Contacts of the helix formed by residues 233 - 258 (chain B) in PDB entry 3RK6
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 MET 233 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 3.5 42.2 - - - +
231B ASN* 2.7 18.0 + - - +
232B PRO* 1.3 76.9 - - + +
234B ASP* 1.3 66.8 + - - +
235B ASP* 3.1 11.5 + - - +
236B ASN* 3.1 4.5 + - + +
237B LEU* 2.9 22.4 + - - +
279B CYS* 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO 4.1 0.4 + - - -
233B MET* 1.3 74.2 - - - +
235B ASP* 1.3 58.5 + - + +
237B LEU* 3.2 4.5 + - - +
238B ILE* 2.8 40.1 + - + +
279B CYS* 3.0 13.4 - - - +
280B SER* 2.5 51.2 + - - -
283B VAL* 3.9 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 4.6 9.8 - - - +
185B ARG* 3.1 47.7 + - - +
186B LYS* 4.8 3.3 + - + +
189B HIS* 3.3 27.7 + - + +
233B MET* 3.8 8.7 - - - +
234B ASP* 1.3 76.3 - - - +
236B ASN* 1.3 68.4 + - - +
238B ILE* 3.5 7.4 + - - +
239B CYS* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ALA* 3.0 26.7 + - - +
185B ARG* 3.6 21.9 - - - +
188B PHE* 4.8 0.6 - - - -
189B HIS* 2.6 36.2 + - - -
228B LEU* 3.6 31.2 - - + +
231B ASN* 2.9 32.2 - - - +
233B MET* 3.1 3.9 + - - +
235B ASP* 1.3 82.7 + - - +
237B LEU* 1.3 59.0 + - + +
239B CYS* 3.3 4.2 + - - +
240B ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU 4.4 1.6 - - - +
229B PHE* 3.7 34.3 - - + -
232B PRO* 3.4 35.4 - - + +
233B MET 2.9 15.2 + - - +
234B ASP 3.7 0.4 - - - +
236B ASN* 1.3 75.9 - - - +
238B ILE* 1.3 59.1 + - - +
240B ALA* 3.2 5.0 + - - +
241B VAL* 2.9 32.9 + - - +
273B VAL* 3.6 22.7 - - + -
279B CYS* 3.5 31.4 - - + -
283B VAL* 3.5 18.6 - - + -
287B LEU* 4.2 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ASP* 2.8 31.3 + - + +
235B ASP* 4.0 7.0 - - - +
237B LEU* 1.3 71.9 - - - +
239B CYS* 1.3 63.2 + - - +
241B VAL* 3.3 8.2 + - + +
242B LYS* 2.9 49.9 + - + +
283B VAL* 3.8 26.9 - - + -
286B MET* 4.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B HIS* 3.5 48.5 - - + -
192B VAL* 3.9 14.8 - - - -
193B LEU* 4.3 8.4 - - + +
228B LEU* 3.8 15.7 - - + -
235B ASP 3.0 15.8 + - - +
236B ASN 3.3 9.6 - - - +
237B LEU 3.2 0.2 - - - -
238B ILE* 1.3 77.5 - - - +
240B ALA* 1.3 61.7 + - - +
242B LYS* 3.3 11.1 + - - +
243B LEU* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.7 17.0 - - + -
228B LEU* 3.8 17.8 - - + +
229B PHE* 3.6 32.1 - - + -
236B ASN 2.9 14.2 + - - +
237B LEU 3.2 7.2 + - - +
239B CYS* 1.3 76.8 - - - +
241B VAL* 1.3 61.3 + - - +
243B LEU* 3.3 2.1 + - - +
244B LEU* 2.9 31.1 + - - +
287B LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 2.9 23.6 + - + +
238B ILE* 3.6 9.6 - - + +
240B ALA* 1.3 71.7 - - - +
