6 + - - +
280A ALA* 4.1 13.4 - - + +
285A GLY* 3.1 15.1 + - - +
286A THR 3.7 4.7 - - - +
287A TYR 3.2 0.2 - - - -
288A SER* 1.3 76.9 - - - +
290A ILE* 1.3 62.8 + - - +
292A ASN* 3.2 9.1 - - - +
293A HIS 3.2 0.7 + - - -
296A SER* 2.5 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PRO 3.0 28.9 - - - +
239A ASP 4.3 7.4 - - - +
241A ILE* 3.9 30.1 - - + +
243A PRO* 4.2 20.0 - - + +
246A LEU* 3.9 19.1 - - + -
262A TRP* 4.3 5.8 - - + -
278A PHE* 3.7 27.1 - - + -
286A THR* 2.9 25.7 + - + +
287A TYR* 3.3 5.3 + - - +
289A LYS* 1.3 71.7 - - - +
291A MET* 1.3 66.0 + - + +
292A ASN 3.1 1.6 - - - -
293A HIS* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PRO* 3.3 37.2 - - + +
246A LEU* 3.7 23.8 - - + -
247A LYS* 3.6 29.8 - - + +
287A TYR* 3.2 16.5 + - + +
288A SER* 3.9 6.5 - - - +
290A ILE* 1.3 76.2 - - - +
292A ASN* 1.3 58.4 + - + +
293A HIS* 3.4 10.0 + - - -
294A LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER 3.0 18.0 + - - +
289A LYS* 3.2 8.5 - - - +
290A ILE 3.1 0.4 - - - -
291A MET* 1.3 77.8 - - - +
293A HIS* 1.3 55.5 + - - +
294A LYS* 3.1 9.3 - - - +
295A ASN* 3.1 33.9 + - - +
296A SER* 2.8 30.6 + - - +
----------------------------------------------------------
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