Contacts of the helix formed by residues 286 - 298 (chain D) in PDB entry 4BUR
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 286 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D GLU* 5.3 6.9 - - - +
165D ASP* 3.9 32.4 - - - +
166D PRO* 5.6 1.2 - - - +
170D TYR* 4.0 11.0 - - - +
172D ARG* 4.4 3.4 - - - +
175D LEU* 4.0 7.8 - - - +
284D PHE* 5.4 0.7 - - - -
285D ARG* 1.3 86.0 - - + +
287D ILE* 1.3 67.1 + - + +
288D GLY* 3.2 4.7 - - - +
289D ASP* 2.8 35.0 + - - +
290D PHE 3.2 8.7 + - - -
1612D FAD 5.2 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ASP* 5.5 0.4 - - - +
167D GLU* 3.7 41.5 - - + +
170D TYR* 3.4 36.4 + - + +
175D LEU* 4.2 13.9 - - + +
191D LEU* 3.5 36.1 - - + -
203D ILE* 4.2 16.8 - - + -
204D TYR* 4.5 0.7 - - - +
286D LYS* 1.3 74.4 - - + +
288D GLY* 1.3 66.4 + - - +
290D PHE* 3.2 8.7 + - + +
291D ARG* 3.2 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D LYS* 3.2 3.6 - - - +
287D ILE* 1.3 78.9 - - - +
289D ASP* 1.3 57.4 + - - +
290D PHE 3.0 1.6 - - - -
291D ARG* 2.7 31.4 + - - +
292D SER* 3.0 17.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
282D THR* 4.5 10.3 - - + +
283D LEU 3.7 13.5 + - - +
284D PHE* 3.6 17.9 - - + -
285D ARG* 3.2 18.1 + - - +
286D LYS* 2.8 44.2 + - - +
288D GLY* 1.3 73.8 - - - +
290D PHE* 1.3 57.9 + - - +
292D SER* 3.7 8.2 + - - -
293D LEU* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LEU* 3.7 40.2 - - + -
179D LEU* 3.7 36.1 - - + -
180D TRP* 3.5 39.3 - + - -
187D VAL* 5.0 6.1 - - + -
188D THR* 5.0 13.5 - - + -
191D LEU* 4.7 14.1 - - + -
284D PHE* 3.8 12.5 - + + -
286D LYS 3.2 5.4 + - - +
287D ILE* 3.2 12.2 + - + +
288D GLY 2.9 1.2 + - - -
289D ASP* 1.3 77.2 - - - +
291D ARG* 1.3 68.2 + - + +
293D LEU* 3.5 1.0 + - - +
294D GLU* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D GLU* 4.5 7.9 + - - -
188D THR* 2.7 52.6 + - + +
189D LYS* 4.0 16.6 + - - +
191D LEU* 3.5 27.2 - - - +
287D ILE* 3.2 30.4 + - + +
288D GLY* 2.7 17.7 + - - +
290D PHE* 1.3 81.9 - - + +
292D SER* 1.3 63.8 + - - +
294D GLU* 3.4 5.7 + - - +
295D LYS* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D THR* 5.2 5.4 + - - +
288D GLY 3.0 16.3 + - - -
289D ASP* 3.7 11.4 + - - -
291D ARG* 1.3 76.1 - - - +
293D LEU* 1.3 58.2 + - - +
295D LYS* 3.5 7.5 + - - +
296D ILE* 3.0 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TRP* 3.8 22.7 - - + -
282D THR* 3.9 26.0 - - + +
284D PHE* 3.8 19.7 - - + -
289D ASP 3.4 15.8 + - - +
290D PHE 3.5 4.1 + - - +
291D ARG 3.2 0.4 - - - -
292D SER* 1.3 78.9 + - - +
294D GLU* 1.3 60.0 + - - +
295D LYS 3.1 1.1 - - - -
296D ILE* 3.7 5.1 - - + +
297D SER* 2.8 30.5 + - - +
303D ILE* 5.3 4.0 - - + -
315D LEU* 4.9 5.8 - - + -
319D LEU* 4.5 20.0 - - + -
393D HIS* 4.1 12.6 - - + -
395D VAL* 3.9 24.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
180D TRP* 4.0 23.5 - - + -
187D VAL* 6.1 4.9 - - + -
188D THR* 4.0 20.3 + - + +
290D PHE* 3.0 32.3 + - + +
291D ARG* 3.4 5.6 + - - +
293D LEU* 1.3 76.0 - - - +
295D LYS* 1.3 59.3 + - - +
297D SER* 2.9 23.0 + - - +
298D ARG* 3.3 36.6 + - - +
322D LYS* 2.7 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D ARG 3.2 13.9 + - - +
292D SER* 3.7 10.3 - - - +
293D LEU 3.1 0.4 - - - -
294D GLU* 1.3 74.4 + - - +
296D ILE* 1.3 66.4 + - + +
298D ARG* 3.1 49.1 + - - +
299D GLU* 3.3 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D THR* 5.0 2.2 - - - +
292D SER* 3.0 29.4 + - - +
293D LEU* 3.8 8.3 - - + +
295D LYS* 1.3 74.2 - - + +
297D SER* 1.3 63.7 + - - +
299D GLU* 3.1 26.3 + - - +
300D VAL* 3.1 34.1 + - + +
303D ILE* 5.2 4.7 - - + -
393D HIS* 3.7 51.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TRP* 4.2 4.8 - - - -
293D LEU* 2.8 19.4 + - - -
294D GLU* 2.9 21.3 + - - -
296D ILE* 1.3 73.8 - - - +
298D ARG* 1.3 62.5 + - - +
299D GLU 3.2 3.2 + - - -
300D VAL 3.9 8.7 - - - +
303D ILE* 3.9 17.6 - - - +
319D LEU* 3.8 27.8 - - - -
322D LYS* 4.4 14.4 - - - +
326D LEU* 3.9 14.8 - - - +
328D THR* 4.8 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D THR* 5.7 0.4 + - - -
294D GLU* 3.4 38.8 + - - +
295D LYS* 3.1 49.0 + - - +
297D SER* 1.3 78.7 + - - +
299D GLU* 1.3 60.0 + - - +
322D LYS* 5.3 4.7 - - + +
326D LEU* 4.1 30.1 - - + +
----------------------------------------------------------
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