Contacts of the helix formed by residues 197 - 219 (chain B) in PDB entry 1XDM
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 ASP 197 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP 5.5 2.2 + - - -
198B LEU* 1.3 64.7 + - - +
199B GLU* 3.3 21.0 + - - +
200B HIS* 2.8 50.4 + - - +
201B CYS* 3.1 9.6 + - - +
234B THR 5.2 3.5 - - - -
241B LYS* 4.6 16.8 + - + +
243B TYR* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 1.3 73.6 - - - +
199B GLU* 1.3 53.0 + - - +
200B HIS 2.8 13.5 + - - -
201B CYS* 3.0 3.6 + - - -
202B GLN* 2.9 24.4 + - - +
233B VAL* 3.3 35.4 - - + +
234B THR* 3.5 22.9 - - - -
243B TYR* 3.0 48.7 + - + +
247B GLN* 4.0 18.6 - - + -
248B VAL* 4.3 1.6 - - - +
251B ALA* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 3.3 16.2 + - - +
198B LEU* 1.3 77.5 - - - +
200B HIS* 1.3 59.9 + - - +
202B GLN* 3.8 19.5 - - - +
203B TYR* 3.2 24.1 + - + +
364B SO4 4.8 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ILE 5.9 0.2 + - - -
193B ASP* 3.9 36.4 + - - +
197B ASP* 2.8 35.2 + - - +
198B LEU 2.8 1.2 + - - -
199B GLU* 1.3 76.4 - - - +
201B CYS* 1.3 65.5 + - + -
202B GLN 3.0 4.6 + - - -
203B TYR* 3.3 8.3 + - - +
204B VAL* 3.0 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 4.5 16.3 - - - +
191B ILE 5.6 1.6 - - - -
197B ASP 3.1 6.2 + - - +
198B LEU 3.0 7.0 + - - +
200B HIS* 1.3 84.7 - - + +
202B GLN* 1.3 52.0 + - - +
204B VAL* 3.7 7.8 + - - +
205B THR* 2.7 42.1 + - - -
231B ASN* 4.3 9.6 - - - -
232B MET 4.3 1.8 - - - -
233B VAL* 3.9 11.0 - - + -
234B THR* 3.8 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU 2.9 17.2 + - - +
199B GLU* 3.8 17.0 - - - +
201B CYS* 1.3 73.0 - - - +
203B TYR* 1.3 68.6 + - - +
204B VAL 3.0 1.3 - - - -
205B THR* 2.8 15.4 + - - -
206B GLU* 3.0 39.1 + - - +
233B VAL* 3.4 15.4 - - + +
251B ALA* 3.2 31.9 + - + +
254B THR* 3.2 13.7 - - - +
255B ALA* 4.0 5.4 - - + +
364B SO4 3.0 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 5.6 2.5 - - - -
220A HIS* 4.8 25.4 - + + -
199B GLU* 3.2 17.6 + - + +
200B HIS* 3.3 7.2 + - - +
202B GLN* 1.3 79.7 - - - +
204B VAL* 1.3 67.2 + - + +
206B GLU* 3.5 18.0 + - + +
207B LYS* 3.3 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 5.9 2.0 - - + -
190B VAL* 5.0 16.8 - - + -
200B HIS* 3.0 37.2 - - + +
201B CYS* 3.8 7.2 - - - +
202B GLN 3.0 0.6 - - - -
203B TYR* 1.3 80.0 - - + +
205B THR* 1.3 67.8 + - - +
207B LYS* 2.9 19.6 + - + +
208B VAL* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 4.4 6.9 - - - +
201B CYS* 2.7 18.7 + - - -
202B GLN 2.8 13.6 + - - -
204B VAL* 1.3 74.9 - - - +
206B GLU* 1.3 55.7 + - - +
