Contacts of the helix formed by residues 197 - 219 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193Y ASP 4.8 6.3 + - - -
198Y LEU* 1.3 62.1 + - - +
199Y GLU* 3.3 19.1 + - - +
200Y HIS* 2.8 29.4 + - - +
201Y CYS* 2.7 36.4 + - - +
234Y THR 5.0 3.1 - - - -
241Y LYS* 3.4 39.7 - - + +
243Y TYR* 3.2 21.3 + - + +
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Residues in contact with LEU 198 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Y ASP* 1.3 79.4 + - - +
199Y GLU* 1.3 57.9 + - - +
200Y HIS 2.9 0.3 + - - -
201Y CYS* 3.1 0.3 + - - -
202Y GLN* 2.8 31.9 + - - +
233Y VAL* 3.4 26.9 - - + +
234Y THR* 3.7 15.4 - - - -
243Y TYR* 3.1 55.4 + - + +
247Y GLN* 4.0 20.2 - - + -
248Y VAL* 4.3 0.7 - - - +
251Y ALA* 3.3 35.0 - - + -
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Residues in contact with GLU 199 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Y ASP* 3.3 10.4 + - - +
198Y LEU* 1.3 79.6 - - - +
200Y HIS* 1.3 59.7 + - - +
202Y GLN* 3.6 11.7 - - - +
203Y TYR* 3.3 21.8 + - - +
243Y TYR* 4.7 0.2 + - - -
364Y SO4 4.6 16.8 + - - +
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Residues in contact with HIS 200 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193Y ASP* 3.5 38.8 + - - +
197Y ASP* 2.8 28.6 + - - +
199Y GLU* 1.3 75.7 - - - +
201Y CYS* 1.3 66.8 + - - -
202Y GLN 3.0 2.0 + - - -
203Y TYR* 3.0 13.5 + + - +
204Y VAL* 3.0 42.7 + - + +
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Residues in contact with CYS 201 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Y VAL* 4.3 21.7 - - - +
191Y ILE 5.2 3.8 - - - -
193Y ASP 6.0 3.8 - - - -
197Y ASP 2.7 16.9 + - - +
198Y LEU 3.8 3.4 - - - +
200Y HIS* 1.3 77.3 - - + +
202Y GLN* 1.3 57.9 + - - +
204Y VAL* 3.5 7.8 + - - +
205Y THR* 2.7 35.5 + - - -
231Y ASN* 4.6 4.7 - - - -
232Y MET 4.7 1.1 - - - -
233Y VAL* 3.8 12.8 - - + -
234Y THR* 3.8 30.1 - - - +
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Residues in contact with GLN 202 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198Y LEU 2.8 17.2 + - - +
199Y GLU* 3.6 13.5 - - - +
201Y CYS* 1.3 76.7 - - - +
203Y TYR* 1.3 65.9 + - - +
205Y THR* 2.9 15.2 + - - -
206Y GLU* 2.7 47.7 + - - +
233Y VAL* 3.3 12.9 - - + +
251Y ALA* 3.2 34.9 - - + +
254Y THR* 3.3 13.1 - - - +
255Y ALA* 3.9 4.6 - - + +
364Y SO4 3.0 33.7 + - - -
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Residues in contact with TYR 203 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199Y GLU 3.3 11.3 + - - +
200Y HIS* 3.0 16.3 + + - +
202Y GLN* 1.3 79.6 - - - +
204Y VAL* 1.3 68.8 + - + +
206Y GLU* 3.4 16.7 + - + +
207Y LYS* 3.3 54.2 + - + +
217Z ASN* 5.7 2.2 - - - -
220Z HIS* 4.8 24.7 - + + -
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Residues in contact with VAL 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163Y ILE* 5.9 2.0 - - + -
190Y VAL* 4.7 17.3 - - + -
200Y HIS* 3.0 40.1 + - + +
201Y CYS* 3.7 8.5 - - - +
203Y TYR* 1.3 80.0 - - + +
205Y THR* 1.3 65.7 + - - +
207Y LYS* 2.9 21.9 + - + +
208Y VAL* 3.0 32.8 + - + +
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Residues in contact with THR 205 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Y VAL* 4.4 10.0 - - + +
201Y CYS* 2.7 22.2 + - - -
202Y GLN 2.9 9.1 + - - -
204Y VAL* 1.3 75.8 - - - +
206Y GLU* 1.3 57.7 + - - +
208Y VAL* 3.6 6.9 + - - +
209Y LEU* 2.9 54.6 + - + +
230Y PRO* 5.9 2.2 - - + -
231Y ASN* 4.0 21.0 + - - +
233Y VAL* 3.3 27.1 - - + +
255Y ALA* 4.4 7.2 - - + -
256Y LEU* 5.7 2.0 - - + -
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Residues in contact with GLU 206 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202Y GLN* 2.7 42.4 + - - +
203Y TYR* 3.7 17.6 - - + +
