Contacts of the helix formed by residues 197 - 219 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A HIS* 1.3 86.0 - - - +
198A LEU* 1.3 68.0 + - - +
199A GLU* 3.5 19.2 - - + +
200A HIS* 3.0 26.0 + - - +
201A CYS* 2.9 21.9 + - - +
235A ALA* 5.4 1.6 - - - -
243A TYR* 3.5 13.7 - - - +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 1.3 70.2 - - - +
199A GLU* 1.3 54.5 + - - +
200A HIS 2.9 0.7 + - - -
201A CYS* 2.9 7.5 + - - +
202A GLN* 2.6 37.5 + - - +
233A VAL* 3.4 28.9 - - + +
234A THR* 3.4 3.6 - - - -
235A ALA 3.3 28.7 - - - +
243A TYR* 2.7 55.4 + - + +
247A GLN* 3.5 30.5 - - + +
248A VAL* 4.5 3.1 - - + -
251A ALA* 4.0 8.5 - - + -
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 3.5 15.4 + - + +
198A LEU* 1.3 78.0 - - - +
200A HIS* 1.3 60.5 + - - +
202A GLN* 3.6 12.8 + - - +
203A TYR* 3.2 21.7 + - - +
243A TYR* 4.5 0.4 + - - -
251A ALA* 6.0 0.2 - - - +
364A SO4 6.1 1.8 - - - +
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Residues in contact with HIS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A HIS* 3.2 48.2 + + + -
197A ASP* 3.0 29.0 + - - +
199A GLU* 1.3 75.2 - - - +
201A CYS* 1.3 68.8 + - + +
202A GLN 3.0 1.3 - - - -
203A TYR* 2.8 23.0 + + - +
204A VAL* 2.8 31.2 + - + +
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Residues in contact with CYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 6.0 3.8 - - - -
197A ASP 2.9 7.3 + - - +
198A LEU 2.9 7.8 + - - +
200A HIS* 1.3 81.6 - - + +
202A GLN* 1.3 60.2 + - - +
204A VAL* 3.3 10.5 - - - +
205A THR* 2.8 35.2 + - - -
231A ASN* 4.6 6.5 - - - -
233A VAL* 4.0 21.8 - - + -
234A THR 3.7 24.9 - - - +
235A ALA 5.5 1.6 - - - -
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Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU 2.6 19.8 + - - +
199A GLU* 3.6 11.7 - - - +
201A CYS* 1.3 75.3 - - - +
203A TYR* 1.3 61.3 + - - +
205A THR* 3.5 1.9 + - - -
206A GLU* 2.9 52.3 + - - +
233A VAL* 3.7 14.5 - - + +
251A ALA* 3.0 45.4 - - - +
254A THR* 3.2 21.8 - - - +
255A ALA* 3.5 3.8 - - + -
258A ARG* 4.4 1.2 - - - +
364A SO4 3.3 19.7 + - - -
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU 3.2 10.1 + - - +
200A HIS* 2.8 21.3 + + - +
202A GLN* 1.3 75.4 - - - +
204A VAL* 1.3 60.4 + - + +
206A GLU* 3.5 11.2 + - + +
207A LYS* 2.9 62.6 + - + +
217B ASN* 5.7 3.1 - - - -
218B ASP 5.7 1.4 + - - -
220B HIS* 4.4 32.1 - + + +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 5.6 4.7 - - + -
191A ILE* 4.3 27.8 - - + -
200A HIS* 2.8 38.1 + - + +
201A CYS* 3.3 16.8 - - - +
203A TYR* 1.3 75.9 - - + +
205A THR* 1.3 54.0 + - - +
207A LYS* 3.0 11.5 + - + +
208A VAL* 2.7 43.3 + - + +
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Residues in contact with THR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A CYS* 2.8 25.0 + - - -
