Contacts of the helix formed by residues 219 - 242 (chain A) in PDB entry 4WLU
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 PRO 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LYS* 5.2 2.5 - - - +
217A ASP 4.3 4.0 - - - +
218A PHE* 1.3 85.7 - - + +
220A GLN* 1.3 66.3 + - - +
221A ASP* 3.3 10.1 - - - +
222A GLN* 3.1 41.7 + - + +
223A LEU* 3.0 18.5 + - - +
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Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A PHE 3.6 1.7 + - - -
219A PRO* 1.3 73.4 - - - +
221A ASP* 1.3 58.8 + - - +
223A LEU* 3.1 12.6 + - + +
224A THR* 2.8 44.0 + - - +
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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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219A PRO* 3.7 17.8 - - - +
220A GLN* 1.3 77.0 - - - +
222A GLN* 1.3 82.8 + - - +
224A THR* 3.7 5.4 + - - +
225A ALA* 3.2 23.4 + - - +
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Residues in contact with GLN 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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184A LEU* 4.0 29.9 - - + +
185A LYS* 5.8 0.2 + - - -
218A PHE* 3.6 26.5 - - + -
219A PRO* 3.1 29.7 + - + +
221A ASP* 1.3 91.0 + - - +
223A LEU* 1.3 58.6 + - - +
225A ALA* 3.4 5.4 + - - +
226A LEU* 2.8 32.6 + - - +
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Residues in contact with LEU 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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209A ILE* 3.7 43.5 - - + -
218A PHE* 4.1 21.3 - - + +
219A PRO 3.0 13.6 + - - +
220A GLN* 3.1 16.1 + - + +
222A GLN* 1.3 78.1 - - - +
224A THR* 1.3 57.2 + - - +
226A LEU* 3.5 6.5 + - + +
227A THR* 2.8 37.9 + - - +
311A PHE* 4.6 22.2 - - + -
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Residues in contact with THR 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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220A GLN* 2.8 29.2 + - - +
221A ASP* 4.1 6.1 - - - -
223A LEU* 1.3 78.0 - - - +
225A ALA* 1.3 57.2 + - - +
227A THR* 3.5 5.8 + - - -
228A GLY* 3.0 25.3 + - - -
311A PHE* 4.6 20.1 - - + -
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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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184A LEU* 6.5 0.2 - - + -
221A ASP 3.2 17.3 + - - +
222A GLN* 3.7 4.9 - - - +
224A THR* 1.3 76.9 - - - +
226A LEU* 1.3 61.2 + - - +
228A GLY* 3.8 1.2 - - - -
229A ARG* 2.9 31.9 + - - +
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Residues in contact with LEU 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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180A PHE* 3.5 39.7 - - + -
181A VAL* 3.8 13.9 - - + +
184A LEU* 4.1 16.1 - - + +
209A ILE* 4.1 14.6 - - + -
218A PHE* 3.7 37.9 - - + -
222A GLN 2.8 21.3 + - - +
223A LEU* 3.6 6.1 - - + +
225A ALA* 1.3 72.9 - - - +
227A THR* 1.3 62.7 + - - +
229A ARG* 3.2 6.5 + - + +
230A ILE* 3.0 42.6 + - + +
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Residues in contact with THR 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 PRO* 4.0 23.5 + - + +
209A ILE* 4.5 8.2 - - - +
223A LEU* 2.8 29.8 + - - +
224A THR* 3.7 5.6 - - - -
225A ALA 3.4 0.2 - - - -
226A LEU* 1.3 75.7 - - - +
228A GLY* 1.3 64.2 + - - +
