Contacts of the helix formed by residues 220 - 244 (chain E) in PDB entry 5J0Z
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 SER 220 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 4.9 4.9 - - - -
222A GLU* 4.0 25.5 + - - +
277A HIS* 4.9 7.2 - - - -
218E SER* 3.2 10.9 + - - -
219E THR* 1.3 76.5 - - - +
221E TYR* 1.3 55.0 + - - +
222E GLU* 3.2 15.4 + - - +
223E ALA* 3.0 14.0 + - - +
224E ASN* 2.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D THR 3.6 10.7 + - - -
218D SER* 3.2 29.2 - - - -
220D SER* 4.8 2.5 - - - -
223D ALA* 4.1 16.2 - - + -
227D LEU* 3.2 22.0 - - + +
219E THR 3.8 3.4 + - - -
220E SER* 1.3 68.7 - - - +
222E GLU* 1.3 72.7 + - - +
223E ALA 2.9 0.9 + - - -
224E ASN* 2.9 7.4 + - - +
225E VAL* 2.8 49.8 + - + +
273E VAL* 3.6 23.6 - - + -
274E THR* 3.3 29.0 + - + +
277E HIS* 3.4 52.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 5.5 8.7 - - + -
220D SER* 3.8 25.6 + - - +
222D GLU* 5.5 6.7 - - + -
223D ALA* 4.1 19.6 - - + +
226D THR* 5.5 1.7 + - - +
219E THR 5.1 0.5 - - - +
220E SER* 3.5 16.9 + - - +
221E TYR* 1.3 95.4 + - - +
223E ALA* 1.3 54.9 + - - +
225E VAL* 4.5 2.6 - - - +
226E THR* 3.1 19.1 + - - -
277E HIS* 5.1 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 4.0 24.2 - - + -
222A GLU* 4.2 23.7 - - - +
225A VAL* 4.2 8.6 - - + +
220E SER* 3.0 21.4 + - - +
221E TYR 2.9 0.2 + - - -
222E GLU* 1.3 76.0 - - - +
224E ASN* 1.3 60.6 + - - +
225E VAL 3.3 1.6 - - - -
226E THR* 3.1 9.9 + - - -
227E LEU* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 4.6 1.6 - - - -
215E ALA* 3.2 33.2 + - + +
218E SER* 2.7 39.3 + - - -
220E SER 2.7 22.7 + - - +
221E TYR* 2.9 3.7 + - - +
223E ALA* 1.3 69.6 - - - +
225E VAL* 1.3 68.0 + - - +
227E LEU* 3.4 8.3 - - - +
228E VAL* 2.8 28.9 + - - +
273E VAL* 3.7 23.3 - - + +
276E GLN* 3.5 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ALA* 4.0 10.5 - - + +
226D THR* 4.0 10.1 - - + -
227D LEU* 3.8 44.2 - - + +
221E TYR* 2.8 58.3 + - + +
222E GLU 4.5 3.6 - - - +
224E ASN* 1.3 71.3 - - - +
226E THR* 1.3 59.3 + - - +
228E VAL* 5.1 1.3 - - - -
229E VAL* 2.8 44.9 + - + +
273E VAL* 4.7 3.6 - - + -
274E THR* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU 5.5 1.6 + - - +
225A VAL* 4.0 17.0 - - + -
226A THR* 4.1 23.8 + - + +
229A VAL* 5.8 1.1 - - + -
226D THR* 4.0 20.6 + - + +
222E GLU 3.1 15.8 + - - -
223E ALA* 3.1 11.2 + - - -
225E VAL* 1.3 77.6 - - - +
227E LEU* 1.3 62.6 + - - +
229E VAL* 5.1 0.4 - - - -
230E SER* 2.7 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.1 35.7 - - + +
225A VAL* 3.8 22.6 - - + +
229A VAL* 4.7 5.8 - - + +
270A VAL* 5.0 3.1 - - + -
211E ILE* 3.4 34.3 - - + +
212E SER* 4.7 1.3 - - - -
214E THR* 3.1 22.7 - - - +
215E ALA* 4.0 21.1 - - + +
223E ALA 2.8 14.5 + - - +
224E ASN* 3.4 11.7 - - - +
226E THR* 1.3 75.0 - - - +
228E VAL* 1.3 52.7 + - + +
230E SER* 4.2 1.2 - - - -
231E THR* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E SER* 3.8 24.2 - - - +
215E ALA* 4.3 9.6 - - + -
224E ASN 2.8 21.0 + - - +