202A GLN 3.8 4.3 - - - -
204A VAL* 1.3 74.8 - - - +
206A GLU* 1.3 58.1 + - - +
208A VAL* 3.3 6.3 + - + +
209A LEU* 2.8 60.2 + - + +
230A PRO* 5.8 2.7 - - + -
231A ASN* 3.8 32.1 + - - +
233A VAL* 3.6 20.7 - - + +
255A ALA* 5.0 4.3 - - + -
256A LEU* 5.9 2.2 - - + -
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLN* 2.9 52.6 + - - +
203A TYR* 3.6 11.3 - - + +
205A THR* 1.3 79.2 - - - +
207A LYS* 1.3 64.1 + - - +
209A LEU* 4.7 0.4 - - - -
210A ALA* 3.0 27.2 + - - +
254A THR* 4.4 0.5 - - - +
255A ALA* 3.3 31.8 - - + +
258A ARG* 3.9 26.0 + - + +
259A THR* 3.5 15.9 - - + +
217B ASN* 4.4 7.4 + - - +
220B HIS* 5.1 9.9 + - - -
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER 5.8 0.4 - - - -
160A SER* 5.2 12.0 + - - +
163A ILE* 4.0 29.6 - - + +
203A TYR* 2.9 58.3 + - + +
204A VAL* 3.5 11.1 - - + +
206A GLU* 1.3 75.8 - - - +
208A VAL* 1.3 61.9 + - + +
210A ALA* 3.8 3.3 - - - +
211A ALA* 3.6 17.0 + - - +
214B LYS* 5.6 1.2 - - - -
217B ASN* 4.1 18.3 + - - +
218B ASP* 6.1 2.5 - - - -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 4.3 29.8 - - + +
166A ASN* 5.4 9.9 - - - +
188A PRO* 4.2 15.7 - - + -
189A GLU 4.9 10.5 - - - +
191A ILE* 5.0 9.2 - - + -
204A VAL* 2.7 41.1 + - + +
205A THR* 3.5 7.0 - - - +
207A LYS* 1.3 70.6 - - - +
209A LEU* 1.3 61.8 + - + +
210A ALA 3.1 1.6 - - - -
211A ALA* 2.8 23.1 + - + +
212A VAL* 2.9 27.6 + - + +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 3.9 28.9 - - + -
205A THR* 2.8 47.0 + - + +
206A GLU 4.0 0.2 - - - +
208A VAL* 1.3 73.9 - - + +
210A ALA* 1.3 57.4 + - - +
212A VAL* 3.2 5.6 + - + +
213A TYR* 2.9 44.3 + - + +
228A LEU* 3.9 22.4 - - + -
230A PRO* 4.9 5.8 - - + -
255A ALA 4.6 3.4 - - - +
256A LEU* 4.2 20.6 - - + -
259A THR* 3.8 28.7 - - - +
260A VAL* 4.4 1.6 - - + -
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLU 3.0 11.3 + - - +
207A LYS 3.8 5.2 - - - +
209A LEU* 1.3 77.1 - - - +
211A ALA* 1.3 56.5 + - - +
213A TYR* 4.2 2.8 - - - +
214A LYS* 3.0 30.3 + - - +
259A THR* 4.1 9.8 - - + +
213B TYR 5.8 0.2 - - - +
214B LYS* 3.8 13.4 - - + +
217B ASN* 3.3 41.7 - - + +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 3.6 35.7 - - + +
164A GLN* 5.1 3.6 - - + -
167A ALA* 3.8 5.1 - - + +
207A LYS 3.6 6.3 + - - +
208A VAL* 2.8 9.7 + - + +
210A ALA* 1.3 76.5 - - - +
212A VAL* 1.3 60.0 + - - +
214A LYS* 3.8 5.3 - - - +
215A ALA* 2.9 33.3 + - - +
214B LYS* 4.4 16.1 - - - +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE 6.1 0.2 - - - +
166A ASN* 5.6 2.2 - - - +
167A ALA* 4.3 11.3 - - + +
170A LEU* 3.8 15.3 - - + -
186A VAL* 3.7 19.7 - - + -
188A PRO* 4.0 17.5 - - + -
208A VAL* 2.9 38.6 + - + +
209A LEU* 3.3 11.4 - - - +
211A ALA* 1.3 78.5 - - + +
213A TYR* 1.3 65.6 + - + +