208B VAL* 3.7 6.8 + - - +
209B LEU* 2.9 51.6 + - + +
230B PRO* 6.0 1.3 - - + -
231B ASN* 3.8 27.1 + - - +
233B VAL* 3.4 25.7 - - + +
255B ALA* 4.5 7.4 - - + -
256B LEU* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 3.4 13.0 + - - +
220A HIS* 5.4 6.9 + - - -
202B GLN* 3.0 41.1 + - - +
203B TYR* 3.8 16.9 - - + +
205B THR* 1.3 73.2 - - - +
207B LYS* 1.3 64.7 + - + +
209B LEU* 4.4 1.1 - - - -
210B ALA 3.1 16.5 + - - -
255B ALA* 3.2 29.6 - - + +
258B ARG* 3.2 24.7 + - + +
259B THR* 3.1 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 4.4 14.6 - - - +
159B SER 6.0 0.2 - - - -
160B SER* 4.8 12.8 + - - +
163B ILE* 4.7 19.3 - - + +
203B TYR* 3.3 51.0 + - + +
204B VAL* 2.9 14.2 + - + +
206B GLU* 1.3 72.8 - - + +
208B VAL* 1.3 58.4 - - + +
209B LEU 3.0 3.1 - - - -
210B ALA* 2.7 26.3 + - - +
211B ALA* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 4.0 35.2 - - + +
166B ASN* 6.4 0.2 - - + -
188B PRO* 4.4 6.5 - - + -
189B GLU* 3.8 47.1 - - + +
190B VAL* 5.2 1.1 - - + -
204B VAL* 2.9 36.3 - - + +
205B THR* 3.9 6.1 - - - +
207B LYS* 1.3 73.4 - - + +
209B LEU* 1.3 59.0 + - + +
211B ALA* 3.8 2.5 - - - +
212B VAL* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.9 24.2 - - + -
205B THR* 2.9 42.3 + - + +
206B GLU 3.9 0.4 - - - +
207B LYS 3.0 0.2 - - - -
208B VAL* 1.3 76.5 - - + +
210B ALA* 1.3 63.4 + - - +
212B VAL* 3.9 3.1 - - + +
213B TYR* 3.3 44.9 + - + +
228B LEU* 3.9 23.6 - - + -
230B PRO* 5.0 6.1 - - + -
255B ALA 4.8 2.0 - - - +
256B LEU* 3.8 22.9 - - + -
259B THR* 3.4 28.5 - - - +
260B VAL* 4.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LYS* 4.3 15.9 - - + +
217A ASN* 3.5 29.2 - - + +
206B GLU 3.1 12.8 + - - +
207B LYS* 2.7 12.2 + - - +
209B LEU* 1.3 70.9 - - - +
211B ALA* 1.3 69.1 + - - +
212B VAL 3.2 0.2 - - - -
213B TYR* 4.6 2.0 - - - +
214B LYS* 2.9 28.6 + - - +
259B THR* 4.3 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LYS* 4.7 12.5 - - - +
163B ILE* 3.4 34.8 - - + +
164B GLN* 5.2 2.5 - - - +
167B ALA* 3.4 14.2 - - + +
207B LYS 3.0 9.6 + - - +
208B VAL 3.8 2.5 - - - +
210B ALA* 1.3 77.3 - - - +
212B VAL* 1.3 52.1 + - - +
214B LYS* 3.5 5.1 - - - +
215B ALA* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 5.8 0.9 - - + +
166B ASN* 6.3 0.4 - - + -
167B ALA* 4.0 20.2 - - + +
170B LEU* 4.9 9.2 - - + -
186B VAL* 3.6 22.2 - - + -
188B PRO* 4.5 16.8 - - + -
208B VAL* 2.9 23.5 + - + +
209B LEU* 4.0 7.0 - - - +
210B ALA 3.2 0.2 - - - -
211B ALA* 1.3 73.0 - - + +
213B TYR* 1.3 69.1 + - + +
214B LYS 3.1 1.6 - - - -
215B ALA* 3.2 6.7 + - - +
216B LEU* 2.8 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA* 5.8 0.2 - - - +
