Contacts of the helix formed by residues 288 - 308 (chain D) in PDB entry 6JBQ
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 288 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA 4.2 1.1 - - - +
287D ALA* 1.3 93.4 - - + +
289D ASP* 1.3 65.3 + - - +
290D ILE* 3.4 9.3 + - + +
291D ILE* 3.5 36.9 + - + +
292D VAL* 3.6 11.1 + - - +
19F GLN* 4.1 27.4 - - + +
20F LYS* 5.9 1.1 - - + -
22F PHE* 5.0 11.0 - - + -
23F ASN* 5.8 5.8 - - + +
58F TYR* 4.2 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D TYR* 5.2 4.3 + - - -
180D MET* 5.1 9.9 - - - +
288D PRO* 1.3 76.1 - - - +
290D ILE* 1.3 59.0 + - - +
292D VAL* 3.4 13.0 - - - +
293D ARG* 2.9 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO* 3.4 4.5 - - + -
289D ASP* 1.3 76.3 + - - +
291D ILE* 1.3 68.2 + - + +
293D ARG* 3.5 39.0 - - - +
294D ASN* 2.9 30.8 + - + +
23F ASN* 4.0 19.7 - - + -
26F VAL* 3.8 24.9 - - + -
27F VAL* 3.7 28.3 - - + -
30F GLN* 6.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D LEU* 3.9 25.4 - - + -
287D ALA* 4.7 4.7 - - + -
288D PRO* 3.5 35.1 + - + +
289D ASP 3.3 0.4 - - - -
290D ILE* 1.3 84.8 - - + +
292D VAL* 1.3 58.2 + - - +
294D ASN* 3.3 2.6 + - - -
295D GLU 2.9 10.9 + - - -
22F PHE* 4.5 22.7 - - + -
26F VAL* 5.5 7.6 - - + -
51F GLN* 2.6 45.3 + - + +
54F PHE* 5.2 12.3 - - + +
55F ILE* 4.7 6.1 - - + -
58F TYR* 5.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 4.9 2.9 - - + +
282D LEU* 3.9 19.3 - - + +
283D LEU* 3.9 30.5 - - + -
287D ALA* 3.9 28.3 - - + +
288D PRO 3.6 7.1 + - - +
289D ASP* 3.4 21.8 - - - +
291D ILE* 1.3 73.7 - - - +
293D ARG* 1.3 61.9 + - - +
295D GLU* 3.6 8.0 - - + +
296D LYS* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D PHE* 3.3 49.7 + - + +
142D GLU* 5.9 2.6 + - - -
144D TYR* 4.0 11.5 + - - -
162D GLU* 3.7 25.5 + - - -
180D MET* 3.7 29.6 - - + -
289D ASP* 2.9 28.4 + - - +
290D ILE* 3.5 37.4 - - - +
292D VAL* 1.3 77.9 - - - +
294D ASN* 1.3 57.3 + - - +
296D LYS* 3.3 6.9 + - - -
297D ARG* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 2.9 18.7 + - + +
291D ILE* 3.8 4.5 - - - +
293D ARG* 1.3 73.9 - - - +
295D GLU* 1.3 61.3 + - - +
297D ARG* 2.9 41.2 + - - +
298D MET* 2.9 49.6 + - + +
30F GLN* 3.5 25.1 + - - +
51F GLN* 4.3 3.9 - - - +
54F PHE* 6.4 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ARG* 3.9 32.2 - - - +
278D ARG* 3.3 30.5 + - - +
279D LEU* 3.7 30.1 - - + -
282D LEU* 3.7 6.9 - - + +
291D ILE 2.9 10.9 + - - +
292D VAL* 3.6 10.3 - - - +
293D ARG 3.2 0.4 - - - -
294D ASN* 1.3 74.8 - - - +
296D LYS* 1.3 58.7 + - - +
298D MET* 3.3 7.3 + - - +
299D LEU* 2.9 26.7 + - - +
51F GLN* 2.9 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D SER* 4.1 26.2 - - - +
141D PHE* 3.6 25.8 - - + -
180D MET* 5.5 10.8 + - + +
183D GLU* 3.9 23.3 + - - -
279D LEU* 3.7 24.5 - - + -
283D LEU* 5.4 12.0 - - - +
292D VAL* 2.9 31.5 + - + +
293D ARG* 3.3 4.9 + - - +
295D GLU* 1.3 75.7 - - - +
297D ARG* 1.3 56.6 + - - +
299D LEU* 3.4 3.6 + - - +
300D GLN* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU 5.7 0.2 - - - -
140D TYR* 4.1 35.3 - - + +
141D PHE* 3.3 17.8 - - + -
293D ARG 2.9 14.9 + - - +
294D ASN* 2.9 40.6 + - - +
296D LYS* 1.3 73.9 - - - +
298D MET* 1.3 66.4 + - - +
300D GLN* 3.4 4.8 + - - +
301D GLU* 2.9 56.3 + - - +
47F PRO* 5.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ARG* 2.4 45.0 + - - +
294D ASN* 2.9 48.8 + - - +
295D GLU* 3.3 9.6 + - - +
297D ARG* 1.3 80.8 - - - +
299D LEU* 1.3 57.7 + - - +
301D GLU* 3.4 5.7 + - - +
302D ALA 2.9 13.3 + - - -
47F PRO* 3.6 47.3 - - + +
48F ASP* 4.6 5.8 - - - +
50F VAL* 6.5 0.9 - - + -
51F GLN* 3.3 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 4.8 8.3 - - + -
109D SER* 4.6 16.2 - - - +