242B LYS* 1.3 61.3 + - + +
244B LEU* 3.4 1.4 + - - +
245B LYS* 2.9 54.8 + - + +
283B VAL* 5.0 0.7 - - + +
286B MET* 4.1 36.1 - - + +
287B LEU* 3.8 24.9 - - + +
290B LEU* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.6 42.8 + - + +
93A GLN* 4.5 2.0 + - - +
193B LEU* 3.9 28.8 - - + +
238B ILE* 2.9 41.3 + - + +
239B CYS* 3.3 6.9 + - - +
241B VAL* 1.3 80.3 - - + +
243B LEU* 1.3 56.6 + - - +
245B LYS* 3.5 8.6 + - + +
246B LEU* 3.0 29.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
192B VAL* 3.6 28.5 - - + +
193B LEU* 3.9 13.5 - - + -
196B GLY* 3.7 30.5 - - - -
221B LEU* 4.2 23.3 - - + +
224B LEU* 5.1 0.2 - - + -
225B LEU* 3.8 34.8 - - + +
228B LEU* 5.0 1.8 - - + -
239B CYS 3.0 16.8 + - - +
240B ALA* 3.7 3.8 - - - +
242B LYS* 1.3 76.7 - - - +
244B LEU* 1.3 59.3 + - - +
246B LEU* 3.3 4.7 + - + +
247B THR* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.8 27.1 - - + -
229B PHE* 4.1 13.5 - - + -
240B ALA 2.9 20.1 + - - +
241B VAL 3.9 2.5 - - - +
243B LEU* 1.3 75.8 - - - +
245B LYS* 1.3 59.2 + - - +
247B THR* 4.4 0.2 - - - -
248B GLY* 2.6 44.7 + - - +
249B SER 4.5 0.2 + - - -
251B LEU* 4.9 7.6 - - + -
255B TRP* 5.8 1.1 - - + -
263B MET* 4.7 15.5 - - + -
266B ILE* 4.2 11.2 - - + -
270B ILE* 4.0 28.0 - - + -
290B LEU* 4.0 23.3 - - + -
294B ARG* 4.5 10.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A HIS* 5.4 9.6 + - + +
92A GLU* 4.5 18.2 + - - +
93A GLN* 3.4 20.2 + - - +
241B VAL* 2.9 39.6 + - + +
242B LYS* 3.7 5.6 - - - +
244B LEU* 1.3 76.1 - - - +
246B LEU* 1.3 63.6 + - - +
248B GLY 4.4 0.9 + - - -
249B SER 5.5 1.0 + - - -
286B MET* 5.9 4.8 - - - +
290B LEU* 4.3 17.7 - - + +
293B LEU* 6.5 0.4 - - + -
294B ARG* 5.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU 5.6 0.7 - - - +
93A GLN* 3.3 33.8 - - + +
193B LEU* 4.2 12.8 - - + +
196B GLY* 3.8 31.9 - - - -
197B GLU* 3.5 33.7 - - + +
200B LEU* 3.3 40.2 - - + +
242B LYS 3.0 17.7 + - - +
243B LEU* 3.5 6.5 - - + +
245B LYS* 1.3 80.1 - - - +
247B THR* 1.3 62.0 + - + +
250B VAL* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLY* 3.6 34.5 - - - +
199B TYR* 4.2 5.8 - - + -
200B LEU* 4.0 12.1 - - + -
221B LEU* 4.1 8.0 - - + +
243B LEU* 2.8 34.1 + - + +
244B LEU* 4.4 0.2 - - - -
246B LEU* 1.3 87.1 - - + +
248B GLY* 1.3 62.0 + - - +
249B SER 3.3 2.5 - - - -
250B VAL* 3.3 5.8 + - - +
251B LEU* 2.8 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 2.6 42.2 + - - -
245B LYS 4.4 0.4 + - - -
246B LEU 3.7 1.0 - - - -
247B THR* 1.3 72.7 + - - +
249B SER* 1.3 58.2 + - - +
251B LEU* 3.8 4.1 - - - +
252B GLU* 2.8 31.5 + - - +
263B MET* 5.1 1.9 - - - +
