Contacts of the helix formed by residues 241 - 264 (chain D) in PDB entry 6UWZ
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 241 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLY* 2.6 40.2 - - - +
247C GLU 3.5 0.7 - - - -
248C LYS* 2.8 6.4 + - - +
249C MET* 2.7 42.8 + - + +
250C SER* 3.7 3.3 + - - +
302C LEU* 3.7 21.0 - - - +
235D LEU* 3.7 3.7 - - + +
239D SER* 2.8 25.8 + - - +
240D GLY* 1.3 77.9 - - - +
242D LYS* 1.3 65.2 + - - +
243D MET 3.4 2.2 - - - -
244D THR* 3.3 9.6 - - + +
245D LEU* 3.0 24.4 + - - +
250E GLN* 3.1 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 3.4 23.1 + - + +
233D PHE* 6.0 0.4 - - - -
235D LEU* 2.8 41.3 + - + +
236D PRO 3.9 9.2 - - - +
237D THR* 3.7 25.6 + - + +
239D SER 4.1 3.8 - - - +
241D GLU* 1.3 77.3 - - - +
243D MET* 1.3 63.8 + - - +
245D LEU 3.3 0.7 + - - -
246D SER* 2.9 31.9 + - - -
292D THR* 3.7 26.9 - - + +
295D VAL* 4.1 3.9 - - - +
296D ILE* 4.1 17.0 - - + -
407D ASP* 3.0 30.6 + - - -
250E GLN* 3.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LYS* 1.3 74.6 - - - +
244D THR* 1.3 66.8 + - - +
246D SER* 3.6 12.3 - - - +
247D ILE* 2.9 31.8 + - + +
289D ILE* 4.0 14.8 - - + -
292D THR* 3.8 9.2 - - + -
293D VAL* 3.9 23.6 - - + -
296D ILE* 3.2 30.5 - - + -
243E LEU* 4.4 5.6 - - + -
249E GLY 4.0 7.6 - - - +
250E GLN* 2.8 44.4 + - + +
253E THR* 4.7 5.4 - - + -
254E LEU* 4.6 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C MET* 4.2 5.4 - - + -
250C SER* 3.7 40.9 + - - +
253C ILE* 4.5 1.6 - - + -
241D GLU* 3.3 15.5 - - + +
243D MET* 1.3 76.2 - - - +
245D LEU* 1.3 58.1 + - - +
247D ILE* 3.6 5.1 - - - +
248D SER* 2.8 43.2 + - - +
250E GLN* 3.0 21.4 + - - -
253E THR* 4.2 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C MET* 3.9 24.9 - - + -
253C ILE* 3.6 28.0 - - + -
295C VAL* 4.1 12.6 - - + -
299C VAL* 4.2 11.2 - - + -
228D LEU* 4.7 8.3 - - + +
231D LEU* 4.7 4.5 - - + -
232D VAL* 4.0 30.7 - - + +
235D LEU* 4.0 9.9 - - + -
241D GLU 3.0 16.9 + - - +
242D LYS 3.8 2.7 - - - +
244D THR* 1.3 78.6 - - - +
246D SER* 1.3 68.1 + - - +
248D SER* 3.8 3.1 - - - -
249D VAL* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D THR* 6.2 2.7 - - - +
232D VAL* 4.6 13.7 - - - -
242D LYS 2.9 17.9 + - - -
243D MET* 3.2 16.3 + - - +
245D LEU* 1.3 79.4 - - - +
247D ILE* 1.3 66.5 + - - +
249D VAL* 3.2 9.5 + - - +
250D LEU* 3.0 25.1 + - - +
285D VAL* 4.0 7.0 - - - +
288D SER* 5.0 5.4 - - - -
289D ILE* 3.4 31.7 - - - +
292D THR* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D MET 2.9 28.1 + - - +
244D THR* 3.6 6.7 - - - +
246D SER* 1.3 78.9 + - - +
248D SER* 1.3 63.2 + - - +
250D LEU* 3.2 28.5 + - + +
251D LEU* 2.9 32.9 + - + +
289D ILE* 4.2 3.4 - - + -
236E LEU* 4.1 9.0 - - + -
253E THR* 4.6 7.6 - - + +
254E LEU* 3.5 31.2 - - + -
257E SER* 3.4 37.7 - - - +
258E VAL* 4.2 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ILE* 3.2 38.3 - - - +
254C SER* 5.4 0.9 + - - -
257C LEU* 4.9 5.3 - - - +
