Contacts of the helix formed by residues 220 - 243 (chain A) in PDB entry 1X0X
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 GLY 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ASP* 5.0 3.2 - - - +
219A PHE* 1.3 78.4 - - - +
221A ASP* 1.3 61.7 + - - -
222A ASN* 3.5 2.2 - - - -
223A THR* 3.4 7.2 + - - -
224A LYS* 2.9 28.7 + - - +
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Residues in contact with ASP 221 (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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220A GLY* 1.3 69.3 - - - -
222A ASN* 1.3 59.5 + - - +
224A LYS* 3.2 2.3 + - - +
225A ALA* 2.7 37.0 + - - +
266A TYR* 2.8 38.6 + - - +
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Residues in contact with ASN 222 (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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220A GLY 3.5 0.6 - - - -
221A ASP* 1.3 78.6 - - - +
223A THR* 1.3 62.5 + - - +
225A ALA* 3.6 6.1 + - - +
226A ALA* 3.1 21.8 + - - +
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Residues in contact with THR 223 (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 CYS* 3.9 22.7 - - + -
219A PHE* 3.5 43.5 - - + +
220A GLY 3.4 10.8 + - - -
221A ASP 3.1 0.6 - - - -
222A ASN* 1.3 77.7 - - - +
224A LYS* 1.3 67.2 + - - +
226A ALA* 2.9 17.4 + - + +
227A VAL* 2.9 15.1 + - + +
339A ILE* 4.7 2.9 - - + -
342A LEU* 4.6 9.4 - - + -
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Residues in contact with LYS 224 (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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211A ALA* 4.1 18.6 - - + +
214A CYS* 5.5 3.3 - - + +
215A ASP* 2.7 40.8 + - - +
220A GLY 2.9 18.2 + - - +
221A ASP* 3.7 3.6 - - - +
223A THR* 1.3 76.2 - - - +
225A ALA* 1.3 62.8 + - - +
227A VAL* 3.2 9.2 + - - +
228A ILE* 2.9 29.9 + - + +
265A CYS 3.1 26.7 + - - +
266A TYR* 3.4 49.8 + - + +
271A ARG* 3.9 3.8 - - - +
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Residues in contact with ALA 225 (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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221A ASP 2.7 21.1 + - - +
222A ASN* 3.8 7.2 - - - +
224A LYS* 1.3 71.8 - - - +
226A ALA* 1.3 58.6 + - - +
228A ILE* 3.1 11.5 + - - +
229A ARG* 2.8 31.3 + - - +
266A TYR* 5.2 2.1 + - - +
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Residues in contact with ALA 226 (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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222A ASN 3.1 13.4 + - - +
223A THR* 2.9 13.0 + - - +
225A ALA* 1.3 75.7 - - - +
227A VAL* 1.3 57.6 + - - +
229A ARG* 3.1 10.0 + - - +
230A LEU* 2.8 45.1 + - + +
342A LEU* 5.1 8.7 - - + -
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Residues in contact with VAL 227 (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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207A VAL* 3.7 16.9 - - + +
210A GLY* 4.2 4.5 - - - -
211A ALA* 3.8 28.0 - - + +
214A CYS* 3.7 29.8 - - + -
223A THR 2.9 17.4 + - - +
224A LYS* 3.6 10.1 - - - +
226A ALA* 1.3 76.9 - - - +
228A ILE* 1.3 58.5 + - + +
230A LEU* 3.9 1.4 - - - +
231A GLY* 2.9 27.4 + - - -
321A LEU* 4.5 11.3 - - + +
338A PHE* 4.4 2.0 - - + -
342A LEU* 3.8 24.9 - - + -
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Residues in contact with ILE 228 (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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207A VAL* 4.3 5.6 - - - -
224A LYS* 2.9 27.9 + - + +
225A ALA* 3.1 10.5 + - - +
227A VAL* 1.3 76.3 - - + +
229A ARG* 1.3 59.4 + - - +
231A GLY* 3.4 0.7 + - - -
