Contacts of the helix formed by residues 210 - 233 (chain E) in PDB entry 6NHW
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 210 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E PRO 4.4 1.9 + - - -
209E GLY* 1.4 79.9 + - - -
211E LEU* 1.4 65.8 + - - +
212E SER* 3.2 9.4 - - - +
213E GLY* 3.2 16.9 + - - +
214E ILE* 3.8 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E SER* 1.4 77.4 - - - +
212E SER* 1.4 60.4 + - - +
214E ILE* 3.4 31.0 - - + +
215E ILE* 3.5 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E SER* 4.5 6.1 - - - -
211E LEU* 1.4 80.4 - - - +
213E GLY* 1.4 62.7 + - - +
215E ILE* 3.4 16.7 - - - +
216E ILE* 3.4 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E SER* 3.2 11.0 + - - +
212E SER* 1.4 82.7 + - - +
214E ILE* 1.4 59.0 + - - +
216E ILE* 3.4 9.2 - - - +
217E GLY* 3.2 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E SER 3.8 5.0 + - - +
211E LEU* 3.4 33.7 - - + +
213E GLY* 1.4 72.1 - - - +
215E ILE* 1.4 68.9 + - + +
217E GLY* 3.3 1.5 + - - -
218E VAL* 3.1 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ILE* 5.3 13.9 - - + -
211E LEU* 3.5 14.4 - - + +
212E SER* 3.4 20.2 - - - +
214E ILE* 1.4 81.1 - - + +
216E ILE* 1.4 62.3 + - + +
218E VAL* 3.2 24.8 - - + +
219E THR* 3.6 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E SER 3.4 18.6 - - - +
213E GLY* 3.4 11.2 - - - +
215E ILE* 1.4 80.7 - - + +
217E GLY* 1.4 63.8 + - - +
219E THR* 2.6 30.4 + - - +
220E VAL* 3.6 24.8 - - + +
215F ILE* 6.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E GLY 3.2 20.5 + - - -
214E ILE* 3.7 2.9 - - - -
215E ILE 3.3 0.6 - - - -
216E ILE* 1.4 80.2 - - - +
218E VAL* 1.4 59.8 + - - +
220E VAL* 3.2 23.9 - - - +
221E ALA* 3.2 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 4.5 25.7 - - + +
223D VAL* 4.7 19.1 - - + +
214E ILE* 3.1 14.5 + - + +
215E ILE* 3.2 24.9 - - + +
217E GLY* 1.4 75.3 - - - +
219E THR* 1.4 66.7 + - + +
221E ALA* 3.6 13.3 + - + +
222E ALA* 3.7 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ILE* 6.2 0.9 - - + -
219D THR* 4.2 16.6 - - + -
215E ILE* 3.6 17.9 - - + +
216E ILE* 2.6 25.6 + - - +
217E GLY 3.4 0.2 - - - -
218E VAL* 1.4 78.8 - - + +
220E VAL* 1.4 69.7 + - - +
222E ALA* 4.0 7.7 + - - +
223E VAL* 3.6 15.9 - - - +
215F ILE* 5.7 4.5 - - + +
218F VAL* 4.6 16.5 - - + +
219F THR* 4.0 30.9 - - + +
222F ALA* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E ILE* 3.6 24.2 - - + +
217E GLY* 3.2 24.9 - - - +
219E THR* 1.4 88.8 + - - +
221E ALA* 1.4 65.3 + - - +
222E ALA 3.4 0.2 - - - -
223E VAL* 3.2 19.5 + - - +
224E VAL* 3.4 20.9 + - + +
218F VAL* 5.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D VAL* 6.4 1.1 - - + -
217E GLY 3.2 19.5 + - - +
218E VAL* 3.7 11.9 - - - +
219E THR 3.5 0.6 - - - -
220E VAL* 1.4 78.9 - - - +
222E ALA* 1.4 61.1 + - - +
223E VAL 3.4 0.3 + - - -
224E VAL* 3.5 6.8 + - - +
225E LEU* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR 5.6 0.7 - - - +
222D ALA* 4.1 26.0 - - + -
223D VAL* 4.6 14.0 - - + +
226D ILE* 4.5 9.1 - - + +
218E VAL 3.7 8.4 + - - +
219E THR* 4.3 9.0 - - - +
220E VAL 3.4 0.6 - - - -
221E ALA* 1.4 76.5 - - - +
