Contacts of the helix formed by residues 197 - 219 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198Z LEU* 1.3 62.5 + - - +
199Z GLU* 3.4 4.4 - - - +
200Z HIS* 3.0 45.1 + - + +
201Z CYS* 3.0 10.9 + - - +
243Z TYR* 4.2 13.4 + - - -
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Residues in contact with LEU 198 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Z ASP* 1.3 72.0 - - - +
199Z GLU* 1.3 54.2 + - - +
200Z HIS 2.8 4.9 + - - -
201Z CYS* 2.9 6.4 + - - +
202Z GLN* 2.8 35.3 + - - +
233Z VAL* 3.3 31.1 - - + +
234Z THR* 3.4 25.6 - - - +
243Z TYR* 3.2 58.8 + - + +
247Z GLN* 4.0 24.0 - - + +
248Z VAL* 5.1 2.5 - - + -
251Z ALA* 4.4 11.9 - - + -
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Residues in contact with GLU 199 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Z ASP* 5.2 3.1 - - - +
198Z LEU* 1.3 78.5 - - - +
200Z HIS* 1.3 56.5 + - - +
202Z GLN* 3.6 13.6 - - - +
203Z TYR* 3.2 23.9 + - - +
243Z TYR* 4.8 0.8 + - - -
364Z SO4 5.6 6.5 - - - +
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Residues in contact with HIS 200 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Z ASP* 3.0 42.6 - - + +
198Z LEU 2.8 0.2 - - - -
199Z GLU* 1.3 76.5 - - - +
201Z CYS* 1.3 58.5 - - + -
202Z GLN 3.0 1.1 - - - -
203Z TYR* 2.9 21.9 + + - +
204Z VAL* 2.7 45.5 + - + +
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Residues in contact with CYS 201 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Z ASP 3.0 12.0 + - - +
198Z LEU* 2.9 10.0 + - - +
200Z HIS* 1.3 78.4 - - + +
202Z GLN* 1.3 57.8 + - - +
204Z VAL* 3.4 10.9 - - - +
205Z THR* 2.7 38.7 + - - -
231Z ASN* 4.5 6.3 - - - -
233Z VAL* 3.9 11.7 - - + -
234Z THR* 3.7 33.0 - - - -
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Residues in contact with GLN 202 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198Z LEU 2.8 14.4 + - - +
199Z GLU* 3.6 12.4 - - - +
201Z CYS* 1.3 78.3 - - - +
203Z TYR* 1.3 56.5 + - - +
205Z THR* 3.7 1.6 - - - -
206Z GLU* 2.7 62.4 + - - +
233Z VAL* 3.5 14.3 - - + +
251Z ALA* 3.2 35.0 - - - +
254Z THR* 3.2 14.8 - - - +
255Z ALA* 3.4 13.5 - - + -
258Z ARG* 4.3 2.2 - - - +
364Z SO4 3.1 27.4 + - - -
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Residues in contact with TYR 203 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217Y ASN* 5.3 6.7 + - - -
218Y ASP 5.3 4.9 + - - -
220Y HIS* 4.2 35.1 + + + +
199Z GLU 3.2 10.8 + - - +
200Z HIS* 2.9 17.3 + + - +
202Z GLN* 1.3 79.4 - - - +
204Z VAL* 1.3 60.3 + - + +
206Z GLU* 3.6 12.1 - - + +
207Z LYS* 2.8 64.2 + - + +
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Residues in contact with VAL 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163Z ILE* 5.6 6.5 - - + -
200Z HIS* 2.7 41.5 + - + +
201Z CYS* 3.4 16.4 - - - +
203Z TYR* 1.3 74.2 - - + +
205Z THR* 1.3 53.5 + - - +
207Z LYS* 3.0 9.8 + - + +
208Z VAL* 2.7 50.1 + - + +
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Residues in contact with THR 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Z CYS* 2.7 26.5 + - - -
202Z GLN 3.7 4.0 - - - -
204Z VAL* 1.3 75.6 - - - +
206Z GLU* 1.3 57.5 + - - +
208Z VAL* 3.5 6.6 - - - +
209Z LEU* 2.8 60.4 + - + +
230Z PRO* 5.6 2.5 - - + -
231Z ASN* 3.9 34.2 + - - +
