Contacts of the helix formed by residues 242 - 258 (chain B) in PDB entry 5DQZ
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 GLU 242 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 5.8 4.0 - - - +
240B PRO* 4.4 3.2 - - - +
241B GLY* 1.3 77.8 - - - +
243B PRO* 1.3 67.6 - - + +
244B ASP* 3.3 20.5 + - + +
245B ARG* 3.8 29.8 + - + +
246B GLU* 4.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 4.1 22.4 - - + -
178B GLN* 4.2 20.2 - - + +
179B CYS* 3.6 27.8 - - - +
235B ILE* 4.8 0.2 - - + -
240B PRO* 4.0 19.9 - - + +
241B GLY 3.4 10.5 - - - +
242B GLU* 1.3 85.9 - - + +
244B ASP* 1.3 71.6 + - - +
246B GLU* 2.9 8.4 + - + +
247B VAL* 2.9 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 5.6 2.8 - - - +
81B ALA* 3.9 36.6 + - - +
82B GLY* 4.7 2.5 - - - +
178B GLN* 4.9 6.9 - - - +
182B ALA* 4.1 11.5 - - + +
242B GLU* 3.3 21.0 + - + +
243B PRO* 1.3 81.1 - - - +
245B ARG* 1.3 57.9 + - - +
247B VAL* 3.4 8.6 + - - +
248B ARG* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLU* 3.8 30.5 + - + +
243B PRO 3.3 1.0 - - - -
244B ASP* 1.3 77.4 - - - +
246B GLU* 1.3 64.4 + - + +
248B ARG* 3.1 21.7 + - - +
249B LEU* 3.0 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 3.2 24.3 - - + +
238B ARG* 3.5 30.1 + - - +
240B PRO* 3.6 31.3 - - + +
242B GLU 4.2 9.2 - - - +
243B PRO 2.9 9.1 + - - +
245B ARG* 1.3 80.5 - - + +
247B VAL* 1.3 56.8 + - - +
249B LEU* 3.5 7.8 + - - +
250B ALA* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B CYS* 4.2 22.9 - - + -
182B ALA* 4.0 7.4 - - + -
183B ALA* 3.5 43.3 - - + +
186B CYS* 5.1 1.8 - - - -
232B ALA* 5.4 3.1 - - - -
235B ILE* 3.4 26.0 - - + -
243B PRO* 2.9 22.5 + - + +
244B ASP* 3.6 10.8 - - - +
246B GLU* 1.3 75.1 - - - +
248B ARG* 1.3 59.8 + - + +
250B ALA* 3.7 0.7 - - + +
251B CYS* 2.9 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 3.8 7.2 - - + +
19B PHE* 3.3 58.5 - - + +
21B GLN* 6.0 0.6 - - - +
55B GLU* 2.9 43.6 + - - +
78B VAL* 5.8 0.8 - - - +
82B GLY* 5.6 5.7 - - - -
182B ALA* 6.5 0.4 - - + -
186B CYS* 4.7 4.5 - - - -
244B ASP* 2.9 43.9 + - - +
245B ARG* 3.1 18.8 + - + +
247B VAL* 1.3 77.5 - - + +
249B LEU* 1.3 64.7 + - - +
251B CYS* 3.3 2.2 + - - +
252B ARG* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 3.0 16.7 + - + +
246B GLU* 3.9 7.2 - - - +
248B ARG* 1.3 75.6 - - - +
250B ALA* 1.3 64.0 + - - +
252B ARG* 3.2 33.2 + - - +
253B ASP* 3.0 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS* 3.4 32.9 - - + +
234B GLU* 6.4 0.7 - - - -
235B ILE* 3.5 16.8 - - + -
238B ARG* 5.2 4.5 - - - +
246B GLU 2.9 18.6 + - - +
247B VAL* 3.7 2.5 - - - +
248B ARG 3.3 0.2 - - - -
249B LEU* 1.3 77.8 - - - +
251B CYS* 1.3 57.9 + - - +
253B ASP* 3.3 9.2 + - - +
254B ILE* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 3.8 15.3 - - + -
183B ALA* 3.8 41.3 - - - -
186B CYS* 4.3 3.4 - - + -
228B VAL* 4.2 15.5 - - - -
231B LYS* 5.5 2.9 - - - -
247B VAL* 2.9 25.8 + - - +
248B ARG 3.7 3.6 - - - +
250B ALA* 1.3 74.4 - - - +
252B ARG* 1.3 61.6 + - - +
254B ILE* 3.1 6.6 - - - +
255B PHE* 2.9 44.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 5.0 7.4 - - - +
16B SER* 3.9 18.4 + - - +
17B MET* 3.4 39.8 + - + +
18B ILE* 6.3 0.2 - - - +
19B PHE* 6.0 3.0 - - - -
248B ARG* 2.9 20.1 + - - +
249B LEU* 3.6 43.3 - - - +
251B CYS* 1.3 76.9 - - - +
253B ASP* 1.3 59.4 + - - +
255B PHE* 3.6 2.4 - - - +
256B ARG* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS* 5.1 7.4 - - - +
249B LEU* 3.0 37.2 + - - +
250B ALA* 3.6 9.8 - - - +
252B ARG* 1.3 77.8 - - - +
254B ILE* 1.3 58.0 + - - +
256B ARG* 3.2 12.2 + - - +
257B SER* 2.9 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASP 5.0 4.5 - - - +
227B THR* 3.5 49.8 - - + +
228B VAL* 4.8 2.9 - - + -
231B LYS* 4.4 26.8 - - + +
250B ALA 2.9 16.5 + - - +
251B CYS* 3.1 19.7 - - + +
253B ASP* 1.3 76.7 - - - +
255B PHE* 1.3 66.1 + - + +
257B SER* 3.2 13.9 + - - +
258B SER* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 4.1 27.4 - - - +
17B MET* 4.2 18.2 - - + -
186B CYS* 4.3 3.8 - - + -
187B LEU* 3.9 29.2 - - + -
190B VAL* 4.0 19.5 - - + -
227B THR* 3.7 22.2 - - + -
228B VAL* 3.7 21.5 - - + -
251B CYS* 2.9 29.2 + - + +
252B ARG* 3.6 4.7 - - - +
254B ILE* 1.3 77.1 - - - +
256B ARG* 1.3 61.5 + - - +
259B LYS* 3.2 2.8 + - - -
260B THR* 3.0 53.6 + - + +
261B LEU* 4.6 5.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG 2.9 17.2 + - - +
253B ASP* 3.7 11.4 - - - +
255B PHE* 1.3 76.3 - - - +
257B SER* 1.3 66.6 + - - +
259B LYS* 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASP 2.9 15.6 + - - -
254B ILE* 3.2 24.4 + - - +
256B ARG* 1.3 81.5 - - - +
258B SER* 1.3 62.0 + - - +
259B LYS* 3.3 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASP 6.1 0.9 - - - -
227B THR* 4.5 10.2 + - - +
254B ILE* 2.8 26.3 + - - +
257B SER* 1.3 80.7 + - - +
259B LYS* 1.3 66.9 + - - +
260B THR* 3.2 14.4 + - - -
263B LYS* 3.1 28.3 + - - +
----------------------------------------------------------
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