Contacts of the helix formed by residues 246 - 270 (chain D) in PDB entry 2QJK
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 PRO 246 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D PRO* 4.8 0.9 - - + -
244D PHE 3.4 1.1 - - - -
245D TRP* 1.3 121.7 - - + +
247D TYR* 1.3 83.0 + - + +
248D PHE 3.4 2.7 - - - -
249D ILE 4.0 0.4 - - - -
250D ILE* 2.9 33.6 + - + +
251E LEU* 3.3 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D VAL* 3.8 14.4 - - + -
243D PRO* 3.3 51.4 - - + +
244D PHE 3.2 1.0 + - - -
246D PRO* 1.3 86.9 - - + +
248D PHE* 1.3 60.2 + - - +
250D ILE* 3.9 2.8 - - - +
251D LYS 3.5 8.8 + - - -
248E ASN* 4.0 0.2 - - - +
251E LEU* 3.2 50.5 + - + +
252E TRP* 3.0 48.1 + + + +
254E GLY 4.9 2.6 + - - -
255E VAL* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 3.3 35.4 - - + -
38D PRO 3.2 21.8 - - - -
39D ARG 4.7 1.1 - - - -
41D LEU* 3.8 23.8 - - + -
242D VAL* 4.0 10.5 - - + -
244D PHE* 2.7 51.6 + + + -
247D TYR* 1.3 71.4 - - - +
249D ILE* 1.3 64.7 + - - +
250D ILE 2.6 6.6 + - - -
251D LYS* 2.8 25.0 + - + +
252D ASP* 2.7 29.9 + - - +
504D ANJ 3.7 14.6 - + - +
252E TRP* 3.6 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.4 29.8 - - + -
244D PHE* 3.4 23.8 + - + -
245D TRP* 3.7 42.6 - - + -
246D PRO 3.3 7.6 + - - +
248D PHE* 1.3 76.9 - - - +
250D ILE* 1.3 61.2 + - + +
252D ASP* 3.6 8.1 - - + +
253D VAL* 3.0 34.5 + - + +
504D ANJ 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D TRP* 5.7 2.5 - - + -
246D PRO* 2.9 24.5 + - + +
247D TYR 3.9 2.5 - - - +
248D PHE 2.6 4.8 + - - -
249D ILE* 1.3 77.5 - - + +
251D LYS* 1.3 57.2 + - - +
252D ASP 3.0 0.9 - - - -
253D VAL* 2.9 7.8 + - + +
254D PHE* 2.6 34.0 + - + +
244E LEU* 4.5 12.5 - - + +
247E THR* 3.9 24.9 - - + +
248E ASN* 3.2 34.5 - - + +
251E LEU* 3.7 22.9 - - + -
16F TYR* 6.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU 3.6 22.6 + - - -
42D ASN* 4.4 6.1 - - - +
43D TRP* 3.0 56.0 - - + -
46D ILE* 5.8 1.1 - - - -
247D TYR 3.5 8.9 + - - +
248D PHE* 2.8 41.7 + - + +
250D ILE* 1.3 76.6 - - - +
252D ASP* 1.3 55.2 + - - +
254D PHE* 3.3 7.1 - - - +
255D ALA* 2.7 36.9 + - - +
504D ANJ 4.9 8.7 + - - -
248E ASN* 3.3 16.3 + - - +
252E TRP* 3.6 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 5.6 4.7 - - - -
49D VAL* 2.8 31.6 - - + +
244D PHE* 4.7 2.2 - - - -
248D PHE* 2.7 28.2 + - - +
249D ILE* 3.6 8.7 - - - +
251D LYS* 1.3 76.9 - - - +
253D VAL* 1.3 53.2 + - + +
255D ALA* 3.7 4.1 - - - +
256D LEU* 2.7 39.8 + - - +
504D ANJ 2.5 58.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 3.0 23.8 - - + +
250D ILE* 2.9 9.0 + - + +
252D ASP* 1.3 77.1 - - + +
254D PHE* 1.3 64.6 + - - +