204Y VAL 3.1 0.2 - - - -
205Y THR* 1.3 72.6 - - - +
207Y LYS* 1.3 66.6 + - + +
209Y LEU* 3.4 1.1 + - - -
210Y ALA 3.1 14.0 + - - -
255Y ALA* 3.2 25.8 - - + +
258Y ARG* 3.2 28.0 + - - +
259Y THR* 3.2 26.3 - - + +
364Y SO4 5.3 0.2 + - - -
217Z ASN* 3.4 13.5 + - - +
220Z HIS* 5.3 6.9 + - - -
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Residues in contact with LYS 207 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159Y SER 6.1 0.2 - - - -
160Y SER* 4.6 15.9 + - - +
163Y ILE* 4.6 19.1 - - + +
203Y TYR* 3.3 53.2 + - + +
204Y VAL* 2.9 13.1 + - + +
206Y GLU* 1.3 73.1 - - + +
208Y VAL* 1.3 60.2 + - + +
209Y LEU 2.9 3.4 - - - -
210Y ALA* 2.7 26.5 + - - +
211Y ALA* 3.0 12.7 + - - +
217Z ASN* 4.4 15.7 - - - +
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Residues in contact with VAL 208 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163Y ILE* 3.9 33.4 - - + +
166Y ASN* 6.3 0.2 - - + -
188Y PRO* 4.3 14.1 - - + -
189Y GLU* 3.5 40.8 - - - +
190Y VAL* 5.0 1.1 - - + -
204Y VAL* 3.0 36.3 + - + +
205Y THR* 3.9 6.7 - - - +
207Y LYS* 1.3 74.1 - - + +
209Y LEU* 1.3 57.8 + - + +
211Y ALA* 3.8 2.1 - - - +
212Y VAL* 2.9 31.4 + - + +
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Residues in contact with LEU 209 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188Y PRO* 4.1 18.2 - - + -
205Y THR* 2.9 42.3 + - + +
206Y GLU 3.8 1.1 - - - +
207Y LYS 2.8 0.6 + - - -
208Y VAL* 1.3 77.2 - - + +
210Y ALA* 1.3 63.5 + - - +
211Y ALA 3.4 0.4 - - - -
212Y VAL* 3.9 3.1 - - + +
213Y TYR* 3.3 42.5 + - + +
228Y LEU* 3.9 29.8 - - + -
230Y PRO* 5.1 4.7 - - + -
255Y ALA 4.8 2.7 - - - +
256Y LEU* 3.8 23.3 - - + -
259Y THR* 3.4 29.9 - - - +
260Y VAL* 4.0 2.9 - - + -
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Residues in contact with ALA 210 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206Y GLU 3.1 12.4 + - - +
207Y LYS* 2.7 12.7 + - - +
209Y LEU* 1.3 71.0 - - - +
211Y ALA* 1.3 68.1 + - - +
212Y VAL 3.1 0.4 - - - -
213Y TYR* 4.0 2.0 - - - +
214Y LYS* 2.9 29.1 + - - +
259Y THR* 4.4 8.1 - - + -
214Z LYS* 4.0 15.8 - - + +
217Z ASN* 3.5 28.9 - - + +
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Residues in contact with ALA 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Y ILE* 3.4 35.9 - - + +
164Y GLN* 5.1 2.0 - - - +
167Y ALA* 3.4 14.1 - - + +
207Y LYS 3.0 8.9 + - - +
208Y VAL 3.8 2.5 - - - +
210Y ALA* 1.3 77.6 - - - +
212Y VAL* 1.3 51.7 + - - +
214Y LYS* 3.5 4.3 - - - +
215Y ALA* 2.8 35.2 + - - +
214Z LYS* 4.6 12.7 - - - +
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Residues in contact with VAL 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163Y ILE* 5.9 0.7 - - + -
166Y ASN* 6.2 0.7 - - + -
167Y ALA* 3.9 20.6 - - + +
170Y LEU* 4.9 8.3 - - + -
186Y VAL* 3.6 22.4 - - + -
188Y PRO* 4.2 17.7 - - + -
208Y VAL* 2.9 23.1 + - + +
209Y LEU* 4.0 7.2 - - + +
210Y ALA 3.1 0.6 - - - -
211Y ALA* 1.3 73.4 - - + +
213Y TYR* 1.3 67.3 + - + +
214Y LYS 3.1 1.6 - - - -
215Y ALA* 3.2 6.3 + - - +
216Y LEU* 2.8 52.2 + - + +
228Y LEU* 5.4 0.4 - - + -
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Residues in contact with TYR 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Y VAL* 4.9 0.9 - - + +
209Y LEU* 3.3 30.2 + - + +
210Y ALA* 4.7 1.3 - - - +
212Y VAL* 1.3 79.6 - - + +
214Y LYS* 1.3 63.7 + - - +
216Y LEU* 3.9 16.5 - - + +
217Y ASN* 3.4 19.1 + - - +
223Y LEU* 3.6 28.7 - - + +
226Y THR* 4.7 8.1 - - + +
228Y LEU* 2.7 52.0 - - + +
259Y THR 4.3 2.9 - - - +
260Y VAL* 3.6 31.0 - - + +
261Y PRO* 3.6 26.4 - - + +
264Y VAL* 3.4 23.3 - - + +
210Z ALA* 5.8 0.2 - - - +
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Residues in contact with LYS 214 (chain Y).
