Contacts of the helix formed by residues 247 - 259 (chain D) in PDB entry 7CAL
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 TYR 247 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TRP* 3.5 26.4 + + - -
79D PHE* 4.2 21.1 - + - -
83D PHE* 3.5 50.3 - + + -
210D HIS* 3.6 12.1 + + - -
214D CYS* 4.5 9.4 - - - -
244D TRP 4.5 5.4 - - - +
245D ASN* 4.3 11.4 - - - -
246D ARG* 1.3 76.9 - - - +
248D VAL* 1.3 60.1 + - + +
249D THR* 3.1 4.5 - - - +
250D ALA* 3.0 20.2 + - + +
251D LEU* 3.5 39.8 + - + +
701D 3PE 5.1 2.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
271C PRO* 5.1 9.9 - - + +
274C MET* 4.0 23.3 - - + +
275C LEU* 4.0 19.3 - - + -
278C ILE* 3.8 20.6 - - + -
246D ARG* 3.2 49.9 - - + +
247D TYR* 1.3 74.3 - - + +
249D THR* 1.3 56.8 + - - +
250D ALA 3.3 0.2 - - - -
251D LEU* 3.4 7.1 + - + +
252D TYR* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C PRO* 6.1 0.7 - - - +
274C MET* 3.8 20.7 - - + +
230D TRP* 4.0 2.9 - - + -
231D ILE* 4.0 23.1 - - + -
235D TYR* 4.3 14.7 - - + -
246D ARG 5.2 2.8 + - - -
247D TYR* 3.1 2.0 - - - -
248D VAL* 1.3 78.5 - - - +
250D ALA* 1.3 60.2 + - - +
252D TYR* 3.4 3.0 + - - +
253D TRP* 3.2 22.5 + - - +
266D PHE* 3.6 36.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.1 17.3 - - + -
213D GLY* 3.3 35.9 - - - +
217D TYR* 4.7 6.7 - - + -
230D TRP* 3.8 21.0 - - + -
231D ILE* 5.8 0.6 - - + +
247D TYR* 3.0 13.2 + - + +
249D THR* 1.3 78.8 - - - +
251D LEU* 1.3 61.8 + - - +
253D TRP* 3.8 5.0 + - - +
254D SER* 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ILE* 3.9 22.8 - - + +
209D ILE* 3.8 30.5 - - + +
210D HIS* 4.5 9.2 - - - +
213D GLY* 4.6 6.5 - - - -
247D TYR* 3.5 42.9 + - + +
248D VAL* 3.4 7.0 + - - +
249D THR 3.3 0.2 - - - -
250D ALA* 1.3 80.4 - - - +
252D TYR* 1.3 59.3 + - - +
253D TRP 3.2 0.4 - - - -
254D SER* 3.8 3.3 - - - +
255D ILE* 3.0 31.9 + - - +
701D 3PE 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C HIS* 3.8 2.9 - - - +
268C ALA* 3.4 29.1 + - + -
274C MET* 4.0 31.2 - - + -
277C ASP* 3.8 32.6 + - + -
278C ILE* 3.9 7.6 - - + +
281C MET* 4.1 11.9 - - + -
248D VAL 2.8 18.3 + - - +
249D THR* 3.8 4.5 - - - +
250D ALA 3.4 0.2 - - - -
251D LEU* 1.3 77.1 - - - +
253D TRP* 1.3 54.0 + - - +
255D ILE* 3.5 6.4 - - - +
256D THR* 2.3 38.8 + - - -
263D TYR* 3.2 27.6 - + - -
265D ASP* 4.1 7.4 - - - -
266D PHE* 3.7 37.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TYR* 4.5 3.0 + - - -
212D ALA 3.6 4.7 - - - -
216D ASN* 3.3 45.0 - - + +
230D TRP* 3.8 30.6 - + + +
249D THR 3.2 9.0 + - - +
250D ALA 4.0 5.8 - - - +
251D LEU 3.2 0.2 - - - -
252D TYR* 1.3 81.2 - - - +
254D SER* 1.3 88.9 + - - +
256D THR* 3.3 9.6 + - - -
257D THR* 3.2 35.4 - - + +
266D PHE* 3.5 43.3 + - + -
267D HIS* 4.8 3.2 - - - +
276D PHE* 4.1 4.7 - + - -
277D ASP* 3.3 33.0 + - - -
280D PHE* 4.0 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ILE* 3.8 26.9 - - - -
212D ALA* 3.1 27.4 + - - +
213D GLY* 3.2 9.5 + - - -
250D ALA 3.5 8.3 + - - -
251D LEU 3.2 5.4 + - - -
253D TRP* 1.3 89.4 - - - +
255D ILE* 1.3 61.3 + - - +
257D THR* 3.5 4.0 + - - -
258D LEU* 3.1 32.0 + - - +
280D PHE* 4.4 5.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
278C ILE* 3.9 24.2 - - + +
281C MET* 3.7 36.9 - - + +
282C MET* 3.8 20.6 - - + -
285C LEU* 4.9 3.4 - - + -
209D ILE* 3.7 32.9 - - + +
251D LEU 3.0 20.2 + - - +
252D TYR* 3.5 8.7 - - - +
254D SER* 1.3 77.5 - - - +
256D THR* 1.3 60.6 + - - +
258D LEU* 4.1 4.3 - - + -
259D THR* 2.8 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TYR* 5.9 1.6 - - + -
281C MET* 3.9 13.0 - - - +
252D TYR* 2.3 35.6 + - + -
253D TRP* 3.3 8.0 + - - -
254D SER 3.2 1.0 - - - -
255D ILE* 1.3 79.1 - - - +
257D THR* 1.3 60.6 + - + +
259D THR* 4.2 2.2 - - - -
260D THR 3.8 0.2 - - - -
261D THR* 2.9 29.2 + - - -
262D GLY* 3.2 27.3 + - - +
263D TYR* 3.6 35.9 - - + +
265D ASP* 5.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 4.3 11.7 + - - -
263A TYR* 3.2 32.3 - - + +
253D TRP* 3.2 35.5 + - + +
254D SER 3.7 1.4 + - - -
256D THR* 1.3 79.6 - - - +
258D LEU* 1.3 65.3 + - - +
259D THR 3.4 0.4 - - - -
260D THR* 3.2 20.4 + - - +
280D PHE* 3.2 29.0 - - - -
281D MET* 5.0 9.7 - - - +
284D ASN* 3.7 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 3.8 27.5 - - + +
205D THR* 4.8 3.8 - - + +
208D ALA* 4.0 16.6 - - + -
209D ILE* 3.9 29.6 - - + -
254D SER 3.1 15.0 + - - +
255D ILE* 4.5 2.7 - - + +
257D THR* 1.3 81.8 + - - +
259D THR* 1.3 61.6 + - + +
260D THR* 3.5 3.3 + - - +
280D PHE* 4.2 11.4 - - + -
284D ASN* 3.7 30.2 - - - +
287D LEU* 3.9 25.1 - - + -
288D THR* 3.6 23.0 - - + +
291D LEU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C THR* 3.6 19.4 - - - +
281C MET* 3.4 30.9 - - - +
284C ASN* 6.3 1.3 - - - -
285C LEU* 3.8 26.7 - - + -
255D ILE* 2.8 35.7 + - + +
258D LEU* 1.3 74.9 - - + +
260D THR* 1.3 71.9 + - - +
261D THR* 2.8 22.7 + - - -
288D THR* 5.4 1.3 - - - -
----------------------------------------------------------
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