256D LEU* 3.3 14.8 - - + +
257D ALA* 2.9 22.7 + - + +
244E LEU* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TRP* 4.2 30.5 - + - -
250D ILE 2.6 17.7 + - - +
251D LYS* 3.3 9.2 - - - +
253D VAL* 1.3 75.7 - - - +
255D ALA* 1.3 67.2 + - - +
257D ALA* 3.0 14.0 + - - +
258D VAL* 3.2 28.8 + - + +
241E SER* 3.8 28.7 - - - -
244E LEU* 4.0 21.7 - - + +
245E TYR* 3.9 34.8 - + + -
248E ASN* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TRP* 4.6 8.3 - - + -
46D ILE* 3.7 41.5 - - + -
50D VAL* 6.0 0.4 - - + -
251D LYS 2.7 18.2 + - - +
252D ASP 3.7 2.7 - - - +
254D PHE* 1.3 76.5 - - + +
256D LEU* 1.3 56.9 + - - +
258D VAL* 2.7 33.2 + - - +
259D VAL* 2.9 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 3.4 32.1 - - + -
50D VAL* 4.1 22.4 - - + +
53D PHE* 4.1 29.4 - - + -
252D ASP 2.7 19.8 + - - +
253D VAL* 3.3 16.8 - - + +
255D ALA* 1.3 72.6 - - - +
257D ALA* 1.3 56.3 + - - +
259D VAL* 3.6 6.1 - - + +
260D LEU* 2.9 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D VAL 2.9 11.2 + - - +
254D PHE 3.1 11.4 - - - +
255D ALA 2.8 0.8 + - - -
256D LEU* 1.3 74.8 - - - +
258D VAL* 1.3 66.5 + - - +
260D LEU* 3.1 5.4 + - - +
261D LEU* 2.8 23.6 + - - +
237E LEU* 3.9 19.2 - - + +
240E LEU* 4.8 3.1 - - + -
241E SER* 3.8 20.0 - - - +
244E LEU* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D PHE* 3.3 45.3 - - + +
255D ALA* 2.7 14.0 + - - +
257D ALA* 1.3 71.1 - - - +
259D VAL* 1.3 65.2 + - + +
261D LEU* 3.0 28.5 - - + +
262D VAL* 3.2 14.7 + - + +
241E SER* 4.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 4.7 10.1 - - + -
47D TRP* 5.2 6.7 - - + -
50D VAL* 4.0 36.1 - - + -
103D LEU* 4.1 22.4 - - + -
255D ALA 2.9 20.6 + - - +
256D LEU* 3.6 9.6 - - + +
258D VAL* 1.3 77.7 - - + +
260D LEU* 1.3 56.3 + - + +
262D VAL* 2.9 10.9 + - - +
263D PHE* 2.7 31.4 + - - +
503D LOP 4.7 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PHE* 3.4 55.6 - - + -
103D LEU* 4.9 5.4 - - + -
256D LEU* 2.9 32.0 + - + +
257D ALA* 3.1 4.7 + - - +
259D VAL* 1.3 78.4 - - + +
261D LEU* 1.3 57.5 + - - +
263D PHE* 3.8 21.1 - - + -
264D PHE* 2.7 51.7 + - + -
237E LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ALA 2.8 12.0 + - - +
258D VAL* 3.0 20.4 - - + +
260D LEU* 1.3 78.6 - - - +
262D VAL* 1.3 68.9 + - + +
264D PHE* 3.9 2.3 - - - +
265D ALA* 3.0 21.3 + - + +
234E VAL* 3.3 44.2 - - + +
237E LEU* 4.1 13.4 - - + +
238E THR* 3.6 27.8 - - + +
241E SER* 4.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D VAL* 3.4 20.6 - - + +
259D VAL* 2.9 6.9 + - - +
261D LEU* 1.3 78.6 - - + +
263D PHE* 1.3 67.9 + - - +
265D ALA* 3.0 22.8 - - + +
266D ILE* 3.1 19.7 + - + +
431D BGL 4.2 26.7 - - + -
