Contacts of the helix formed by residues 288 - 293 (chain C) in PDB entry 2EWY
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 THR 288 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 4.7 1.9 + - - +
292B TYR* 5.2 0.4 + - - -
283C TRP* 5.5 0.2 - - - -
286C SER 4.6 6.1 - - - +
287C GLU* 1.3 88.2 + - - +
289C PRO* 1.3 67.6 - - - +
290C TRP* 3.1 51.3 + - + +
291C SER* 4.2 9.7 + - - -
292C TYR* 4.4 2.4 - - - -
330C GLU* 5.2 5.6 - - - +
332C TYR* 4.0 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C PHE* 4.7 2.7 - - + -
283C TRP* 3.8 38.4 - - + -
287C GLU 3.8 3.1 - - - +
288C THR* 1.3 84.6 - - - +
290C TRP* 1.3 60.6 + - + +
291C SER 3.6 0.9 - - - -
292C TYR* 3.6 19.1 + - + +
293C PHE* 3.0 33.3 - - + -
319C ILE* 4.7 6.7 - - + -
332C TYR* 3.1 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA 6.4 1.3 - - - -
288C THR* 3.1 42.8 - - + +
289C PRO* 1.3 77.7 - - + +
291C SER* 1.3 55.8 + - - +
292C TYR 2.7 16.6 + - - -
293C PHE* 3.0 15.3 + - - +
315C PRO* 3.5 32.9 - - + +
316C GLN* 3.3 53.2 - - + +
319C ILE* 3.1 38.8 + - + +
321C PRO* 4.3 19.7 - - + -
332C TYR* 4.4 14.3 - + - -
374C ILE* 4.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 3.3 18.2 + - - -
286B SER* 5.1 6.7 + - - -
287B GLU* 3.0 40.1 + - - -
288C THR* 4.2 3.8 + - - -
290C TRP* 1.3 75.0 - - - +
292C TYR* 1.3 79.5 + - - +
293C PHE 3.5 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TRP* 4.8 18.0 + + - -
285B ASN* 4.4 23.8 - - + +
287B GLU* 3.7 21.5 + - + +
288B THR 5.0 0.7 + - - -
292B TYR* 3.3 30.8 + - - -
264C ALA 3.2 7.1 - - - +
265C SER* 2.8 35.6 - - - -
267C ILE* 4.8 15.9 - - + -
268C PRO* 4.9 12.6 - - + -
283C TRP* 5.8 3.1 - + - -
287C GLU* 5.7 0.2 - - + -
288C THR 4.4 7.6 - - - -
289C PRO* 3.7 24.0 - - + +
290C TRP 2.7 7.5 + - - -
291C SER* 1.3 94.7 - - - +
293C PHE* 1.3 60.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C VAL* 3.8 25.1 - - + -
264C ALA 5.2 0.7 - - - -
265C SER* 4.4 12.6 - - - -
268C PRO* 5.2 7.9 - - + -
270C PHE* 3.9 25.1 - + - -
275C TRP* 4.5 13.2 - + - -
289C PRO* 3.0 38.8 - - + -
290C TRP* 3.0 12.7 + - - +
291C SER 4.4 3.8 - - - +
292C TYR* 1.3 83.8 - - + +
294C PRO* 1.3 68.0 - - + +
315C PRO* 3.6 19.1 - - + +
318C TYR* 3.5 9.2 - - - +
319C ILE* 3.7 39.7 - - + -
----------------------------------------------------------
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