215A ALA* 3.5 2.6 - - - +
216A LEU* 2.9 49.5 + - + +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 5.1 3.1 - - + +
209A LEU* 2.9 31.9 + - + +
210A ALA* 4.5 2.0 - - - +
212A VAL* 1.3 78.7 - - + +
214A LYS* 1.3 66.9 + - - +
216A LEU* 3.0 18.0 + - + +
217A ASN* 2.8 23.9 + - - +
223A LEU* 4.2 22.2 - - + +
226A THR* 4.7 7.0 - - + +
227A LEU 4.9 0.2 - - - -
228A LEU* 3.2 52.4 + - + +
259A THR 4.3 7.2 - - - +
260A VAL* 4.3 11.2 - - + +
261A PRO* 3.9 28.5 - - + -
264A VAL* 3.7 28.9 - - + +
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ALA 3.0 21.7 + - - +
211A ALA 3.8 4.3 - - - +
212A VAL 3.3 0.2 - - - -
213A TYR* 1.3 74.6 - - - +
215A ALA* 1.3 64.7 + - - +
217A ASN* 3.0 8.2 + - - +
218A ASP* 2.9 52.0 + - - +
210B ALA* 4.0 17.3 - - + +
211B ALA* 4.7 15.5 - - - +
214B LYS* 3.7 48.2 - - + +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLN* 6.2 0.4 - - + -
167A ALA* 3.7 31.6 - - + +
168A ASN* 3.9 16.2 - - - +
171A ALA* 4.0 2.2 - - - -
211A ALA 2.9 18.8 + - - +
212A VAL 3.5 4.3 - - - +
214A LYS* 1.3 77.9 - - - +
216A LEU* 1.3 64.9 + - - +
218A ASP* 2.9 23.3 + - - +
219A HIS* 3.1 15.5 + - + -
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 5.2 0.7 - - + -
171A ALA* 4.1 14.8 - - - +
174A ALA* 4.0 15.9 - - + -
186A VAL* 4.1 20.9 - - + -
212A VAL* 2.9 44.3 + - + +
213A TYR* 3.0 20.2 + - + +
215A ALA* 1.3 77.1 - - - +
217A ASN* 1.3 62.2 + - - +
219A HIS 3.1 4.7 + - - -
221A VAL* 3.0 68.2 + - + +
223A LEU* 4.5 13.9 - - + -
226A THR* 5.0 2.5 - - + +
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Residues in contact with ASN 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR 2.8 15.4 + - - +
214A LYS* 3.3 8.7 - - - +
216A LEU* 1.3 72.1 - - - +
218A ASP* 1.3 60.8 + - - +
220A HIS* 2.7 27.6 + - - +
221A VAL 5.0 2.0 - - - +
223A LEU* 5.4 4.2 - - - +
203B TYR* 5.6 1.6 - - - -
206B GLU* 3.4 31.5 + - - +
207B LYS* 4.4 17.0 - - - +
210B ALA* 3.5 21.3 - - + +
258B ARG* 5.8 1.4 + - - +
259B THR* 3.8 11.5 - - - +
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS* 2.9 52.1 + - - +
215A ALA* 2.9 17.7 + - - +
217A ASN* 1.3 79.2 - - - +
219A HIS* 1.3 59.4 + - + +
220A HIS* 3.6 2.3 + - - +
161D LEU* 4.2 36.1 - - + +
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Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASN* 4.0 8.2 + - - +
171A ALA* 3.0 42.7 - - + +
172A ARG* 4.1 16.6 + - + +
175A SER* 4.2 14.4 + - - -
215A ALA* 3.1 15.5 + - - -
216A LEU 3.1 3.1 + - - +
217A ASN 2.8 1.2 + - - -
218A ASP* 1.3 81.0 - - + +
220A HIS* 1.3 69.5 + - - +
221A VAL* 3.0 12.5 + - + +
161D LEU* 3.8 18.8 - - + +
165D GLU* 3.0 32.0 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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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