Contacts of the helix formed by residues 279 - 301 (chain D) in PDB entry 4UQJ
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 LYS 279 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 3.4 21.1 + - - +
25D GLU* 5.0 2.0 - - - +
229D ASP* 3.2 16.8 - - + +
278D ILE* 1.3 77.7 - - - +
280D TYR* 1.3 61.5 + - + +
281D THR* 3.8 16.8 - - - +
282D SER* 2.9 5.8 + - - +
283D ALA* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D PRO 5.4 2.0 - - - -
114D ARG* 5.4 4.0 - - + -
141D ARG* 4.9 13.5 - - - -
197D GLU* 6.1 1.4 - - - -
198D ARG* 6.0 7.0 - - + -
224D ASN* 4.7 14.4 - - + +
225D LEU* 3.7 41.1 - - + +
226D GLY* 3.6 18.2 - - - -
229D ASP* 2.9 23.3 + - + +
246D GLN* 5.9 0.2 - - - +
247D ILE* 3.5 25.1 - - + +
248D VAL* 4.2 13.5 - - + -
278D ILE 3.5 1.2 + - - -
279D LYS* 1.3 72.3 - - + +
281D THR* 1.3 80.9 + - + +
283D ALA* 3.7 0.9 - - - +
284D LEU* 3.0 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLU* 2.8 30.4 + - - +
76D PHE* 5.2 7.6 - - + -
99D PRO* 3.9 11.0 - - + +
279D LYS* 3.8 10.7 - - + +
280D TYR* 1.3 111.7 - - + +
282D SER* 1.3 60.0 + - - +
284D LEU* 3.5 8.0 + - - +
285D THR* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 3.3 39.0 + - - +
25D GLU* 3.3 23.2 + - - +
28D ALA* 3.4 8.5 - - - +
278D ILE* 3.6 19.1 - - - -
279D LYS* 2.9 8.7 + - - +
281D THR* 1.3 77.5 + - - +
283D ALA* 1.3 64.5 + - - +
285D THR* 3.1 17.9 + - - -
286D TYR* 3.1 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ILE* 6.0 0.2 - - + -
248D VAL* 3.6 30.5 - - + -
278D ILE* 3.5 17.9 - - + +
279D LYS 2.9 12.5 + - - +
280D TYR 3.7 3.4 - - - +
282D SER* 1.3 75.6 - - - +
284D LEU* 1.3 60.3 + - + +
286D TYR* 3.4 4.5 + - - +
287D ASP* 3.1 32.5 + - - +
341D LEU* 4.1 20.3 - - + +
342D SER* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D PRO* 3.7 28.9 - - + +
113D MET* 3.3 30.3 - - + +
114D ARG* 3.6 32.5 - - + +
115D PRO* 4.8 4.0 - - + -
225D LEU* 5.3 0.2 - - + -
247D ILE* 5.4 3.8 - - + -
280D TYR* 3.0 35.2 + - + +
281D THR* 3.8 0.9 - - - +
282D SER 3.2 0.2 - - - -
283D ALA* 1.3 74.7 - - + +
285D THR* 1.3 55.8 + - - +
287D ASP* 3.2 5.5 + - + +
288D ALA* 2.8 34.2 + - - +
342D SER* 3.6 31.9 - - - +
353D ARG* 4.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D PHE* 4.4 0.7 - - + -
25D GLU* 3.3 27.4 + - - +
28D ALA* 4.6 0.2 - - - -
29D PHE* 3.6 22.0 - - + +
74D PHE* 3.4 29.0 - - + -
76D PHE* 3.7 9.0 - - - -
99D PRO* 3.7 11.2 - - - +
281D THR 3.0 14.6 + - - -
282D SER* 3.1 12.2 + - - -
284D LEU* 1.3 79.4 - - - +
286D TYR* 1.3 61.8 - - - +
288D ALA* 3.1 15.4 + - - +
289D VAL* 3.3 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA* 3.9 18.8 + - + +
