Contacts of the helix formed by residues 218 - 245 (chain A) in PDB entry 3PWH
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 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLN* 4.3 4.2 + - - +
216A LEU* 3.7 15.4 - - - +
217A PRO* 1.3 83.7 - - - +
219A GLU* 1.3 59.8 + - - +
220A ARG* 3.1 11.1 + - - -
221A ALA* 3.3 16.5 + - - +
222A ARG* 3.7 10.0 + - - +
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Residues in contact with GLU 219 (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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217A PRO* 3.7 24.2 - - + +
218A GLY* 1.3 73.8 - - - +
220A ARG* 1.3 62.6 + - - +
221A ALA 3.3 0.2 - - - -
222A ARG* 3.5 41.9 + - - +
223A SER* 2.8 42.7 + - - +
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Residues in contact with ARG 220 (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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218A GLY* 3.1 3.1 - - - -
219A GLU* 1.3 81.9 + - - +
221A ALA* 1.3 61.0 + - - +
223A SER* 4.3 9.1 + - - -
224A THR* 2.7 38.1 + - - -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A MET* 3.6 22.0 - - - -
214A GLN* 6.0 0.9 - - - +
218A GLY* 3.3 10.5 + - - +
219A GLU 3.3 0.2 - - - -
220A ARG* 1.3 77.5 - - - +
222A ARG* 1.3 61.2 + - - +
224A THR* 3.9 2.7 - - - -
225A LEU* 2.8 34.1 + - - +
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 5.0 5.4 + - + +
211A MET* 2.8 56.3 + - + +
212A GLU* 3.8 16.4 + - - +
214A GLN* 3.9 9.3 - - - +
217A PRO 5.0 0.2 - - - -
218A GLY 3.7 6.9 + - - +
219A GLU* 3.4 40.8 + - - +
221A ALA* 1.3 79.2 - - - +
223A SER* 1.3 57.4 + - - +
225A LEU* 3.2 1.8 + - - +
226A GLN* 2.8 52.8 + - - +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLU* 2.8 31.8 + - - +
220A ARG* 4.3 12.7 + - - -
222A ARG* 1.3 72.9 - - - +
224A THR* 1.3 63.7 + - - +
226A GLN* 3.5 8.8 + - - +
227A LYS* 3.2 30.2 + - - +
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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 ARG* 2.7 29.5 + - - -
221A ALA* 3.9 3.6 - - - -
223A SER* 1.3 76.1 - - - +
225A LEU* 1.3 59.5 + - - +
227A LYS* 3.1 8.2 + - - +
228A GLU* 2.9 43.2 + - + +
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Residues in contact with LEU 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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106A ILE* 4.2 30.1 - - + +
109A PRO* 6.4 1.6 - - + -
204A ALA 4.0 4.9 - - - +
207A GLN* 3.4 35.7 - - + -
208A LEU* 3.6 14.8 - - + -
211A MET* 3.5 20.9 - - + -
221A ALA 2.8 23.0 + - - +
222A ARG 3.6 2.9 - - - +
224A THR* 1.3 74.6 - - - +
226A GLN* 1.3 52.0 + - - +
228A GLU* 2.9 12.5 + - + +
229A VAL* 2.7 44.9 + - + +
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Residues in contact with GLN 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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208A LEU* 4.4 25.0 - - + +
222A ARG* 2.8 40.3 + - - +
223A SER* 3.9 8.2 - - - +
225A LEU* 1.3 71.5 - - - +
227A LYS* 1.3 61.5 + - + +
229A VAL* 3.8 9.8 - - - +
230A HIS* 3.0 23.9 + - - +
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Residues in contact with LYS 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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223A SER* 3.2 15.6 + - - +
224A THR* 3.1 10.2 + - - +
225A LEU 3.0 0.6 - - - -
226A GLN* 1.3 83.9 - - - +
228A GLU* 1.3 61.1 + - - +
229A VAL 3.1 1.1 - - - -
230A HIS* 3.5 21.4 + - + +
231A ALA* 2.9 29.1 + - - +
293A ARG* 3.3 41.7 - - - +
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Residues in contact with GLU 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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102A ARG* 3.3 35.1 + - - -
105A ALA* 4.0 13.3 - - + +
106A ILE* 3.7 21.2 - - + +
224A THR* 2.9 34.2 + - + +
225A LEU* 2.9 13.1 + - + +
227A LYS* 1.3 75.9 - - - +
