Contacts of the helix formed by residues 229 - 240 (chain D) in PDB entry 2PGW
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 229 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D GLN* 5.9 0.2 + - - -
226D VAL* 3.5 13.7 + - - +
227D SER 3.2 4.9 - - - +
228D TRP* 1.3 76.2 - - - +
230D ILE* 1.3 62.8 + - - +
231D PRO* 3.7 8.7 - - - +
232D ALA* 3.1 31.3 + - - +
233D MSE 3.3 17.3 + - - +
249D ALA* 5.7 0.5 - - - +
254E TYR* 4.5 11.6 - - - -
257E TYR* 5.9 1.0 - - - -
290G ALA 4.4 2.6 + - - -
291G ALA* 3.7 9.9 + - - -
292G GLY* 4.3 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D SER 4.5 2.9 - - - +
228D TRP 3.8 4.8 + - - +
229D SER* 1.3 69.6 - - - +
231D PRO* 1.3 75.7 - - + +
233D MSE 3.1 8.6 + - + +
234D ALA* 3.0 19.8 + - - +
249D ALA* 3.7 34.1 - - + +
255D ASP* 5.1 3.6 - - + +
258D GLU* 4.6 10.5 - - + -
259D ILE* 3.6 31.0 - - + +
262D GLN* 3.4 26.2 - - - +
264D ALA* 3.5 20.8 - - + +
258E GLU* 6.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 3.5 9.6 - - - +
230D ILE* 1.3 96.7 - - + +
232D ALA* 1.3 56.3 + - - +
234D ALA* 3.3 6.3 + - + +
235D HIS* 2.9 28.9 + - - +
262D GLN* 3.9 10.5 - - - +
257E TYR* 5.3 3.4 - - + -
258E GLU* 3.5 27.4 - - - +
261E ARG* 3.9 26.5 - - - +
263G ARG* 3.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D VAL* 4.3 6.6 - - + +
225D THR* 4.2 11.2 - - - +
226D VAL* 5.3 1.6 - - + +
229D SER* 3.1 30.5 + - - +
230D ILE 3.2 0.2 - - - -
231D PRO* 1.3 76.6 - - - +
233D MSE 1.3 62.1 + - - +
235D HIS* 3.2 4.3 - - - +
236D VAL* 3.1 26.2 + - - +
263G ARG* 3.7 14.5 - - - +
291G ALA 4.0 11.4 - - - +
292G GLY* 4.3 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D GLN* 3.9 20.6 - - - +
224D PRO* 5.2 2.5 - - + -
225D THR* 3.6 18.1 + - - +
229D SER 3.3 7.1 + - - +
230D ILE* 3.1 10.1 + - + +
232D ALA* 1.3 77.0 - - - +
234D ALA* 1.3 59.9 + - - +
236D VAL* 3.3 4.4 + - - +
237D ARG* 2.9 27.5 + - - +
244D ILE* 4.2 17.8 - - + +
245D VAL 4.8 0.2 - - - +
246D ALA* 3.7 41.5 - - + -
249D ALA* 3.9 16.2 - - + -
259D ILE* 4.1 10.3 - - + -
264D ALA* 3.5 33.4 - - + +
265D ALA* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D ILE 3.0 13.3 + - - +
231D PRO* 3.6 11.9 - - + +
233D MSE 1.3 76.5 - - - +
235D HIS* 1.3 57.4 + - - +
237D ARG* 3.7 2.2 - - - +
238D GLU* 2.9 46.6 + - - +
262D GLN* 4.3 13.9 - - + +
263D ARG 4.6 1.6 - - - +
264D ALA* 3.8 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D VAL* 3.6 17.3 - - + +
207D ILE* 5.0 0.4 - - + -
231D PRO 2.9 13.8 + - - +
232D ALA 3.2 12.6 - - - +
234D ALA* 1.3 78.8 - - - +
236D VAL* 1.3 63.2 + - - +
238D GLU* 3.6 7.1 + - - +
239D LYS* 3.4 21.1 + - + +
237G ARG* 3.2 31.7 + - - +
263G ARG* 3.1 40.3 + - + +
265G ALA 3.4 21.1 - - - -
266G ASP* 2.7 28.8 + - - -
293G LEU* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D VAL* 3.9 29.6 - - + +
206D ALA* 3.9 16.6 - - + -
207D ILE* 4.7 3.1 - - + -
210D CYS* 5.2 0.7 - - - -
224D PRO* 4.3 15.9 - - + -
225D THR* 3.7 23.6 - - + -
232D ALA 3.1 14.7 + - - +
233D MSE 3.3 7.4 + - - +
235D HIS* 1.3 74.7 - - - +
237D ARG* 1.3 67.8 + - - +
239D LYS* 2.9 14.9 + - - -
240D VAL* 2.9 34.9 + - + +
244D ILE* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C HIS* 3.3 29.3 + - - +
239C LYS* 3.1 44.2 + - + +
233D MSE 2.9 18.0 + - - +
234D ALA 3.7 3.6 + - - +
236D VAL* 1.3 77.0 - - - +
238D GLU* 1.3 87.4 + - - +
239D LYS 3.3 0.7 + - - -
240D VAL* 3.5 7.1 - - - +
242D ILE 5.3 1.0 - - - +
244D ILE* 3.9 23.1 - - + +
263D ARG* 2.7 36.9 + - - +
264D ALA* 3.7 5.4 - - - +
265D ALA* 3.6 25.4 - - - +
266D ASP* 3.6 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLU* 6.1 0.7 - - - -
239C LYS* 3.5 17.5 + - - +
234D ALA* 2.9 31.4 + - - +
235D HIS* 3.9 7.7 - - - +
237D ARG* 1.3 98.8 + - - +
239D LYS* 1.3 65.1 + - + +
262D GLN 4.9 4.5 - - - +
263D ARG* 5.9 0.5 - - - +
237G ARG* 5.7 3.0 + - - +
238G GLU* 5.0 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C LYS* 4.5 1.6 + - - -
207D ILE* 4.3 33.3 - - + +
235D HIS* 3.4 10.1 + - + +
236D VAL 2.9 7.3 + - - +
238D GLU* 1.3 85.0 - - + +
240D VAL* 1.3 65.6 + - - +
241D GLY 4.0 0.3 + - - -
237G ARG* 2.9 49.1 + - - +
238G GLU* 3.1 24.0 + - + +
239G LYS 3.9 2.2 + - - -
240G VAL 2.7 29.6 + - - -
241G GLY* 5.0 3.3 - - - -
242G ILE 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C LYS* 2.8 27.3 + - - +
207D ILE* 3.8 27.6 - - + +
210D CYS* 3.6 32.5 - - + -
236D VAL* 2.9 26.7 + - + +
237D ARG 3.5 4.5 - - - +
239D LYS* 1.3 78.5 - - - +
241D GLY* 1.3 61.5 + - - +
242D ILE 3.4 19.0 - - - +
244D ILE* 3.7 22.9 - - + -
----------------------------------------------------------
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