Contacts of the helix formed by residues 247 - 257 (chain D) in PDB entry 3PRJ
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 247 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C SER* 4.8 3.4 + - - -
241D CYS* 4.0 2.5 - - - -
246D ALA* 1.3 78.1 - - - +
248D VAL* 1.3 68.0 + - - +
249D GLU* 2.9 14.6 + - - +
250D GLU* 3.0 34.7 + - + +
251D VAL* 3.0 20.9 + - - +
443D ARG* 3.0 26.9 + - - -
463D GLY 3.4 3.4 - - - +
464D LYS* 4.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ILE* 3.9 31.2 - - + +
237D ILE* 4.4 5.6 - - + -
238D SER* 3.8 24.7 - - - +
241D CYS* 3.7 17.2 - - - -
247D ASP* 1.3 74.3 + - - +
249D GLU* 1.3 58.6 + - + +
251D VAL* 3.2 1.9 + - - -
252D ALA* 2.6 38.8 + - + +
268D ALA* 4.0 18.4 - - + -
443D ARG* 3.5 20.2 - - - +
462D ILE 3.9 2.5 - - - +
463D GLY* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ASP* 2.9 10.5 + - - +
248D VAL* 1.3 82.9 - - + +
250D GLU* 1.3 60.0 + - + +
252D ALA* 3.4 8.2 - - - +
253D THR* 2.9 28.1 + - - -
266D LEU 4.7 2.1 - - - +
267D LYS* 3.4 43.5 + - - +
268D ALA 4.2 10.9 + - - -
443D ARG* 3.4 43.8 - - - +
446D ASP* 3.6 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C THR* 3.3 25.5 + - - -
212C ASN* 5.1 2.6 + - - -
215C SER* 4.1 10.9 + - - +
247D ASP* 3.0 32.0 + - + +
249D GLU* 1.3 75.9 - - + +
251D VAL* 1.3 67.0 + - - +
253D THR* 3.1 17.0 + - - -
254D ALA* 3.2 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C SER* 4.0 15.9 - - - +
218C LEU* 4.2 22.0 - - + -
219C SER* 3.8 34.5 - - - +
222C ALA* 4.5 2.5 - - + -
234D ILE* 5.7 0.2 - - + -
237D ILE* 4.2 16.2 - - + -
241D CYS* 4.2 7.2 - - - -
246D ALA* 4.5 1.6 - - + -
247D ASP 3.0 14.2 + - - +
248D VAL* 3.7 8.7 - - - +
250D GLU* 1.3 73.9 - - - +
252D ALA* 1.3 63.4 + - - +
254D ALA* 3.0 4.5 + - - +
255D ILE* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ILE* 4.1 9.6 - - + -
248D VAL 2.6 21.5 + - - +
249D GLU* 3.4 13.5 - - - +
251D VAL* 1.3 73.7 - - - +
253D THR* 1.3 51.5 + - - +
255D ILE* 3.2 14.0 + - - +
256D GLY* 2.7 34.8 + - - -
266D LEU* 3.8 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C LEU* 4.9 11.2 - - + -
249D GLU 2.9 15.0 + - - -
250D GLU* 3.1 9.5 + - - -
252D ALA* 1.3 77.2 - - - +
254D ALA* 1.3 62.3 + - - +
256D GLY* 3.1 2.6 + - - -
257D MET* 3.1 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C PHE* 6.3 0.4 - - + -
177C ARG* 3.0 29.9 + - + +
179C LEU* 4.4 12.3 - - + -
209C LEU* 4.0 21.7 - - + +
219C SER* 3.7 27.4 - - - +
223C ALA* 5.6 0.4 - - - -
250D GLU 3.2 7.0 + - - +
251D VAL 3.0 9.3 + - - +
253D THR* 1.3 77.2 - - - +
255D ILE* 1.3 65.8 + - - +
257D MET* 3.7 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ARG* 4.2 5.2 - - - +
219C SER 4.2 4.5 - - - +
222C ALA* 3.8 14.8 - - + -
223C ALA* 4.1 18.8 - - - +
226C PHE* 4.1 25.8 - - + -
234D ILE* 4.0 22.9 - - + -
237D ILE* 5.1 0.9 - - + -
251D VAL* 2.9 42.3 + - + +
252D ALA* 3.5 4.5 - - - +
254D ALA* 1.3 75.4 - - - +
256D GLY* 1.3 63.4 + - - +
257D MET 3.2 0.9 + - - -
258D ASP* 3.3 21.7 + - - +
261D ILE* 3.7 30.6 - - + +
266D LEU* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ALA 2.7 22.0 + - - -
253D THR* 3.1 4.4 + - - -
255D ILE* 1.3 74.1 - - - +
257D MET* 1.3 60.8 + - - +
258D ASP 3.3 3.1 + - - +
259D GLN* 5.3 0.5 - - - -
262D GLY* 3.4 23.9 - - - +
263D ASN* 3.2 26.5 - - - +
266D LEU* 3.8 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASP* 3.5 33.7 - - - +
177C ARG* 3.9 25.8 - - + +
206C GLU 4.4 16.2 - - - +
207C LYS* 4.6 7.2 - - + -
209C LEU* 3.8 31.0 - - - -
253D THR* 3.1 24.1 + - + +
254D ALA 4.2 0.4 - - - +
255D ILE 3.2 1.2 + - - -
256D GLY* 1.3 73.8 - - - +
258D ASP* 1.3 64.6 + - - +
259D GLN* 3.1 10.4 + - - +
263D ASN* 5.3 2.0 - - + +
----------------------------------------------------------
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