244D THR* 2.8 27.1 + - - +
247D ILE* 1.3 78.5 - - - +
249D VAL* 1.3 59.2 + - - +
251D LEU* 3.2 14.7 + - - +
252D SER* 2.8 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ILE* 3.8 19.7 - - + +
256C LEU* 5.9 0.2 - - + -
225D PHE* 3.8 21.9 - - + +
228D LEU* 4.1 21.8 - - + +
229D THR* 3.4 30.1 - - + -
245D LEU* 2.9 27.2 + - + +
246D SER* 3.4 10.1 - - - +
248D SER* 1.3 75.3 - - - +
250D LEU* 1.3 57.8 + - - +
252D SER* 3.3 7.6 + - - -
253D LEU* 2.9 27.2 + - - +
285D VAL* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D SER 3.0 12.1 + - - +
247D ILE* 3.3 18.6 - - + +
248D SER 3.2 0.4 - - - -
249D VAL* 1.3 78.6 - - - +
251D LEU* 1.3 54.0 + - + +
253D LEU* 3.3 7.4 + - - +
254D THR* 2.6 39.2 + - - +
282D MET* 4.5 7.7 - - - +
285D VAL* 4.1 11.9 - - + +
286D ILE* 3.6 25.1 - - + -
289D ILE* 3.5 26.2 - - + -
233E ILE* 3.8 35.4 - - + -
236E LEU* 3.6 10.3 - - + -
257E SER 5.8 0.4 - - - +
258E VAL* 5.9 0.2 - - + -
261E ALA* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 4.1 21.1 - - + -
247D ILE* 2.9 21.8 + - + +
248D SER* 3.2 17.9 + - - +
250D LEU* 1.3 75.3 - - + +
252D SER* 1.3 65.4 + - - +
254D THR* 3.0 5.3 + - - -
255D VAL* 2.9 28.6 + - + +
257E SER* 3.6 36.6 - - - +
260E LEU* 4.1 26.0 - - + -
261E ALA* 3.9 22.7 - - + +
264E ILE* 4.5 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ILE* 4.5 3.5 + - - +
256C LEU* 4.1 4.2 - - - +
257C LEU* 3.7 33.1 + - - +
260C THR* 3.7 16.2 - - - +
225D PHE* 3.5 28.5 - - - -
248D SER 2.8 18.5 + - - -
249D VAL* 3.6 4.8 - - - -
251D LEU* 1.3 75.2 - - - +
253D LEU* 1.3 57.4 + - - +
255D VAL 3.4 0.5 + - - -
256D PHE* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D CYS* 4.2 15.7 - - - -
225D PHE* 3.2 38.5 - - + -
249D VAL 2.9 17.6 + - - +
250D LEU* 3.6 5.4 - - - +
251D LEU 3.2 0.2 - - - -
252D SER* 1.3 76.9 - - - +
254D THR* 1.3 57.5 + - - +
256D PHE* 3.4 5.4 + - + +
257D LEU* 2.8 25.8 + - - +
260D ILE* 5.4 0.7 - - + +
278D MET* 4.9 8.4 - - + +
281D THR* 3.9 26.7 - - + -
282D MET* 3.6 42.4 - - + +
285D VAL* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D LEU* 2.6 33.8 + - - +
251D LEU* 3.0 9.5 + - - -
253D LEU* 1.3 74.0 - - - +
255D VAL* 1.3 65.4 + - - +
257D LEU* 2.9 20.0 + - + +
258D LEU* 3.0 16.6 + - + +
282D MET* 4.6 2.6 - - - +
233E ILE* 4.2 5.9 - - - +
261E ALA* 4.3 5.9 - - + +
264E ILE* 3.9 27.6 - - + -
265E PHE* 3.6 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 3.8 16.8 - - + -
260C THR* 4.2 22.0 - - + +
261C VAL* 4.4 15.0 - - + -
264C LEU* 4.2 23.5 - - + +
251D LEU 2.9 16.6 + - - +
252D SER 3.8 3.8 - - - +
254D THR* 1.3 74.6 - - - +
256D PHE* 1.3 57.7 + - - +
258D LEU* 3.1 17.0 - - + +
259D VAL* 3.0 24.5 + - - +
264E ILE* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C THR* 4.3 11.8 - - + +
263C LEU* 4.1 11.2 - - + -
217D ASN 2.9 29.4 - - - -
218D VAL* 3.0 28.0 - - - -
221D PRO* 3.4 28.9 - - + -
222D CYS* 3.4 21.8 - - - -
225D PHE* 3.9 15.3 - + + -
252D SER 2.9 18.7 + - - +