31D VAL* 4.2 7.6 - - + -
32D GLY* 3.7 25.4 - - - -
35D GLN* 3.3 27.0 - - + +
36D PHE* 3.5 31.7 - + - -
254D LEU* 5.8 4.2 - - + +
258D PHE* 3.4 37.8 - + + -
282D SER 3.1 8.2 + - - +
283D ALA* 3.6 7.9 - - - +
284D LEU 3.3 0.2 - - - -
285D THR* 1.3 78.5 - - - +
287D ASP* 1.3 78.5 + - - +
288D ALA 3.3 0.5 + - - -
289D VAL* 3.3 15.8 + - - +
290D GLN* 3.5 8.2 + - - -
340D GLY* 6.0 0.4 - - - -
341D LEU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D MET* 4.3 4.0 - - - -
283D ALA 3.1 19.2 + - - +
284D LEU* 3.7 7.4 - - + +
286D TYR* 1.3 87.5 - - - +
288D ALA* 1.3 64.1 + - - +
290D GLN* 3.4 9.2 + - - +
291D VAL* 3.1 28.4 + - - +
340D GLY* 3.5 11.1 - - - -
341D LEU* 3.0 20.6 + - - +
342D SER* 3.0 38.7 + - - +
345D ILE* 3.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D PHE* 3.4 32.8 - - + -
97D ILE* 3.9 5.3 - - + +
113D MET* 3.7 19.5 - - + -
284D LEU 2.8 13.6 + - - +
285D THR 3.1 11.0 + - - +
287D ASP* 1.3 75.3 - - - +
289D VAL* 1.3 66.0 + - + +
291D VAL* 3.1 4.4 + - - +
292D MET* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 3.8 43.7 - - + +
32D GLY* 3.4 33.4 - - - +
33D MET* 3.9 14.8 - - - +
36D PHE* 4.1 5.6 - - + -
43D LEU* 4.9 4.8 - - + +
285D THR 3.3 13.4 + - - +
286D TYR 3.6 7.4 - - - +
287D ASP 3.3 0.2 - - - -
288D ALA* 1.3 77.1 - - + +
290D GLN* 1.3 56.8 + - - +
292D MET* 3.3 11.0 + - - +
293D THR* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D PHE* 3.5 49.5 - - + -
286D TYR* 3.5 5.4 + - - +
287D ASP* 3.4 15.6 + - - +
288D ALA 3.2 0.4 - - - -
289D VAL* 1.3 79.0 - - - +
291D VAL* 1.3 57.5 + - - +
293D THR* 3.4 2.3 + - - -
294D GLU* 3.0 28.5 + - + +
338D VAL* 3.3 36.3 - - + +
339D GLU 3.3 26.4 + - - +
340D GLY* 4.0 9.5 - - - -
345D ILE* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 5.8 2.0 - - + -
111D ILE* 5.0 3.4 - - + -
113D MET* 4.3 10.3 - - + -
287D ASP 3.1 17.4 + - - +
288D ALA* 3.1 8.2 + - - +
290D GLN* 1.3 77.8 - - - +
292D MET* 1.3 58.7 + - + +
295D ALA* 3.0 27.2 + - - +
333D LEU* 4.1 18.4 - - + +
336D VAL* 3.5 30.1 - - + +
338D VAL* 4.9 2.7 - - + -
345D ILE* 4.2 28.7 - - + -
347D PHE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.7 43.7 - - + -
29D PHE* 5.4 3.8 - - - -
43D LEU* 4.5 12.3 - - + +
72D ALA* 4.1 19.7 - - + -
74D PHE* 4.1 26.2 - - + -
97D ILE* 4.3 18.2 - - + -
288D ALA 3.0 20.8 + - - +
289D VAL* 3.7 8.5 - - - +
291D VAL* 1.3 74.4 - - + +
293D THR* 1.3 63.7 + - - +
295D ALA* 3.5 1.4 + - - +
296D PHE* 3.1 24.8 + - - +
333D LEU* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D PHE* 3.7 38.0 + - + +
38D THR* 5.4 4.3 - - + -