186B VAL* 4.9 1.0 - - + +
209B LEU* 3.3 28.4 + - + +
210B ALA* 4.7 1.3 - - - +
212B VAL* 1.3 81.1 - - + +
214B LYS* 1.3 62.9 + - - +
216B LEU* 3.8 15.5 - - + +
217B ASN* 3.4 18.5 + - - +
223B LEU* 3.6 29.1 - - + +
226B THR* 4.7 8.1 - - + +
228B LEU* 2.9 46.9 - - + +
259B THR 4.2 3.4 - - - +
260B VAL* 3.6 36.4 - - + +
261B PRO* 3.6 25.9 - - + +
264B VAL* 3.4 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 5.5 6.3 - - - +
207A LYS 5.6 1.1 - - - -
210A ALA* 3.8 19.1 - - + +
211A ALA* 4.4 19.9 - - - +
214A LYS* 3.7 49.3 - - + +
210B ALA 2.9 20.6 + - - +
211B ALA* 3.5 4.0 - - - +
213B TYR* 1.3 77.2 - - - +
215B ALA* 1.3 58.5 + - - +
217B ASN* 2.8 23.8 + - - +
218B ASP* 2.9 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 3.4 35.7 - - + +
168B ASN* 3.8 11.7 - - - +
171B ALA* 4.0 2.5 - - + -
211B ALA 2.8 19.7 + - - +
212B VAL 3.2 5.8 - - - +
214B LYS* 1.3 75.9 - - - +
216B LEU* 1.3 63.6 + - - +
217B ASN 2.9 1.7 + - - -
218B ASP* 2.9 17.4 + - - +
219B HIS* 2.8 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU 4.2 0.2 - - - +
171B ALA* 4.0 11.4 - - + -
174B ALA* 3.5 22.4 - - + -
186B VAL* 4.1 18.8 - - + -
212B VAL* 2.8 47.1 + - + +
213B TYR* 3.8 28.3 - - + +
215B ALA* 1.3 72.5 - - - +
217B ASN* 1.3 56.7 + - - +
219B HIS 3.9 0.4 - - - -
220B HIS 3.2 2.8 + - - -
221B VAL* 2.8 70.3 + - + +
223B LEU* 4.2 11.7 - - + -
226B THR* 5.4 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 5.7 3.1 - - - -
206A GLU* 3.9 14.6 + - - +
207A LYS* 4.1 21.7 + - - +
210A ALA* 3.3 33.4 - - + +
258A ARG* 5.1 4.2 + - - +
259A THR* 4.0 11.5 - - - +
213B TYR 3.4 12.1 + - - +
214B LYS* 2.8 11.5 + - - +
216B LEU* 1.3 77.6 - - - +
218B ASP* 1.3 63.3 + - - +
219B HIS 3.0 1.6 - - - -
220B HIS* 2.8 22.2 + - - +
221B VAL 5.8 0.2 - - - -
223B LEU* 5.4 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 5.7 1.4 + - - -
207A LYS* 6.1 2.2 - - - -
168B ASN* 4.5 5.5 - - - +
214B LYS* 2.9 51.6 + - - +
215B ALA* 2.9 13.1 + - - +
217B ASN* 1.3 79.8 - - - +
219B HIS* 1.3 61.8 + - + +
220B HIS* 3.5 2.1 + - - +
161C LEU* 3.4 35.9 - - + +
164C GLN* 5.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASN* 3.3 37.8 + - - -
171B ALA* 3.6 15.6 - - + +
172B ARG* 3.7 16.7 + - + +
175B SER* 4.4 11.3 + - - +
215B ALA 2.8 27.5 + - - +
216B LEU 3.7 0.2 - - - -
217B ASN 3.0 1.0 - - - -
218B ASP* 1.3 82.3 - - + +
220B HIS* 1.3 72.6 + - - +
221B VAL* 3.4 16.7 + - + +
161C LEU* 4.5 15.5 - - + +
165C GLU* 2.8 29.3 + - - -
----------------------------------------------------------
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