233Z VAL* 3.9 18.2 - - + +
255Z ALA* 5.0 3.8 - - + -
256Z LEU* 5.9 1.8 - - + -
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Residues in contact with GLU 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217Y ASN* 4.4 6.5 + - - +
220Y HIS* 5.1 6.9 + - - -
202Z GLN* 2.7 62.0 + - - +
203Z TYR* 3.6 14.2 + - + +
205Z THR* 1.3 77.2 - - - +
207Z LYS* 1.3 63.9 + - - +
209Z LEU* 3.4 0.4 + - - -
210Z ALA* 3.0 26.9 + - - +
255Z ALA* 3.2 30.2 - - + +
258Z ARG* 4.0 23.6 + - + +
259Z THR* 3.5 16.4 - - + +
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Residues in contact with LYS 207 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214Y LYS* 5.7 1.2 - - - -
217Y ASN* 4.2 16.8 - - - +
218Y ASP* 6.2 2.0 - - - -
159Z SER* 5.6 1.8 - - - +
160Z SER* 5.2 10.4 - - - +
163Z ILE* 4.0 28.6 - - + +
203Z TYR* 2.8 64.1 + - + +
204Z VAL* 3.4 9.6 - - + +
206Z GLU* 1.3 73.7 - - - +
208Z VAL* 1.3 64.2 + - + +
210Z ALA* 3.8 3.3 - - - +
211Z ALA* 3.6 16.8 + - - +
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Residues in contact with VAL 208 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163Z ILE* 4.3 30.3 - - + +
166Z ASN* 5.4 8.3 - - - +
188Z PRO* 4.1 21.5 - - + -
189Z GLU* 5.7 5.8 - - + -
204Z VAL* 2.7 41.1 + - + +
205Z THR* 3.5 7.6 - - + +
207Z LYS* 1.3 70.2 - - - +
209Z LEU* 1.3 62.1 + - + +
210Z ALA 3.1 1.3 - - - -
211Z ALA* 2.9 22.2 + - - +
212Z VAL* 2.9 27.7 + - + +
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Residues in contact with LEU 209 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188Z PRO* 3.9 27.4 - - + -
205Z THR* 2.8 45.0 + - + +
206Z GLU 4.0 0.2 - - - +
208Z VAL* 1.3 74.6 - - + +
210Z ALA* 1.3 57.0 - - - +
212Z VAL* 3.2 7.0 + - + +
213Z TYR* 2.9 44.9 + - + +
228Z LEU* 4.1 23.3 - - + -
230Z PRO* 4.9 4.9 - - + -
255Z ALA 4.6 3.6 - - - +
256Z LEU* 4.3 19.7 - - + -
259Z THR* 3.9 28.3 - - - +
260Z VAL* 4.4 1.6 - - + -
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Residues in contact with ALA 210 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214Y LYS* 3.8 11.5 - - + +
217Y ASN* 3.3 41.3 - - + +
206Z GLU 3.0 11.7 + - - +
207Z LYS 3.8 5.4 - - - +
209Z LEU* 1.3 78.6 - - - +
211Z ALA* 1.3 57.1 + - - +
213Z TYR* 4.4 2.4 - - - +
214Z LYS* 3.0 30.0 + - - +
259Z THR* 4.1 9.1 - - + +
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Residues in contact with ALA 211 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214Y LYS* 4.4 15.4 - - - +
163Z ILE* 3.7 36.3 - - + +
164Z GLN* 5.1 2.7 - - + -
167Z ALA* 3.9 4.5 - - + +
207Z LYS 3.6 6.8 + - - +
208Z VAL 2.9 8.6 + - - +
210Z ALA* 1.3 76.2 - - - +
212Z VAL* 1.3 61.3 + - + +
214Z LYS* 3.7 5.6 - - - +
215Z ALA* 2.9 32.9 + - - +
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Residues in contact with VAL 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Z ILE 6.1 0.2 - - - +
166Z ASN* 5.6 2.7 - - - +
167Z ALA* 4.3 12.1 - - + +
170Z LEU* 3.9 16.2 - - + -
186Z VAL* 3.7 20.9 - - + -
188Z PRO* 4.4 15.0 - - + -
208Z VAL* 2.9 39.3 + - + +
209Z LEU* 3.3 12.1 - - + +
211Z ALA* 1.3 78.9 - - + +
213Z TYR* 1.3 66.8 + - + +
215Z ALA* 3.4 2.6 + - - +
216Z LEU* 2.9 49.3 + - + +
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Residues in contact with TYR 213 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Z VAL* 5.0 3.9 - - + +