503D LOP 4.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PHE* 5.2 0.4 - + - -
57D LEU* 3.8 19.7 - - + -
96D LEU* 3.4 47.3 - - + -
99D ASN* 3.6 26.9 - - + -
100D GLY* 4.1 2.7 - - - -
103D LEU* 4.1 13.9 - - + -
259D VAL 2.7 17.4 + - - +
260D LEU* 3.5 28.0 - - + +
262D VAL* 1.3 72.0 - - - +
264D PHE* 1.3 71.7 + + - +
266D ILE* 3.0 16.9 + - - +
267D VAL* 2.9 33.3 + - + +
503D LOP 3.6 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PHE* 5.6 3.4 - + - -
92D MET* 5.4 10.1 - - - -
96D LEU* 4.2 32.1 - - + -
260D LEU* 2.7 46.2 + - + +
261D LEU 3.9 2.7 - - - +
263D PHE* 1.3 80.1 - + - +
265D ALA* 1.3 57.2 + - - +
267D VAL* 3.7 7.8 - - + +
268D GLY* 2.5 36.0 + - - -
230E GLY* 5.2 3.1 - - - -
233E ALA* 3.7 33.0 - - + -
234E VAL* 5.1 2.5 - - + +
237E LEU* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D LEU* 3.0 15.9 + - + +
262D VAL* 3.0 18.6 - - - +
264D PHE* 1.3 75.7 - - - +
266D ILE* 1.3 52.4 + - + +
269D PHE* 2.8 54.7 + - + +
270D MET* 4.8 0.6 - - - +
431D BGL 4.9 20.6 - - + +
234E VAL* 4.6 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN* 4.1 15.9 - - - +
262D VAL* 3.1 22.2 - - + +
263D PHE* 3.2 8.5 - - - +
265D ALA* 1.3 72.2 - - - +
267D VAL* 1.3 62.3 + - + +
268D GLY 3.0 1.8 - - - -
270D MET* 2.6 78.8 + - + +
271D PRO 2.9 0.7 - - - -
273D TYR* 5.3 1.3 - - + -
274D LEU* 5.1 7.9 - - + -
431D BGL 4.3 22.0 - - + -
503D LOP 4.3 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D MET* 4.3 12.4 - - - +
95D TYR* 3.9 26.8 - - + +
96D LEU* 4.0 25.1 - - + +
99D ASN* 4.3 8.5 - - + +
263D PHE* 2.9 52.5 + - + +
264D PHE* 3.7 10.3 - - + +
266D ILE* 1.3 75.1 - - + +
268D GLY* 1.3 60.2 + - - +
271D PRO* 3.7 18.8 - - - +
226E ARG* 3.8 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D MET* 5.3 3.6 - - - -
264D PHE* 2.5 21.4 + - - -
265D ALA 3.8 0.4 - - - -
267D VAL* 1.3 75.7 - - - +
269D PHE* 1.3 62.2 + - - +
226E ARG* 2.8 44.2 + - - +
227E LYS* 4.2 7.1 - - - +
230E GLY* 4.4 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ALA* 2.8 35.8 + - + +
268D GLY* 1.3 75.7 - - - +
270D MET* 1.3 58.6 + - - +
271D PRO* 3.6 4.8 - - - +
431D BGL 2.6 60.5 + - + +
16E PRO* 3.6 41.5 - - + -
226E ARG* 3.8 7.8 + - - +
227E LYS* 3.9 24.0 - - + -
230E GLY* 4.2 5.8 - - - -
231E PHE* 3.9 31.9 - + - -
234E VAL* 4.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN* 4.7 0.2 - - - +
266D ILE* 2.6 52.5 + - + +
269D PHE* 1.3 75.8 - - - +
271D PRO* 1.3 64.1 - - - +
272D ASN 3.3 2.5 - - - -
273D TYR* 3.2 53.4 + - + +
431D BGL 3.6 42.6 - - + +
121E LEU* 3.7 29.6 - - + +
----------------------------------------------------------
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