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 2.9 20.8 + - - +
211Y ALA 3.5 3.4 - - - +
213Y TYR* 1.3 76.4 - - - +
215Y ALA* 1.3 56.8 + - - +
217Y ASN* 2.8 23.9 + - - +
218Y ASP* 2.9 45.9 + - - +
164Z GLN* 5.5 6.5 - - - +
207Z LYS 5.7 1.1 - - - -
210Z ALA* 3.8 17.5 - - + +
211Z ALA* 4.4 19.7 - - - +
214Z LYS* 3.7 49.5 - - + +
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Residues in contact with ALA 215 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Y ALA* 3.3 35.7 - - + +
168Y ASN* 3.8 12.1 - - - +
171Y ALA* 4.0 2.2 - - + -
211Y ALA 2.8 19.7 + - - +
212Y VAL 3.2 6.5 - - - +
214Y LYS* 1.3 75.3 - - - +
216Y LEU* 1.3 62.8 + - - +
217Y ASN 2.9 1.7 + - - -
218Y ASP* 2.9 16.1 + - - -
219Y HIS* 2.8 24.5 - - - -
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Residues in contact with LEU 216 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170Y LEU 4.2 0.4 - - - +
171Y ALA* 3.9 12.1 - - + +
174Y ALA* 3.6 21.8 - - + -
186Y VAL* 4.1 17.9 - - + -
212Y VAL* 2.8 46.3 + - + +
213Y TYR* 3.9 27.4 - - + +
214Y LYS 3.3 0.2 - - - -
215Y ALA* 1.3 73.1 - - - +
217Y ASN* 1.3 56.7 + - - +
219Y HIS 3.9 0.4 - - - -
220Y HIS 3.3 2.8 + - - -
221Y VAL* 2.8 71.6 + - + +
223Y LEU* 4.2 13.0 - - + -
226Y THR* 5.4 2.5 - - + +
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Residues in contact with ASN 217 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213Y TYR 3.4 12.3 + - - +
214Y LYS 2.8 11.4 + - - +
216Y LEU* 1.3 77.7 - - - +
218Y ASP* 1.3 64.5 + - - +
219Y HIS 3.0 1.3 - - - -
220Y HIS* 2.8 21.9 + - - +
221Y VAL 4.9 0.4 - - - +
223Y LEU* 5.4 9.2 - - + +
203Z TYR* 5.3 6.1 + - - -
206Z GLU* 4.0 13.4 + - - +
207Z LYS* 4.2 20.8 + - - +
210Z ALA* 3.3 33.5 - - + +
258Z ARG* 5.1 4.0 + - - +
259Z THR* 4.1 10.9 - - - +
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Residues in contact with ASP 218 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X LEU* 3.3 37.2 - - + +
164X GLN* 5.7 2.2 + - - -
168Y ASN* 4.5 5.6 - - - +
214Y LYS* 2.9 52.7 + - - +
215Y ALA* 2.9 12.3 + - - +
217Y ASN* 1.3 79.2 - - - +
219Y HIS* 1.3 62.6 + - + +
220Y HIS* 3.5 1.6 + - - +
203Z TYR* 5.3 4.5 + - - -
207Z LYS* 6.2 1.8 - - - -
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Residues in contact with HIS 219 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X LEU* 4.5 15.6 - - + +
165X GLU* 2.8 29.7 + - - -
168Y ASN* 3.3 37.8 + - - -
171Y ALA* 3.5 15.1 - - + +
172Y ARG* 3.7 15.9 + - + +
175Y SER* 4.5 10.7 + - - +
215Y ALA 2.8 29.2 + - - +
217Y ASN 3.0 0.8 - - - -
218Y ASP* 1.3 83.0 - - + +
220Y HIS* 1.3 71.8 + - - +
221Y VAL* 3.4 16.5 + - + +
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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