Contacts of the helix formed by residues 251 - 264 (chain B) 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 GLN 251 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU 3.3 1.6 + - - -
250B PRO* 1.3 68.5 - - - +
252B LYS* 1.3 67.0 + - - +
254B PHE* 2.8 31.9 + - - +
255B ASP* 2.9 43.3 + - - +
338B PRO* 3.9 16.2 - - - +
339B SER 2.9 16.5 + - - +
340B THR* 5.2 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 4.7 22.5 - - + +
232B GLU* 2.9 35.5 + - - +
250B PRO* 3.1 3.2 + - + +
251B GLN* 1.3 76.5 - - - +
253B VAL* 1.3 63.2 + - + +
255B ASP* 3.6 9.6 + - - +
256B ALA* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.8 29.6 - - + -
226B LEU* 4.0 9.4 - - + -
228B LEU* 4.4 8.1 - - + -
232B GLU* 4.4 12.8 - - + +
233B TYR* 3.8 25.4 - - + -
249B LEU* 3.9 15.9 - - + -
250B PRO* 2.7 32.2 + - + +
252B LYS* 1.3 71.7 - - + +
254B PHE* 1.3 67.2 + - - +
256B ALA* 3.0 6.6 + - - +
257B VAL* 2.8 21.1 + - - +
343B LEU* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 3.9 25.4 - - + +
250B PRO 3.1 2.4 + - - -
251B GLN* 2.8 23.3 + - - +
253B VAL* 1.3 75.5 - - - +
255B ASP* 1.3 63.9 + - - +
257B VAL* 3.1 2.7 + - + +
258B VAL* 2.8 51.0 + - + +
275B TRP* 3.5 29.2 - - + -
276B THR* 5.5 1.6 - - - -
334B PHE* 3.8 9.6 - + - -
336B ILE* 3.4 33.9 - - + -
337B SER 3.7 11.0 - - - -
338B PRO* 3.5 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B GLN* 2.9 44.5 + - - +
252B LYS* 3.7 10.6 - - - +
254B PHE* 1.3 82.7 - - - +
256B ALA* 1.3 64.4 + - - +
258B VAL* 3.6 5.1 - - - +
259B GLU* 2.8 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.9 27.1 - - + +
228B LEU* 4.2 15.0 - - + -
252B LYS 3.2 10.2 + - - +
253B VAL 3.0 8.6 + - - +
255B ASP* 1.3 78.9 - - - +
257B VAL* 1.3 62.9 + - - +
259B GLU* 3.5 14.3 + - - +
260B ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.9 7.0 - - + -
221B ILE* 3.5 31.6 - - + -
226B LEU* 3.8 13.0 - - + -
249B LEU* 3.5 24.2 - - + -
253B VAL 2.8 20.9 + - - +
254B PHE* 3.4 6.7 - - + +
256B ALA* 1.3 70.5 - - - +
258B VAL* 1.3 58.0 + - + +
260B ALA* 2.9 4.3 + - - +
261B VAL* 2.7 48.9 + - + +
296B ILE* 4.7 4.0 - - + -
334B PHE* 5.3 1.8 - - + -
336B ILE* 4.3 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 2.8 58.3 + - + +
255B ASP* 3.6 5.6 - - - +
257B VAL* 1.3 74.6 - - + +
259B GLU* 1.3 67.3 + - - +
261B VAL* 3.1 6.6 + - - +
262B ALA* 2.8 23.8 + - + +
275B TRP* 3.8 37.9 - - + +
334B PHE* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ASP 2.8 20.2 + - - +
256B ALA* 3.5 11.4 - - - +
258B VAL* 1.3 74.5 - - - +
260B ALA* 1.3 59.5 + - - +
262B ALA* 3.2 6.0 + - - +
263B ARG* 2.8 65.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 3.8 29.4 - - + -
226B LEU* 4.7 6.7 - - + -
256B ALA 3.0 14.0 + - - +
257B VAL 2.9 10.6 + - - +
259B GLU* 1.3 80.6 + - - +
261B VAL* 1.3 65.1 + - - +
262B ALA 3.0 1.0 + - - -
263B ARG* 3.1 8.8 + - - +
264B ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 4.5 9.6 - - + -
257B VAL* 2.7 40.7 + - + +
258B VAL* 3.7 7.2 - - - +
260B ALA* 1.3 72.3 - - - +
262B ALA* 1.3 64.5 + - - +
264B ALA* 3.7 6.8 + - - +
265B SER* 3.4 13.3 + - - -
275B TRP* 4.3 17.4 - - + -
293B PHE* 3.8 26.0 - - + -
294B PRO* 4.1 11.5 - - + +
296B ILE* 4.6 7.6 - - + -
318B TYR* 3.8 24.5 - - + +
334B PHE* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B VAL* 2.8 15.9 + - + +
259B GLU* 3.3 11.7 - - - +
261B VAL* 1.3 75.5 - - - +
263B ARG* 1.3 68.7 + - - +
265B SER* 2.8 18.0 + - - -
266B LEU* 3.1 25.3 + - + +
275B TRP* 4.5 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU* 2.8 56.4 + - + +
260B ALA* 3.7 7.0 - - - +
262B ALA* 1.3 70.9 - - - +
264B ALA* 1.3 57.1 + - - +
265B SER 2.9 6.4 + - - -
266B LEU* 3.7 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 6.0 0.7 - - + -
222B GLY* 6.1 1.1 - - - -
260B ALA 3.1 14.5 + - - +
261B VAL 4.0 4.7 - - - +
262B ALA 2.9 1.6 + - - -
263B ARG* 1.3 73.0 - - - +
265B SER* 1.3 64.7 + - - +
292B TYR 3.2 8.8 - - - +
293B PHE 5.2 0.2 - - - -
294B PRO* 4.1 24.9 - - + +
----------------------------------------------------------
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