209Z LEU* 2.9 31.5 + - + +
210Z ALA* 4.4 2.0 - - - +
212Z VAL* 1.3 79.0 - - + +
214Z LYS* 1.3 67.5 + - - +
216Z LEU* 3.0 19.2 + - + +
217Z ASN* 2.8 24.7 + - - +
223Z LEU* 4.2 20.4 - - + +
226Z THR* 4.7 6.6 - - + +
227Z LEU 4.8 0.7 + - - -
228Z LEU* 3.4 50.2 + - + +
259Z THR 4.3 7.4 - - - +
260Z VAL* 4.3 11.6 - - + +
261Z PRO* 3.9 29.2 - - + -
264Z VAL* 3.7 29.2 - - + +
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Residues in contact with LYS 214 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y ALA* 4.0 17.3 - - + +
211Y ALA* 4.6 15.3 - - - +
214Y LYS* 3.7 49.4 - - + +
210Z ALA 3.0 21.4 + - - +
211Z ALA* 3.7 4.9 - - - +
213Z TYR* 1.3 76.5 - - - +
215Z ALA* 1.3 65.1 + - - +
217Z ASN* 3.0 8.5 + - - +
218Z ASP* 2.9 52.5 + - - +
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Residues in contact with ALA 215 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164Z GLN* 6.3 0.4 - - + -
167Z ALA* 3.8 32.1 - - + +
168Z ASN* 3.9 15.3 - - - +
171Z ALA* 4.0 2.2 - - - -
211Z ALA 2.9 19.1 + - - +
212Z VAL 3.6 4.0 - - - +
214Z LYS* 1.3 76.7 - - - +
216Z LEU* 1.3 66.0 + - - +
218Z ASP* 2.9 22.3 + - - +
219Z HIS* 3.0 15.9 + - + -
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Residues in contact with LEU 216 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Z ALA 5.8 0.2 - - - +
170Z LEU* 5.3 0.9 - - + -
171Z ALA* 4.1 14.8 - - - +
174Z ALA* 4.0 15.7 - - + -
186Z VAL* 4.2 20.2 - - + -
212Z VAL* 2.9 43.8 + - + +
213Z TYR* 3.0 23.3 + - + +
215Z ALA* 1.3 76.7 - - - +
217Z ASN* 1.3 63.7 + - - +
219Z HIS 3.1 4.9 + - - -
221Z VAL* 3.1 68.7 + - + +
223Z LEU* 4.5 13.5 - - + -
226Z THR* 5.1 2.5 - - + +
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Residues in contact with ASN 217 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203Y TYR* 5.7 1.9 - - - -
206Y GLU* 3.4 30.5 + - - +
207Y LYS* 4.4 16.3 + - - +
210Y ALA* 3.5 21.3 - - + +
258Y ARG* 5.8 1.2 + - - +
259Y THR* 3.8 12.3 - - - +
213Z TYR 2.8 15.6 + - - +
214Z LYS* 3.0 8.9 + - - +
216Z LEU* 1.3 73.1 - - - +
218Z ASP* 1.3 59.5 + - - +
220Z HIS* 2.7 28.2 + - - +
221Z VAL 5.0 1.6 - - - +
223Z LEU* 5.4 4.4 - - + +
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Residues in contact with ASP 218 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161W LEU* 4.1 35.9 - - + +
210Y ALA* 5.7 0.2 - - - +
214Z LYS* 2.9 52.2 + - - +
215Z ALA* 2.9 17.4 + - - +
217Z ASN* 1.3 79.5 - - - +
219Z HIS* 1.3 57.4 - - + +
220Z HIS* 3.6 2.4 + - - +
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Residues in contact with HIS 219 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161W LEU* 3.7 20.8 - - + +
165W GLU* 3.0 32.7 + - + -
168Z ASN* 4.1 7.4 + - + -
171Z ALA* 3.0 40.8 - - + +
172Z ARG* 4.1 16.9 + - + +
175Z SER* 4.2 14.9 + - - -
215Z ALA* 3.0 15.9 + - + -
216Z LEU 3.8 5.2 - - - +
217Z ASN 2.8 2.0 + - - -
218Z ASP* 1.3 78.4 - - + +
220Z HIS* 1.3 69.4 + - - +
221Z VAL* 3.0 11.8 + - + +
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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) + - + + + + + -
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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