230A ILE* 3.3 5.2 + - - +
231A GLN* 3.1 31.4 + - - +
311A PHE* 4.0 15.4 - - + -
315A MET* 3.7 31.8 - - + +
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Residues in contact with GLY 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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224A THR 3.0 14.7 + - - -
225A ALA* 3.9 2.7 - - - -
227A THR* 1.3 76.4 - - - +
229A ARG* 1.3 56.6 + - - +
231A GLN* 3.2 13.1 + - - +
232A GLU* 3.0 36.6 + - - +
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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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180A PHE* 3.6 48.1 - - + +
183A GLU* 4.7 8.3 + - - -
225A ALA 2.9 22.0 + - - +
226A LEU* 3.2 8.3 + - + +
228A GLY* 1.3 71.6 - - - +
230A ILE* 1.3 58.1 + - - +
232A GLU* 3.4 2.9 + - - -
233A ALA* 2.9 32.5 + - - +
236A GLU* 5.3 14.8 - - - +
69B SER* 5.3 2.8 + - - -
70B HIS* 4.3 10.9 + - - -
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Residues in contact with ILE 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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173A ASP* 4.1 22.3 - - + +
176A ARG* 4.9 5.4 + - + -
177A ALA* 3.7 28.7 - - + +
180A PHE* 3.8 24.0 - - + -
196A VAL* 5.1 1.1 - - + -
205A ILE* 4.1 20.4 - - + +
207A PRO* 3.7 32.5 - - + -
209A ILE* 4.4 4.5 - - + -
226A LEU* 3.0 36.9 + - + +
227A THR 3.6 5.6 - - - +
229A ARG* 1.3 76.6 - - - +
231A GLN* 1.3 62.7 + - - +
233A ALA* 3.5 12.2 + - - +
234A GLY 5.1 0.2 + - - -
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.9 4.9 + - - -
202A GLY* 3.5 26.0 + - - +
203A LYS* 4.0 19.7 + - - +
205A ILE* 2.9 51.8 + - + +
207A PRO* 4.7 1.8 - - + -
227A THR* 3.1 29.1 + - + +
228A GLY* 3.2 13.8 + - - +
230A ILE* 1.3 75.3 - - - +
232A GLU* 1.3 68.1 + - + +
233A ALA 3.8 0.5 + - - -
234A GLY 5.0 1.6 + - - -
315A MET* 4.0 21.6 - - - +
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Residues in contact with GLU 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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202A GLY* 4.2 15.2 - - - -
203A LYS 5.1 0.3 + - - -
228A GLY* 3.0 19.8 + - - +
229A ARG* 3.7 3.4 - - - +
231A GLN* 1.3 85.2 - - + +
233A ALA* 1.3 63.5 + - - +
234A GLY 3.3 2.7 - - - -
235A THR* 3.0 27.7 + - - +
236A GLU* 2.9 36.2 + - + +
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Residues in contact with ALA 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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176A ARG* 3.5 32.8 - - - +
180A PHE* 4.2 7.9 - - + -
229A ARG* 2.9 18.7 + - - +
230A ILE 3.6 7.4 - - - +
231A GLN 3.4 2.4 - - - -
232A GLU* 1.3 76.7 - - - +
234A GLY* 1.3 62.4 + - - +
236A GLU* 3.2 7.3 + - - +
237A VAL* 3.1 27.4 + - - +
70B HIS* 3.6 14.9 - - + -
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Residues in contact with GLY 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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104A ARG* 3.3 7.0 - - - -
110A ARG* 3.7 11.0 - - - +
176A ARG* 3.5 22.2 - - - +
231A GLN 5.0 0.4 + - - -
232A GLU 3.3 0.8 - - - -
233A ALA* 1.3 78.2 - - - +
235A THR* 1.3 57.3 + - - +
237A VAL* 3.4 4.2 + - - +
238A VAL* 3.1 30.1 + - - +
246A SER* 5.3 0.3 - - - -
247A ALA 5.5 0.2 + - - -
401A LMR 3.7 17.3 - - - +