225E VAL* 4.2 2.0 - - - +
227E LEU* 1.3 73.6 - - - +
229E VAL* 1.3 62.4 + - + +
231E THR* 2.8 17.6 + - - -
232E LEU* 3.1 13.0 + - + +
266E TYR* 3.8 20.5 - - + +
269E ALA* 4.3 16.4 - - + -
270E VAL* 3.3 35.7 - - + +
273E VAL* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ILE* 4.4 20.2 - - + -
226D THR* 4.9 1.3 - - + +
227D LEU* 4.5 7.6 - - + +
230D SER* 3.2 36.6 - - - +
231D THR* 4.3 15.0 - - + +
234D ALA* 6.4 0.4 - - + -
225E VAL* 2.8 40.9 + - + +
226E THR* 4.5 1.1 - - - +
228E VAL* 1.3 74.3 - - + +
230E SER* 1.3 57.9 + - - +
232E LEU* 3.2 13.5 + - + +
233E ILE* 3.0 27.8 + - + +
270E VAL* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 3.2 26.6 - - - +
233A ILE* 3.6 14.4 - - - +
226D THR* 6.0 0.7 - - - +
226E THR* 2.7 37.4 + - - +
229E VAL* 1.3 74.0 - - - +
231E THR* 1.3 62.0 + - - +
233E ILE* 3.1 13.9 + - - +
234E ALA* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.4 11.2 - - + -
232A LEU* 5.6 2.9 - - + -
208E ILE* 3.4 30.8 - - + +
211E ILE* 3.6 26.2 - - + -
212E SER* 3.6 6.2 - - - +
227E LEU 2.7 23.8 + - - +
228E VAL* 2.8 16.3 + - - -
230E SER* 1.3 78.4 - - - +
232E LEU* 1.3 54.5 + - - +
234E ALA* 3.4 9.6 + - + +
235E HIS* 2.9 27.7 + - - +
266E TYR* 3.4 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 4.1 16.6 - - + -
211D ILE* 3.8 30.7 - - + -
231D THR* 5.5 3.1 - - + -
234D ALA* 5.4 4.7 - - + -
228E VAL* 3.1 17.4 + - + +
229E VAL* 3.3 18.2 - - + +
230E SER 3.2 0.2 - - - -
231E THR* 1.3 71.7 + - - +
233E ILE* 1.3 62.0 + - - +
235E HIS* 3.4 6.3 + - + +
236E ILE* 2.9 42.2 + - + +
263E TYR* 4.6 18.4 - - + +
266E TYR* 3.4 33.4 - - + -
270E VAL* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 3.6 22.2 - - + -
402A LMT 4.1 20.4 - - + -
403A LMT 5.8 2.7 - - + -
230D SER* 3.5 32.5 - - - +
233D ILE* 3.7 19.5 - - + -
234D ALA* 4.1 19.7 - - + +
403D LMT 4.8 8.9 - - + +
229E VAL* 3.0 15.8 + - + +
230E SER* 3.1 11.0 + - - +
232E LEU* 1.3 74.0 - - + +
234E ALA* 1.3 67.2 + - - +
236E ILE* 2.9 19.6 + - - +
237E ALA* 3.0 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 6.3 0.7 - - + -
232A LEU* 5.3 4.9 - - + -
233A ILE* 4.1 13.2 - - + -
236A ILE* 3.7 25.1 - - + -
403A LMT 5.5 0.9 - - - -
208E ILE* 4.0 12.3 - - + -
230E SER 2.9 12.6 + - - +
231E THR* 3.5 13.2 - - - +
233E ILE* 1.3 77.9 - - - +
235E HIS* 1.3 61.1 + - - +
237E ALA* 3.1 22.5 - - - +
238E PHE* 3.4 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E MET* 3.8 37.8 + - + +
208E ILE* 3.2 22.6 - - + +
231E THR 2.9 14.0 + - - +
232E LEU* 3.6 9.0 - - + +
233E ILE 3.2 0.2 - - - -
234E ALA* 1.3 71.9 - - - +
236E ILE* 1.3 65.7 + - - +
238E PHE* 3.1 8.8 + - - +
239E ASN* 3.0 18.2 + - + +
259E ILE* 3.9 8.3 + - + +
262E ILE* 3.1 36.9 - - + +
263E TYR* 3.4 40.6 - + - -
266E TYR* 3.8 13.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 4.1 15.5 - - + -
234D ALA* 3.5 31.4 - - + -
237D ALA* 3.7 21.5 - - + -
238D PHE* 3.5 30.1 - - + -
403D LMT 4.0 9.6 - - + +
232E LEU* 2.9 23.1 + - + +
233E ILE* 2.9 10.1 + - - +
235E HIS* 1.3 76.5 - - - +