41D PHE* 3.5 24.7 - - + -
43D LEU* 4.2 14.0 - - - +
289D VAL* 3.0 19.8 + - - +
290D GLN 3.7 5.4 - - - -
292D MET* 1.3 75.3 - - - +
294D GLU* 1.3 62.9 + - - +
296D PHE 3.3 0.9 + - - -
297D ARG* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D GLN* 3.0 17.7 + - + +
293D THR* 1.3 78.0 - - - +
295D ALA* 1.3 56.4 + - - +
297D ARG* 3.5 7.7 + - - +
298D ASN* 3.1 59.6 + - - +
336D VAL* 3.8 26.7 - - + -
337D GLN 5.0 1.1 - - - +
338D VAL* 3.9 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D VAL 3.0 19.4 + - - +
292D MET 3.7 2.9 - - - +
294D GLU* 1.3 74.4 - - - +
296D PHE* 1.3 64.4 + - - +
297D ARG 3.1 1.9 + - - -
298D ASN* 3.3 11.2 + - - +
299D LEU* 3.4 10.4 + - - +
329D ILE* 6.4 0.2 - - + -
332D ALA* 3.7 19.2 - - + +
333D LEU* 3.4 37.5 - - + +
336D VAL* 3.6 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 3.6 33.6 - - + +
41D PHE* 4.1 11.9 - - + -
43D LEU* 5.6 2.0 - - + -
292D MET 3.1 15.3 + - - +
293D THR 4.0 2.9 - - - +
295D ALA* 1.3 78.5 - - - +
297D ARG* 1.3 60.1 + - - +
298D ASN 3.5 0.2 - - - -
299D LEU* 3.6 14.4 + - - +
300D ARG* 3.5 18.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
41D PHE* 3.7 21.7 - - + -
293D THR* 3.0 19.5 + - + +
294D GLU* 3.7 13.2 - - - +
296D PHE* 1.3 75.4 - - - +
298D ASN* 1.3 63.3 + - - +
299D LEU 3.1 4.7 - - - -
300D ARG* 3.3 5.2 + - - +
301D LYS* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D GLU* 3.1 47.5 + - - +
295D ALA* 3.3 6.9 + - - +
297D ARG* 1.3 77.8 - - - +
299D LEU* 1.3 63.6 + - + +
301D LYS* 4.2 7.4 - - - +
302D GLN* 3.0 25.5 + - - +
332D ALA* 5.1 5.8 + - + +
335D GLN* 5.2 5.7 + - - +
336D VAL* 4.8 12.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
295D ALA 3.4 8.0 + - - +
296D PHE* 3.8 15.0 - - + +
297D ARG 3.1 0.4 - - - -
298D ASN* 1.3 85.3 - - + +
300D ARG* 1.3 61.2 + - - +
301D LYS 3.4 0.4 - - - -
302D GLN* 3.5 2.4 + - - -
303D ARG 3.4 2.8 + - - -
304D ILE* 3.1 60.5 + - + +
306D ILE* 3.9 28.0 - - + -
328D GLU* 4.3 7.4 - - - +
329D ILE* 4.2 17.0 - - + +
332D ALA* 3.3 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 5.8 3.6 - - - +
40D GLU* 6.5 0.9 - - + -
41D PHE* 5.4 8.5 - - + -
296D PHE 3.5 10.1 + - - +
297D ARG* 3.3 10.8 + - - +
299D LEU* 1.3 78.9 - - - +
301D LYS* 1.3 61.2 + - - +
302D GLN 3.1 1.6 - - - -
303D ARG* 3.2 13.0 + - - +
304D ILE 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ARG 3.2 13.3 + - - +
298D ASN* 4.3 6.1 - - - +
300D ARG* 1.3 78.6 - - - +
302D GLN* 1.3 57.6 + - - +
303D ARG* 3.3 2.2 + - - +
----------------------------------------------------------
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