232A LEU* 2.9 30.2 + - + +
258A VAL* 5.2 4.7 - - + +
261A LEU* 3.7 24.4 - - + +
262A ILE* 3.4 39.3 - - + -
265A CYS* 3.8 37.5 - - + -
266A TYR* 4.4 7.4 - - + -
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Residues in contact with ARG 229 (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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225A ALA 2.8 16.8 + - - +
226A ALA* 3.1 10.0 + - - +
228A ILE* 1.3 78.6 - - - +
230A LEU* 1.3 80.9 + - - +
232A LEU* 3.2 9.9 + - + +
233A MET* 3.0 49.7 + - - +
347A GLU* 4.0 9.5 + - - +
348A HIS* 5.4 3.8 - - - -
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Residues in contact with LEU 230 (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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226A ALA* 2.8 27.0 + - + +
229A ARG* 1.3 95.4 - - - +
231A GLY* 1.3 64.9 + - - +
233A MET* 3.3 16.8 + - + +
234A GLU* 3.0 28.0 + - - +
321A LEU* 4.1 13.9 - - + -
342A LEU* 3.7 35.9 - - + +
345A HIS* 3.8 41.1 + - + +
346A PRO 4.7 1.8 - - - +
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Residues in contact with GLY 231 (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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207A VAL* 3.9 20.2 - - - -
227A VAL 2.9 17.7 + - - -
228A ILE 3.8 1.1 - - - -
230A LEU* 1.3 79.5 - - - +
232A LEU* 1.3 56.3 + - - +
234A GLU* 3.1 6.7 + - - +
235A MET* 2.8 38.6 + - - +
321A LEU* 4.5 10.3 - - - +
322A PHE* 4.3 1.0 - - - -
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Residues in contact with LEU 232 (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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228A ILE* 2.9 19.8 + - + +
229A ARG* 3.5 8.7 - - + +
231A GLY* 1.3 71.3 - - - +
233A MET* 1.3 66.4 + - - +
235A MET* 3.2 10.4 + - + +
236A ILE* 3.0 41.1 + - + +
252A PHE* 3.9 38.1 - - + +
253A LEU* 5.5 6.5 - - + -
258A VAL* 4.7 22.9 - - + +
261A LEU* 3.9 19.4 - - + +
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Residues in contact with MET 233 (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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229A ARG* 3.0 33.8 + - - +
230A LEU* 3.4 19.1 - - + +
232A LEU* 1.3 80.0 - - - +
234A GLU* 1.3 61.7 + - - +
236A ILE* 3.7 6.7 + - - +
237A ALA* 3.3 21.5 + - - +
345A HIS* 3.6 23.8 - - - -
346A PRO 3.7 9.9 - - - +
347A GLU* 3.1 29.4 - - - +
348A HIS* 4.0 7.6 - - - +
349A MET* 3.9 25.6 - - + +
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Residues in contact with GLU 234 (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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230A LEU 3.0 16.9 + - - +
231A GLY 3.1 7.6 + - - +
233A MET* 1.3 75.5 - - - +
235A MET* 1.3 56.8 + - - +
237A ALA 3.5 0.2 + - - -
238A PHE* 2.8 33.4 + - - +
319A PHE* 3.5 16.4 - - + +
320A PRO* 3.2 7.7 - - - +
321A LEU* 2.9 28.0 + - - -
322A PHE* 3.0 48.4 + - + +
345A HIS* 2.7 27.9 + - - +
349A MET* 3.9 16.8 - - + -
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Residues in contact with MET 235 (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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200A CYS* 3.8 46.9 - - + +
203A LEU* 3.8 32.2 - - + +
204A LYS* 4.3 4.5 - - + +
207A VAL* 4.2 5.4 - - - -
231A GLY 2.8 20.8 + - - +
232A LEU* 3.5 8.5 - - + +
234A GLU* 1.3 73.9 - - - +
236A ILE* 1.3 60.7 + - - +
238A PHE* 3.7 1.0 - - - +
239A ALA* 2.8 31.5 + - - +
252A PHE* 4.0 11.5 - - + -
256A CYS 5.3 0.4 - - - +
257A GLY* 5.2 4.3 - - - +
261A LEU* 3.7 39.5 - - + -
322A PHE* 4.0 7.6 - - + -