237E ALA* 1.3 60.9 + - - +
239E ASN* 3.1 11.1 + - - +
240E ILE* 3.2 15.4 + - + +
263E TYR* 3.5 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.7 14.6 - - + -
240A ILE* 3.3 16.4 - - + +
403A LMT 3.1 36.6 - - + -
403D LMT 3.3 27.1 - - - +
233E ILE 3.0 6.9 + - - +
234E ALA 3.1 17.9 - - - +
236E ILE* 1.3 76.2 - - - +
238E PHE* 1.3 55.8 + - + +
241E LEU 3.4 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.5 35.2 - - + -
239A ASN* 4.4 3.8 - - - -
240A ILE* 4.4 7.9 - - + -
263A TYR* 3.5 30.1 - + - -
200E ASN 3.9 15.5 - - - -
201E ILE* 4.3 17.8 - - + +
204E PRO* 3.8 20.4 - - + -
205E MET* 3.3 34.6 - - + +
208E ILE* 5.5 4.5 - - + -
234E ALA 3.4 13.5 - - - -
235E HIS* 3.1 8.3 + - - +
237E ALA* 1.3 79.1 - - + +
239E ASN* 1.3 63.2 + - - +
241E LEU* 4.0 19.0 - - + +
242E VAL* 3.5 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D PRO 5.4 2.4 + - - -
200D ASN* 4.5 14.1 + - - +
204D PRO* 4.8 3.6 - - - +
238D PHE* 4.3 9.9 - - - -
205E MET* 4.5 0.6 - - - +
235E HIS* 3.0 10.6 + - + +
236E ILE 3.1 4.0 + - - +
238E PHE* 1.3 75.8 - - - +
240E ILE* 1.3 63.0 + - + +
242E VAL* 3.3 2.1 + - - +
243E GLU* 3.0 40.4 + - - +
259E ILE* 3.7 28.5 - - + +
263E TYR* 2.7 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ALA* 3.2 40.6 - - + +
238D PHE* 4.2 17.3 - - + -
241D LEU* 3.6 35.2 - - + -
402D LMT 3.6 30.3 - - + -
403D LMT 4.1 20.4 - - + +
236E ILE* 3.2 12.6 + - + +
239E ASN* 1.3 76.6 - - + +
241E LEU* 1.4 54.2 + - - +
243E GLU* 4.2 7.2 - - - +
244E THR* 2.5 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 3.4 36.1 - - + -
243A GLU* 3.6 31.0 - - - +
244A THR* 4.8 13.5 - - + -
403D LMT 3.9 18.7 - - + +
201E ILE* 4.8 17.9 - - + -
237E ALA 3.4 18.6 + - - +
238E PHE* 4.3 14.8 - - + +
239E ASN 3.3 1.2 - - - -
240E ILE* 1.4 78.1 - - - +
242E VAL* 1.4 51.7 - - - +
244E THR* 4.2 2.3 + - - -
245E ASN* 2.7 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E TYR* 5.1 6.5 - - + -
201E ILE* 3.7 43.1 - - + -
238E PHE 3.5 15.2 + - - +
239E ASN* 3.3 3.6 + - - +
241E LEU* 1.4 73.6 - - + +
243E GLU* 1.3 69.4 + - + +
244E THR 3.2 3.7 + - - -
245E ASN* 3.5 24.8 + - - +
246E LEU* 3.9 17.9 + - + +
255E THR* 4.1 18.6 - - + -
256E GLY* 5.8 2.7 - - - +
259E ILE* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D ASN* 3.8 43.1 - - - +
201D ILE* 4.7 5.6 - - - +
238D PHE* 5.5 0.5 - - - -
241D LEU* 3.2 37.1 - - - +
239E ASN* 3.0 40.1 + - - +
240E ILE* 4.2 5.7 - - - +
241E LEU 3.7 0.2 - - - -
242E VAL* 1.3 80.5 - - + +
244E THR* 1.3 59.3 + - - +
246E LEU* 3.5 20.7 - - - +
247E PRO 5.5 0.9 - - - +
248E LYS* 5.6 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D LEU* 4.5 20.6 - - + -
245D ASN* 6.0 0.9 - - - +
402D LMT 5.6 7.8 - - + +
33E LYS* 3.3 34.2 - - - +
240E ILE* 2.5 29.0 + - + +
241E LEU* 4.2 3.9 + - - -
242E VAL 3.2 0.4 - - - -
243E GLU* 1.3 82.4 - - - +
245E ASN* 1.3 62.5 + - - +
246E LEU 3.2 3.4 - - - -
----------------------------------------------------------
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