110D PRO 5.7 0.2 - - - +
111D THR* 3.7 28.5 - - + -
272D VAL* 5.1 5.2 - - + +
275D ARG* 4.0 14.3 - - + +
276D ASN* 3.8 41.1 - - + +
279D LEU* 3.7 24.0 - - + -
295D GLU* 2.9 16.1 + - - +
296D LYS* 3.8 4.3 - - - +
297D ARG 3.3 0.2 - - - -
298D MET* 1.3 76.5 - - - +
300D GLN* 1.3 58.9 + - + +
302D ALA* 3.4 3.7 + - + +
303D VAL* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PRO 4.3 4.3 - - - +
111D THR* 3.6 12.7 - - - +
112D ALA* 3.0 49.0 + - - +
114D ILE* 6.0 0.8 - - - +
117D LEU* 5.9 2.6 - - - +
139D LEU* 4.8 23.4 - - + +
140D TYR* 4.6 19.3 - - + -
141D PHE* 5.8 2.0 - - + -
182D ALA* 4.8 1.7 - - - +
296D LYS 2.9 18.3 + - - +
297D ARG* 3.8 6.3 - - - +
299D LEU* 1.3 75.6 - - + +
301D GLU* 1.3 59.4 + - - +
303D VAL* 3.3 5.7 + - - +
304D ASP* 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 5.0 17.4 - - + +
275D ARG* 4.3 5.6 + - - +
297D ARG* 2.9 49.5 + - + +
298D MET* 3.6 8.1 - - - +
299D LEU 3.3 0.2 - - - -
300D GLN* 1.3 76.5 - - - +
302D ALA* 1.3 56.0 + - - +
304D ASP* 2.8 20.2 - - - +
305D ALA* 2.9 20.8 + - - +
316D ILE* 5.2 9.8 - - - +
47F PRO* 6.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 5.6 1.6 - - - +
271D ARG* 5.1 9.0 - - + +
272D VAL* 3.8 25.3 - - + +
275D ARG* 3.4 31.6 - - - +
298D MET 2.9 9.3 + - - +
299D LEU* 3.7 5.4 - - + +
301D GLU* 1.3 76.1 - - - +
303D VAL* 1.3 57.9 + - - +
305D ALA* 3.8 4.9 - - - +
306D LEU* 2.9 30.7 + - - +
316D ILE* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 4.9 7.4 - - + -
111D THR* 3.5 43.1 - - + +
112D ALA 4.4 7.2 - - - +
239D LEU* 5.1 3.4 - - + -
242D LEU* 5.3 10.3 - - + -
272D VAL* 4.8 15.3 - - + -
299D LEU* 2.9 26.8 + - + +
300D GLN* 3.8 5.4 - - - +
302D ALA* 1.3 77.9 - - - +
304D ASP* 1.3 60.1 + - - +
306D LEU* 3.1 7.1 + - - +
307D LEU* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ALA 5.1 0.4 - - - +
114D ILE* 3.5 43.5 - - + +
140D TYR* 3.4 24.0 + - - -
300D GLN* 2.9 30.6 + - - +
301D GLU* 2.8 33.4 - - - +
303D VAL* 1.3 78.1 - - + +
305D ALA* 1.3 59.1 + - - +
307D LEU* 4.1 4.7 - - + +
308D ASP 2.9 23.7 + - - +
312D ARG* 4.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 4.3 8.8 - - + +
301D GLU 2.9 20.2 + - - +
302D ALA* 3.9 3.6 - - - +
304D ASP* 1.3 78.4 - - - +
306D LEU* 1.3 63.4 + - - +
307D LEU 3.4 0.2 - - - -
308D ASP 4.2 3.1 - - - -
309D ASN* 3.4 30.8 + - - +
316D ILE* 3.8 36.3 - - + -
326D SER* 3.9 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LEU* 4.4 16.4 - - + -
243D PRO 5.8 0.2 - - - +
265D LEU* 4.9 6.2 - - + +
268D LEU* 3.7 43.7 - - + +
269D TYR* 3.6 44.6 - - + +
272D VAL* 3.9 10.3 - - + -
302D ALA 2.9 18.1 + - - +
303D VAL* 3.6 6.1 - - - +
305D ALA* 1.3 77.3 - - - +
307D LEU* 1.3 70.4 + - + +
326D SER* 2.8 16.8 + - - -
327D LEU* 3.8 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333C LEU* 3.8 31.6 - - + +
1334C GLY 5.6 0.2 - - - +
113D HIS* 3.6 44.0 - - + +
114D ILE* 3.9 20.6 - - + +
115D TRP* 4.4 3.1 + - + -
239D LEU* 4.1 16.2 - - + -
242D LEU* 4.7 8.5 - - + -
303D VAL* 2.9 31.6 + - + +
304D ASP* 4.5 1.3 - - - -
306D LEU* 1.3 90.8 - - + +
308D ASP* 1.3 60.7 + - - +
326D SER* 2.9 8.8 + - - -
327D LEU* 4.3 3.2 + - + +
328D ALA* 3.5 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ILE* 3.8 13.1 - - + +
115D TRP* 3.6 16.1 + - - +
304D ASP 2.9 19.5 + - - +
305D ALA 3.9 0.2 - - - -
307D LEU* 1.3 82.0 - - - +
309D ASN* 1.3 70.9 + - - +
310D GLY 3.6 2.1 + - - -
311D ARG* 2.6 55.5 + - - +
312D ARG* 4.9 1.6 + - - +
326D SER* 3.5 2.7 - - - -
328D ALA* 3.4 18.3 - - - +
329D ASP* 4.1 6.6 - - - +
332D LYS* 4.6 4.8 + - - -
1329D THR* 4.8 0.2 - - - +
----------------------------------------------------------
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