229A VAL* 1.3 58.2 + - - +
231A ALA* 3.5 4.6 + - - +
232A ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 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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106A ILE* 3.8 14.6 - - + -
200A ILE* 6.4 0.4 - - + -
201A PHE* 4.2 22.7 - - + -
204A ALA* 3.8 28.5 - - + -
205A ARG* 5.0 10.3 - - - +
208A LEU* 6.1 4.5 - - + -
225A LEU* 2.7 29.4 + - + +
226A GLN* 3.8 9.0 - - - +
228A GLU* 1.3 75.4 - - - +
230A HIS* 1.3 55.6 + - - +
231A ALA 3.2 0.2 - - - -
232A ALA* 3.1 1.5 + - - +
233A LYS* 2.7 36.1 + - + +
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Residues in contact with HIS 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 GLN 3.0 20.5 + - - +
227A LYS* 3.2 26.2 + - + +
229A VAL* 1.3 76.5 - - - +
231A ALA* 1.3 54.8 + - - +
233A LYS* 4.5 2.5 - - - -
234A SER* 2.8 38.7 + - - -
291A ARG* 2.9 59.1 + - - +
292A ILE* 4.9 4.9 - - + -
293A ARG* 5.1 11.6 + - - -
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Residues in contact with ALA 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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102A ARG* 3.3 32.0 - - - +
227A LYS 2.9 16.1 + - - +
228A GLU 3.8 0.9 - - - +
229A VAL 3.2 0.2 - - - -
230A HIS* 1.3 76.7 - - + +
232A ALA* 1.3 60.5 + - - +
234A SER* 3.5 6.6 + - - -
235A ALA* 2.9 27.7 + - - +
292A ILE* 5.2 7.9 - - + -
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Residues in contact with ALA 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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102A ARG* 3.8 28.0 - - + +
106A ILE* 3.9 15.5 - - + -
197A TYR* 3.3 11.6 - - - -
200A ILE* 4.1 15.3 - - + -
201A PHE* 3.9 5.4 - - + -
228A GLU 3.0 17.3 + - - +
229A VAL* 3.5 4.9 - - - +
231A ALA* 1.3 74.8 - - - +
233A LYS* 1.3 60.7 + - - +
235A ALA* 3.1 1.6 + - - +
236A ALA 2.8 22.9 + - - -
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Residues in contact with LYS 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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201A PHE* 3.3 26.4 - - + -
205A ARG* 6.3 0.7 - - - +
229A VAL* 2.7 23.4 + - + +
230A HIS* 3.8 1.8 - - - +
232A ALA* 1.3 70.9 - - - +
234A SER* 1.3 64.3 + - - +
236A ALA* 3.0 6.2 + - + +
237A ILE* 2.9 38.3 + - + +
291A ARG* 3.5 31.7 - - - +
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Residues in contact with SER 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 HIS* 2.8 29.2 + - - -
231A ALA* 3.7 5.4 - - - -
232A ALA 3.3 0.2 - - - -
233A LYS* 1.3 75.8 - - - +
235A ALA* 1.3 59.2 + - - +
237A ILE* 3.4 7.9 + - - +
238A ILE* 3.0 29.4 + - - +
287A ILE* 4.4 1.7 - - - +
288A TYR* 6.6 0.4 - - - -
291A ARG* 2.8 44.2 + - - +
292A ILE* 4.0 13.9 - - - +
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Residues in contact with ALA 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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95A LEU* 5.8 0.3 - - - +
98A ILE* 3.8 24.7 - - + -
102A ARG* 4.3 4.0 - - + -
197A TYR* 3.2 20.4 + - + +
231A ALA 2.9 16.1 + - - +
232A ALA* 3.3 12.1 - - - +
233A LYS 3.1 0.2 - - - -
234A SER* 1.3 75.4 - - - +
236A ALA* 1.3 64.1 + - - +
238A ILE* 3.1 22.7 + - + +
239A ALA* 3.1 11.6 + - - +
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Residues in contact with ALA 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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197A TYR* 3.4 37.6 + - + -
201A PHE* 4.5 6.1 - - + -
232A ALA 2.8 7.6 + - - +
233A LYS* 3.0 13.7 + - + +
235A ALA* 1.3 76.9 - - - +
237A ILE* 1.3 59.2 + - + +
239A ALA* 3.5 1.8 + - - +
240A GLY* 2.9 26.9 + - - -
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Residues in contact with ILE 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 LYS* 2.9 27.1 + - + +
234A SER* 3.7 6.5 - - - +
235A ALA 3.2 0.2 - - - -