294B ARG* 3.6 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS 5.5 1.0 + - - -
247B THR 3.3 0.4 - - - -
248B GLY* 1.3 75.5 - - - +
250B VAL* 1.3 68.6 + - - +
252B GLU* 3.4 4.4 + - - +
253B ASP* 3.0 32.5 + - - +
294B ARG* 3.5 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.6 26.9 - - + +
200B LEU* 3.7 22.4 - - + -
213B ARG* 3.5 36.6 - - - +
246B LEU 5.6 0.7 - - - +
247B THR* 3.3 8.3 + - - +
249B SER* 1.3 81.3 + - - +
251B LEU* 1.3 61.6 + - - +
253B ASP* 3.4 7.4 + - - +
254B ALA* 3.0 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.6 29.4 - - + +
218B GLN* 3.8 27.4 - - + +
221B LEU* 4.3 17.7 - - + -
225B LEU* 4.8 11.9 - - + -
244B LEU* 4.9 2.7 - - + -
247B THR* 2.8 40.3 + - - +
248B GLY* 3.8 6.5 - - - +
250B VAL* 1.3 69.7 - - - +
252B GLU* 1.3 62.2 + - - +
254B ALA* 3.1 2.8 + - - +
255B TRP* 2.8 70.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY 2.8 21.9 + - - +
249B SER* 3.6 6.4 - - - +
251B LEU* 1.3 73.9 - - - +
253B ASP* 1.3 62.8 + - - +
255B TRP* 3.5 13.0 + - - +
256B LYS* 3.0 35.4 + - + +
263B MET* 3.9 15.4 - - + +
293B LEU 5.0 1.7 - - - +
294B ARG* 3.2 56.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
249B SER* 3.0 23.6 + - - +
250B VAL* 3.8 6.6 - - - +
252B GLU* 1.3 82.2 - - - +
254B ALA* 1.3 57.6 + - - +
256B LYS* 3.9 7.3 - - - +
257B GLU* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.9 13.5 - - - +
218B GLN* 3.6 23.1 - - - +
250B VAL* 3.0 17.9 + - + +
251B LEU* 3.6 4.0 - - - +
253B ASP* 1.3 76.6 - - - +
255B TRP* 1.3 63.2 + - - +
257B GLU* 3.8 6.3 - - - +
258B LYS* 3.3 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLN* 3.9 28.4 + - + +
222B ARG* 4.1 23.2 - - + +
225B LEU* 5.1 4.3 - - + -
244B LEU* 5.8 1.3 - - + -
251B LEU* 2.8 56.4 + - + +
252B GLU* 3.8 4.3 - - - +
254B ALA* 1.3 75.5 - - - +
256B LYS* 1.3 66.1 + - - +
258B LYS 3.0 7.6 + - - -
260B LYS* 2.9 62.7 + - + +
262B ASP* 3.5 26.9 - - + +
263B MET* 3.6 52.7 - - + +
266B ILE* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLU* 3.0 24.5 + - + +
253B ASP* 3.9 7.6 - - - +
255B TRP* 1.3 75.0 - - - +
257B GLU* 1.3 58.1 + - - +
259B GLY* 3.0 19.9 + - - -
260B LYS 4.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASP 3.0 18.9 + - - +
254B ALA* 3.8 8.7 - - - +
256B LYS* 1.3 77.3 - - - +
258B LYS* 1.3 76.7 + - + +
259B GLY 3.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLN* 5.5 5.2 - - - +
254B ALA 3.3 17.7 + - - +
255B TRP 3.0 5.6 + - - +
257B GLU* 1.3 97.4 + - + +
259B GLY* 1.3 63.9 + - - +
260B LYS* 3.2 23.3 + - + +
----------------------------------------------------------
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