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Residues in contact with ILE 236 (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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232A LEU* 3.0 31.4 + - + +
233A MET* 4.1 5.4 - - - +
235A MET* 1.3 74.6 - - - +
237A ALA* 1.3 59.6 + - - +
239A ALA* 3.2 2.4 + - - +
240A LYS* 2.9 53.9 + - + +
249A SER* 3.7 27.4 - - - +
252A PHE* 3.7 40.8 - - + -
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Residues in contact with ALA 237 (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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233A MET 3.3 16.5 + - - +
234A GLU 3.7 3.6 - - - +
236A ILE* 1.3 81.1 - - - +
238A PHE* 1.3 60.3 + - - +
240A LYS* 3.5 7.4 + - - +
241A LEU* 3.1 27.6 + - + +
319A PHE* 4.1 4.5 - - + -
349A MET* 3.8 44.0 - - + +
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Residues in contact with PHE 238 (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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129A LEU* 4.6 5.4 - - + -
199A ILE* 4.6 14.8 - - + -
203A LEU* 3.8 19.3 - - + -
234A GLU 2.8 22.4 + - - +
235A MET 3.7 2.9 - - - +
237A ALA* 1.3 70.4 - - - +
239A ALA* 1.3 69.7 + - - +
241A LEU 4.6 0.2 - - - +
242A PHE* 3.1 61.8 + + + +
306A LEU* 3.7 28.7 - - + -
309A ILE* 4.3 15.5 - - + -
310A LEU* 4.0 17.0 - - + -
319A PHE* 3.6 24.0 - + + -
322A PHE* 4.0 16.4 - + + -
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Residues in contact with ALA 239 (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 ILE* 3.9 20.0 - - + -
235A MET 2.8 18.5 + - - +
236A ILE 3.6 4.0 - - - +
238A PHE* 1.3 81.0 - - - +
240A LYS* 1.3 57.7 + - - +
243A CYS* 2.9 45.1 + - - +
247A VAL* 3.8 11.7 - - + -
252A PHE* 3.6 20.4 - - + -
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Residues in contact with LYS 240 (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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236A ILE* 2.9 39.7 + - + +
237A ALA* 3.8 6.7 - - - +
239A ALA* 1.3 77.7 - - - +
241A LEU* 1.3 62.5 + - + +
243A CYS 4.3 7.3 - - - +
247A VAL* 3.8 29.5 - - + +
249A SER* 3.7 11.3 + - - +
1003A SO4 3.1 34.1 + - - -
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Residues in contact with LEU 241 (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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237A ALA* 3.1 18.5 + - + +
238A PHE 4.6 0.2 - - - -
240A LYS* 1.3 80.9 - - + +
242A PHE* 1.3 87.4 + - + +
243A CYS 3.8 2.6 + - - +
315A LEU* 4.0 21.5 - - + -
318A LYS* 6.2 0.4 - - + -
319A PHE* 4.3 15.9 - - + -
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Residues in contact with PHE 242 (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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128A GLY* 5.4 1.6 - - - -
129A LEU* 3.8 38.7 + - + +
238A PHE* 3.1 48.1 + + + +
241A LEU* 1.3 97.6 - - + +
243A CYS* 1.3 62.1 + - - +
244A SER* 3.9 2.3 + - - -
309A ILE* 3.4 27.1 - - + -
310A LEU* 3.7 23.3 - - + -
313A LYS* 3.7 27.6 - - + -
315A LEU* 4.3 15.3 - - + -
319A PHE* 4.6 0.2 - + - -
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Residues in contact with CYS 243 (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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129A LEU* 4.2 16.4 - - - -
131A LEU* 5.7 2.0 - - - -
195A ASP* 4.7 19.7 - - + -
196A THR 5.0 0.4 - - - -
199A ILE* 4.2 18.4 - - - -
239A ALA* 2.9 42.1 + - - +
240A LYS 4.3 8.5 - - - +
241A LEU 3.6 2.3 - - - +
242A PHE* 1.3 74.4 - - - +
244A SER* 1.3 65.3 + - - +
245A GLY 3.6 5.9 - - - +
247A VAL* 3.6 15.3 - - + +
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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