253D LEU* 3.6 6.1 - - + +
255D VAL* 1.3 75.0 - - - +
257D LEU* 1.3 60.0 + - - +
259D VAL* 3.2 23.5 + - + +
260D ILE* 2.8 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU 2.8 13.8 + - - +
254D THR* 2.9 14.5 + - + +
256D PHE* 1.3 73.8 - - - +
258D LEU* 1.3 63.6 + - - +
260D ILE* 3.3 11.3 + - + +
261D VAL* 2.9 29.4 + - + +
278D MET* 3.3 41.3 - - + -
282D MET* 4.8 5.8 - - + -
225E ASN* 3.4 32.1 - - + +
229E PRO* 4.3 7.2 - - + -
265E PHE* 3.6 31.0 - - + -
268E LEU* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 4.0 24.7 - - + -
254D THR* 3.0 13.4 + - + +
255D VAL* 3.1 14.4 - - + +
257D LEU* 1.3 77.0 - - + +
259D VAL* 1.3 63.8 + - - +
261D VAL* 3.3 4.0 + - - +
262D GLU* 2.9 23.2 + - - +
264E ILE* 3.4 32.5 - - + +
265E PHE* 5.7 0.4 - - + -
267E PHE* 3.3 36.1 - - + -
268E LEU* 3.4 33.9 - - + -
271E GLN* 5.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C THR 4.8 3.1 - - - +
263C LEU* 4.6 6.1 - - + +
264C LEU* 3.5 45.5 - - + +
267C ALA* 4.7 4.9 - - + -
217D ASN* 4.3 8.1 - - + +
255D VAL 3.0 15.3 + - - +
256D PHE* 3.2 37.9 + - + +
258D LEU* 1.3 74.3 - - - +
260D ILE* 1.3 65.4 + - + +
262D GLU* 3.1 4.7 + - - +
263D LEU* 2.9 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 3.8 20.4 - - + -
222D CYS* 4.3 5.2 - - - -
253D LEU* 5.4 0.7 - - + +
256D PHE* 2.8 52.3 + - + +
257D LEU* 3.6 15.5 - - + +
259D VAL* 1.3 74.7 - - - +
261D VAL* 1.3 61.1 + - + +
263D LEU* 2.9 5.1 + - - +
264D ILE* 2.7 65.8 + - + +
274D ILE* 4.1 6.5 - - + -
278D MET* 4.0 24.9 - - + -
225E ASN* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LEU* 2.9 23.7 + - + +
258D LEU 3.8 3.1 - - - +
260D ILE* 1.3 76.6 - - + +
262D GLU* 1.3 63.1 + - - +
263D LEU 3.5 0.3 + - - -
264D ILE* 3.6 13.4 - - - +
266D SER* 4.7 4.7 + - - -
221E PHE* 3.9 25.1 - - + -
225E ASN* 4.5 17.0 - - + +
268E LEU* 4.3 26.5 - - + -
271E GLN* 5.3 7.2 - - - +
272E LYS* 3.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 3.8 25.0 - - - +
267C ALA* 4.5 12.5 - - + +
268C ASP* 3.7 24.1 - - + +
258D LEU 2.9 11.6 + - - +
259D VAL 3.1 9.2 + - - +
261D VAL* 1.3 80.4 - - - +
263D LEU* 1.3 66.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ALA* 3.7 32.3 - - + +
213D TYR* 3.6 33.8 - - + +
214D PHE* 4.1 13.7 - - + -
217D ASN* 3.7 28.7 - - + -
218D VAL* 3.7 16.2 - - + -
259D VAL* 2.9 31.4 + - + +
260D ILE 2.9 4.7 + - - +
262D GLU* 1.3 84.6 - - + +
264D ILE* 1.3 72.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D PHE* 3.7 17.0 - - + -
214D PHE* 3.9 17.9 - - + -
218D VAL* 4.0 13.9 - - + -
260D ILE* 2.7 46.9 + - + +
261D VAL* 3.6 16.8 - - - +
262D GLU 4.6 0.5 - - - +
263D LEU* 1.3 77.3 - - - +
265D PRO* 1.3 82.3 - - + +
266D SER* 3.9 0.9 + - - -
272D PRO* 5.5 6.7 - - + -
274D ILE* 3.5 23.8 - - + -
275D GLY* 5.1 4.9 - - - +
221E PHE* 5.1 2.4 - - + -
225E ASN* 4.9 11.2 - - - +
----------------------------------------------------------
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