Contacts of the helix formed by residues 239 - 252 (chain B) in PDB entry 5K7W
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 239 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ARG* 4.4 0.2 - - - +
197B GLU* 4.8 4.8 + - - +
213B TRP* 3.7 18.6 - - + +
238B GLY* 1.3 70.2 - - - -
240B GLY* 1.3 59.4 + - - +
241B LEU 3.1 0.2 - - - -
242B ASP* 3.0 19.9 + - - +
243B LEU* 2.9 46.4 + - + +
276B ASP* 5.0 2.6 + - - -
278B LYS* 4.6 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLU* 4.9 2.4 + - - -
213B TRP* 3.5 25.9 - - - +
235B CYS* 3.5 27.9 + - - +
238B GLY 3.1 2.6 + - - -
239B GLU* 1.3 79.3 - - - +
241B LEU* 1.3 59.4 + - - +
242B ASP 3.1 0.4 - - - -
243B LEU 4.2 1.6 - - - -
244B GLY* 2.7 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.7 8.1 + - - +
451A ARG* 3.5 26.5 - - - +
454A GLU* 3.5 24.7 - - + +
235B CYS* 4.1 7.2 - - + +
236B GLY 3.3 28.9 - - - +
237B SER* 3.8 19.1 - - - +
238B GLY 3.1 5.6 + - - +
240B GLY* 1.3 77.3 - - - +
242B ASP* 1.3 58.8 + - - +
245B ARG* 2.9 37.6 + - - +
258B ASP* 5.6 0.2 - - - +
285B LYS* 5.1 0.4 - - - +
287B HIS* 3.7 39.9 - - + +
289B LEU* 4.2 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 2.8 35.2 + - - +
451A ARG* 2.9 44.5 + - - +
239B GLU* 3.0 12.1 + - - +
241B LEU* 1.3 77.2 - - - +
243B LEU* 1.3 69.7 + - + +
244B GLY 3.3 0.2 - - - -
245B ARG* 3.2 16.5 + - - +
246B VAL* 3.4 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 3.7 40.2 - - + -
217B MET* 4.5 6.3 - - + +
239B GLU* 2.9 44.3 + - + +
242B ASP* 1.3 78.0 - - + +
244B GLY* 1.3 65.9 + - - +
246B VAL* 3.1 18.8 + - + +
247B CYS* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 3.8 19.8 - - - -
233B LEU* 3.8 11.8 - - - +
235B CYS* 4.0 3.4 - - - -
240B GLY 2.7 24.6 + - - -
243B LEU* 1.3 72.5 - - - +
245B ARG* 1.3 55.2 + - - +
247B CYS* 3.2 4.5 + - - +
248B LEU* 3.0 30.8 + - - +
289B LEU* 4.1 6.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
437A MET* 3.6 19.8 - - - +
438A GLU* 2.8 37.9 + - + +
441A ARG* 3.4 41.8 - - - +
454A GLU* 5.1 2.6 + - - -
241B LEU* 2.9 28.0 + - - +
242B ASP 3.2 9.0 + - - +
243B LEU 3.2 0.4 - - - -
244B GLY* 1.3 77.9 - - - +
246B VAL* 1.3 62.0 + - + +
248B LEU* 3.3 9.6 + - - +
249B ARG* 3.1 31.9 + - + +
255B ARG* 3.6 22.8 - - + +
258B ASP* 4.7 9.1 + - - +
289B LEU* 3.8 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B MET* 3.8 23.6 - - + -
242B ASP 3.6 14.4 - - - +
243B LEU* 3.1 20.8 + - + +
245B ARG* 1.3 73.5 - - + +
247B CYS* 1.3 66.2 + - - +
249B ARG* 3.2 39.6 + - - +
250B LYS* 2.9 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 3.8 25.4 - - - -
216B ILE* 4.0 5.2 - - - -
217B MET* 3.9 42.4 - - - -
233B LEU* 4.5 0.9 - - + -
243B LEU 3.0 18.0 + - - -
244B GLY* 3.2 10.1 + - - +
246B VAL* 1.3 76.9 - - - +
248B LEU* 1.3 62.2 + - - +
250B LYS* 3.1 2.8 + - - +
251B TRP* 2.9 51.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.5 29.8 - - + -
233B LEU* 4.5 12.6 - - + -
244B GLY 3.0 20.4 + - - +
245B ARG* 3.5 8.7 - - - +
246B VAL 3.3 0.2 - - - -
247B CYS* 1.3 75.3 - - - +
249B ARG* 1.3 62.9 + - + +
251B TRP* 3.3 18.2 + - + -
252B GLY 3.1 4.9 + - - -
253B TYR* 2.9 39.5 + - + +
255B ARG* 3.9 41.3 - - + +
289B LEU* 4.4 14.4 - - + +
290B MET 4.3 2.2 - - - +
291B GLY* 4.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 3.1 20.0 + - + +
246B VAL* 3.2 43.4 + - - +
248B LEU* 1.3 76.6 - - + +
250B LYS* 1.3 61.1 + - - +
252B GLY* 3.0 13.9 + - - -
253B TYR 3.9 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B MET* 2.9 51.0 + - + +
218B LYS* 3.7 10.8 + - - +
219B LEU 3.1 17.0 + - - -
220B GLU* 4.5 8.1 - - - +
222B ASP* 4.5 8.9 + - - +
246B VAL* 2.9 14.4 + - + +
247B CYS* 3.1 7.8 + - - +
249B ARG* 1.3 77.0 - - - +
251B TRP* 1.3 71.1 + - + +
252B GLY 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.4 21.5 - - + -
216B ILE* 3.4 31.6 - - + -
217B MET* 3.6 7.8 + - - -
219B LEU* 2.8 27.6 + - + -
221B ILE* 3.5 30.5 - - + +
222B ASP* 3.3 20.8 - - - +
231B ILE* 3.8 29.2 - - + -
233B LEU* 4.2 13.7 - - + -
247B CYS* 2.9 45.7 + - + +
248B LEU* 3.3 8.5 + - + -
250B LYS* 1.3 86.4 - - + +
252B GLY* 1.3 58.1 + - - +
253B TYR* 3.6 15.5 - - + -
293B LYS* 2.8 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG 3.0 14.0 + - - -
250B LYS 3.3 1.4 + - - -
251B TRP* 1.3 80.7 - - - +
253B TYR* 1.3 59.0 + - - +
254B ARG* 5.5 2.1 + - - +
292B ILE 4.3 0.3 - - - +
293B LYS* 3.3 30.3 + - - +
----------------------------------------------------------
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