223E VAL* 1.4 62.1 + - - +
225E LEU* 3.6 9.1 + - - +
226E ILE* 3.5 29.1 + - + +
222F ALA* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E THR 3.6 18.8 - - - +
220E VAL* 3.2 9.6 + - - +
222E ALA* 1.4 76.2 - - - +
224E VAL* 1.4 63.7 + - + +
225E LEU 3.5 0.3 + - - -
226E ILE* 3.5 17.2 + - - +
227E VAL* 3.6 18.5 + - + +
218F VAL* 4.0 30.3 - - + +
221F ALA* 6.1 1.3 - - + -
222F ALA* 4.6 12.8 - - + -
225F LEU* 5.6 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E VAL* 3.4 18.5 + - + +
221E ALA* 4.1 7.9 - - - +
223E VAL* 1.4 79.1 - - + +
225E LEU* 1.4 62.3 + - - +
227E VAL* 3.4 19.1 + - + +
228E ALA* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D VAL* 6.5 0.9 - - + -
226D ILE* 4.0 40.4 - - + -
221E ALA 3.2 18.5 + - - +
222E ALA* 3.8 8.3 - - - +
223E VAL 3.3 0.4 - - - -
224E VAL* 1.4 77.4 - - - +
226E ILE* 1.4 61.8 + - - +
228E ALA* 3.4 22.0 + - + +
229E VAL* 3.7 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ALA* 6.3 0.7 - - + -
226D ILE* 4.6 15.0 - - + -
222E ALA* 3.5 16.4 - - + +
223E VAL* 3.5 9.3 + - - +
224E VAL 3.4 0.4 - - - -
225E LEU* 1.4 76.5 - - - +
227E VAL* 1.4 62.8 + - + +
229E VAL* 3.4 24.9 + - + +
230E PHE* 3.7 23.7 - - + -
222F ALA* 4.0 30.3 - - + +
225F LEU* 3.8 33.9 - - + -
226F ILE* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E VAL* 3.6 18.8 - - + +
224E VAL* 3.4 14.1 + - + +
225E LEU 3.4 0.6 - - - -
226E ILE* 1.4 76.5 - - + +
228E ALA* 1.4 62.7 + - - +
229E VAL 3.3 0.9 + - - -
230E PHE* 3.4 19.6 + - + +
231E VAL* 3.7 12.7 + - + +
225F LEU* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E VAL 3.4 8.6 + - - +
225E LEU* 3.4 19.0 + - + +
226E ILE 3.3 0.4 - - - -
227E VAL* 1.4 79.4 - - - +
229E VAL* 1.4 57.6 + - + +
230E PHE 3.6 0.2 - - - -
231E VAL* 3.2 17.3 - - - +
232E CYS* 3.0 27.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
226D ILE* 6.2 2.2 - - + -
233D LYS* 5.6 10.3 - - - +
225E LEU* 3.7 22.9 - - + +
226E ILE* 3.5 14.4 - - + +
227E VAL 3.2 0.6 - - - -
228E ALA* 1.4 76.8 - - + +
230E PHE* 1.4 67.6 + - + +
232E CYS* 3.4 15.7 + - - +
233E LYS* 3.5 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E ILE* 3.7 35.2 - - + -
227E VAL* 3.4 11.5 + - + +
229E VAL* 1.4 80.6 - - + +
231E VAL* 1.4 60.9 + - - +
233E LYS* 3.4 35.7 + - + +
234E SER* 3.9 3.8 + - - -
225F LEU* 5.8 8.3 - - + -
229F VAL* 5.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E VAL* 3.7 7.7 + - + +
228E ALA* 3.2 27.4 - - - +
230E PHE* 1.4 75.6 - - - +
232E CYS* 1.4 63.4 + - - +
234E SER* 2.6 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E ALA* 3.0 24.7 - - - -
229E VAL* 3.4 11.4 + - + +
230E PHE 3.4 0.4 - - - -
231E VAL* 1.4 80.4 - - - +
233E LYS* 1.4 59.9 + - + +
234E SER 3.4 0.5 + - - -
235E LEU* 3.5 21.4 + - - +
236E LEU* 3.8 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E VAL* 3.5 26.4 + - + +
230E PHE* 3.4 28.4 + - + +
231E VAL 3.2 0.6 - - - -
232E CYS* 1.4 72.7 - - + +
234E SER* 1.4 59.3 + - - +
235E LEU 3.2 2.7 - - - -
236E LEU* 3.0 36.9 + - + +
237E TRP* 3.3 12.1 + - - +
----------------------------------------------------------
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