236A ALA* 1.3 77.2 - - + +
238A ILE* 1.3 60.4 - - - +
240A GLY* 3.9 1.7 - - - +
241A LEU* 3.2 32.2 + - + +
287A ILE* 3.5 19.7 - - + -
291A ARG* 3.7 39.3 - - + +
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Residues in contact with ILE 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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45A VAL* 6.2 0.4 - - + -
48A LEU* 4.2 4.9 - - + -
95A LEU* 4.0 21.7 - - + +
98A ILE* 5.6 7.2 - - + -
234A SER* 3.0 20.0 - - - +
235A ALA* 3.1 16.7 + - + +
237A ILE* 1.3 76.4 - - - +
239A ALA* 1.3 65.7 + - - +
241A LEU* 3.3 13.8 + - - +
242A PHE* 3.4 10.6 + - - +
280A ASN* 4.9 1.4 + - - -
284A ASN* 3.6 27.8 - - - +
287A ILE* 4.0 19.3 - - + -
288A TYR* 3.3 35.4 - - + +
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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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95A LEU* 4.0 31.4 - - + +
190A LEU* 4.6 6.0 - - + +
193A MET* 4.5 14.4 - - + -
197A TYR* 4.5 17.0 - - + +
235A ALA 3.1 10.3 + - - +
236A ALA 4.1 2.9 - - - +
238A ILE* 1.3 79.2 - - - +
240A GLY* 1.3 62.9 + - - +
242A PHE* 3.3 16.1 + - - +
243A ALA* 3.4 9.4 + - - +
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Residues in contact with GLY 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 ALA 2.9 18.7 + - - -
237A ILE* 4.1 2.2 - - - -
238A ILE 3.2 0.2 - - - -
239A ALA* 1.3 78.4 - - - +
241A LEU* 1.3 62.7 + - - +
243A ALA* 3.6 5.4 + - - +
244A LEU* 3.1 24.5 + - - +
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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 ILE* 3.2 23.4 + - + +
238A ILE* 3.3 9.0 + - - +
240A GLY* 1.3 73.6 - - - +
242A PHE* 1.3 60.8 + - - +
244A LEU* 3.6 21.4 - - + -
245A CYS* 2.9 41.0 + - - -
280A ASN* 3.6 11.2 - - - +
283A VAL* 3.7 33.7 - - + -
284A ASN* 5.4 0.2 - - - +
287A ILE* 4.1 17.9 - - + -
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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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48A LEU* 6.0 0.9 - - + -
88A ALA* 3.8 13.9 - - + -
91A SER* 4.0 21.1 - - - -
92A ILE* 3.3 34.5 - - + -
95A LEU* 3.6 26.7 - - + -
186A VAL* 4.8 10.8 - - + -
190A LEU* 4.4 10.3 - - + -
238A ILE 3.4 5.0 + - - +
239A ALA 3.3 10.9 + - - +
240A GLY 3.2 0.4 - - - -
241A LEU* 1.3 76.9 - - - +
243A ALA* 1.3 63.2 + - - +
245A CYS 2.8 17.2 + - - -
246A TRP* 2.9 53.8 + + + -
280A ASN* 2.9 29.5 - - - +
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Residues in contact with ALA 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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190A LEU* 3.7 33.9 - - + -
239A ALA 3.4 5.0 + - - +
240A GLY* 4.0 7.4 - - - +
242A PHE* 1.3 84.8 - - - +
244A LEU* 1.3 57.6 + - - +
246A TRP* 4.8 1.6 - - - -
247A LEU* 2.9 50.2 + - + +
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Residues in contact with LEU 244 (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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240A GLY 3.1 19.8 + - - +
241A LEU* 3.6 25.6 - - + +
242A PHE 3.1 0.2 - - - -
243A ALA* 1.3 76.5 - - - +
245A CYS* 1.3 61.6 + - - +
246A TRP 3.5 0.2 - - - -
247A LEU* 5.3 2.7 - - - -
248A PRO* 3.8 10.6 - - + +
276A LEU* 3.7 13.9 - - - +
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Residues in contact with CYS 245 (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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241A LEU* 2.9 29.9 + - - +
242A PHE 2.8 5.3 + - - +
244A LEU* 1.3 87.2 - - - +
246A TRP* 1.3 59.1 + - - +
248A PRO* 4.4 0.2 - - - -
273A ALA 5.2 0.9 - - - +
276A LEU* 3.6 39.2 - - - +
277A ALA* 3.2 27.5 + - - +
279A THR* 5.3 4.3 - - - -
280A ASN* 3.8 24.5 - - + -
283A VAL* 5.7 5.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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