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Residues in contact with THR 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ARG* 3.0 29.0 + - - +
107A GLY* 5.6 7.6 - - - +
108A MET 5.7 1.3 - - - +
110A ARG* 4.8 2.0 + - - +
232A GLU* 3.0 28.8 + - - +
234A GLY* 1.3 73.0 - - - +
236A GLU* 1.3 65.6 + - - +
238A VAL* 3.3 6.9 + - + +
239A LYS* 2.9 46.2 + - + +
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ARG* 5.3 14.8 - - - +
232A GLU* 2.9 31.3 + - + +
233A ALA* 3.2 10.5 + - - +
235A THR* 1.3 79.4 - - - +
237A VAL* 1.3 57.9 + - + +
239A LYS* 3.4 34.9 + - - +
240A ALA* 2.9 28.2 + - - +
66B ALA* 5.2 1.5 - - - +
70B HIS* 5.5 3.4 - - + +
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Residues in contact with VAL 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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176A ARG* 4.5 6.1 - - - +
233A ALA 3.1 6.1 + - - +
234A GLY 3.9 6.5 - - - +
235A THR 3.3 0.4 - - - -
236A GLU* 1.3 74.4 - - - +
238A VAL* 1.3 65.3 + - - +
240A ALA* 3.2 5.4 + - - +
241A LYS* 2.9 30.5 + - + +
246A SER 4.2 2.9 - - - -
247A ALA* 3.6 33.9 - - + +
63B GLY 4.4 1.3 - - - +
66B ALA* 4.3 4.3 - - + -
67B ASP* 4.2 30.3 - - + +
70B HIS* 3.5 34.3 - - + +
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Residues in contact with VAL 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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104A ARG* 4.1 30.3 - - + +
105A LYS 3.5 9.4 - - - +
106A PRO* 3.2 41.8 - - + +
107A GLY 5.0 0.2 - - - +
108A MET 6.1 0.2 - - - +
234A GLY 3.1 18.3 + - - +
235A THR* 3.3 10.5 + - + +
237A VAL* 1.3 75.9 - - - +
239A LYS* 1.3 60.9 + - + +
241A LYS* 3.2 4.9 + - - +
242A ALA 3.1 17.5 + - - -
243A GLY 4.3 0.3 + - - -
245A GLY 3.9 9.1 - - - +
246A SER* 3.6 27.6 - - - -
401A LMR 4.2 0.4 - - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PRO* 4.6 18.8 - - + +
107A GLY 5.4 2.0 - - - +
235A THR* 2.9 29.7 + - + +
236A GLU* 3.4 37.4 + - - +
238A VAL* 1.3 76.3 - - - +
240A ALA* 1.3 60.8 + - - +
242A ALA* 3.2 16.5 + - - +
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Residues in contact with ALA 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 GLU 2.9 18.5 + - - +
237A VAL 3.2 5.3 + - - +
239A LYS* 1.3 75.4 - - - +
241A LYS* 1.3 60.8 + - - +
242A ALA* 3.6 3.8 + - - +
62B PRO* 4.1 11.2 - - + +
63B GLY* 3.6 19.5 + - - -
66B ALA* 3.9 25.1 - - + -
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Residues in contact with LYS 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 VAL* 2.9 18.4 + - + +
238A VAL 3.2 1.1 + - - +
240A ALA* 1.3 73.8 - - - +
242A ALA* 1.3 69.5 + - - +
243A GLY 3.3 1.3 - - - -
244A ALA* 2.9 40.3 + - + +
245A GLY 3.4 26.7 - - - +
246A SER* 2.7 28.3 + - - +
248A THR* 3.1 24.5 + - - +
38B GLN* 5.0 4.0 + - - +
60B HIS* 5.0 3.5 + - - +
63B GLY* 3.7 33.2 - - - +
64B VAL* 4.5 8.3 - - - +
67B ASP* 3.4 11.9 + - - -
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Residues in contact with ALA 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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106A PRO* 4.2 9.9 - - - -
238A VAL 3.1 8.7 + - - -
239A LYS 3.2 13.4 + - - +
240A ALA 4.4 3.6 - - - +
241A LYS* 1.3 78.8 - - - +
243A GLY* 1.3 56.5 + - - +
58C ILE* 4.3 23.2 - - + +
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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