Contacts of the helix formed by residues 216 - 245 (chain A) in PDB entry 3GIA
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 ASN 216 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 5.4 2.0 - - - +
215A GLU* 1.3 73.5 - - + +
217A PRO* 1.4 63.1 - - - +
218A LYS* 3.3 5.2 + - - +
219A LYS* 3.1 42.6 + - - +
220A ASN* 2.8 37.1 + - - +
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Residues in contact with PRO 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 5.4 5.6 - - - +
63A GLY 4.1 1.7 - - - +
67A VAL* 3.7 27.1 - - + -
211A SER* 3.0 28.9 - - - +
212A GLU* 5.2 0.9 - - - -
214A ILE* 3.1 17.9 - - + +
215A GLU 3.3 2.0 - - - +
216A ASN* 1.4 84.4 - - - +
218A LYS* 1.3 61.5 + - + +
221A VAL* 2.8 47.3 + - + +
222A PRO* 3.4 0.5 - - - +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 3.8 6.7 - - - -
64A ALA* 3.3 33.3 - - - +
65A LYS* 3.6 17.4 + - - +
67A VAL* 3.7 23.1 - - + -
216A ASN* 3.2 5.5 + - - +
217A PRO* 1.3 79.9 - - + +
219A LYS* 1.3 56.7 - - - +
222A PRO* 3.4 19.4 - - - +
435A SER* 2.8 30.8 + - - +
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Residues in contact with LYS 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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216A ASN* 3.1 34.1 + - - +
218A LYS* 1.3 79.9 - - - +
220A ASN* 1.3 70.4 + - - +
221A VAL 3.5 0.4 - - - -
222A PRO* 3.2 15.1 - - - +
223A ARG* 2.9 65.4 + - - +
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Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 5.4 0.2 - - - +
10A LEU* 3.8 39.4 - - + +
13A ALA* 5.3 0.2 - - - +
214A ILE* 3.9 11.9 - - + +
215A GLU* 2.8 34.9 + - - +
216A ASN* 2.8 17.2 + - - +
219A LYS* 1.3 89.9 - - - +
221A VAL* 1.3 59.6 - - - +
223A ARG* 3.9 9.7 + - - -
224A ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR 5.3 0.9 - - - +
63A GLY* 4.7 17.3 - - - +
207A ILE* 3.9 12.9 - - + +
208A THR* 4.2 11.9 - - + -
211A SER* 3.6 35.4 - - - -
214A ILE* 4.0 15.5 - - + -
217A PRO* 2.8 33.1 + - + +
220A ASN* 1.3 73.5 - - - +
222A PRO* 1.4 65.1 - - + +
224A ALA* 3.4 1.6 + - - +
225A ILE* 3.1 42.3 + - + +
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Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.6 50.5 - - + +
63A GLY 4.3 1.8 - - - +
64A ALA* 4.1 9.6 - - + +
217A PRO 3.4 1.6 - - - +
218A LYS 3.4 21.3 - - - +
219A LYS 3.2 12.1 - - - +
221A VAL* 1.4 96.3 - - + +
223A ARG* 1.3 61.4 + - + +
225A ILE* 3.4 1.1 + - + -
226A PHE* 3.1 24.9 + - - +
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.7 28.0 - - + +
219A LYS* 2.9 64.7 + - - +
220A ASN* 3.7 9.5 + - - +
222A PRO* 1.3 77.8 - - + +
224A ALA* 1.3 58.7 + - - +
226A PHE* 3.9 3.0 - - - +
227A ILE* 2.9 43.9 + - + +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.6 6.9 - - + +
13A ALA* 3.9 26.2 - - + -
14A VAL* 3.8 17.2 - - + +
207A ILE* 3.8 15.8 - - + +
220A ASN 2.9 20.5 + - - +
221A VAL 3.9 3.6 - - - +
223A ARG* 1.3 74.1 - - - +
225A ILE* 1.3 61.5 + - - +
228A SER* 2.8 31.2 + - - -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 3.9 16.2 - - + -
59A TYR* 4.0 27.1 - - + -
60A THR* 4.2 6.5 - - + -
203A GLY 6.3 0.4 - - - -
204A PHE* 3.7 33.4 - - + +
207A ILE* 3.7 23.1 - - + -
208A THR* 4.2 13.2 - - + -
221A VAL* 3.1 38.8 + - + +
222A PRO* 3.8 4.9 - - + +
224A ALA* 1.3 76.4 - - - +
226A PHE* 1.3 62.8 + - - +
228A SER* 3.3 2.4 + - - -
229A ILE* 3.2 27.9 + - + +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.7 29.4 - - + -
56A ALA* 5.6 4.9 - - + -
60A THR* 5.1 6.5 - - + -
222A PRO 3.1 17.2 + - - +
223A ARG* 4.0 3.4 - - - +
225A ILE* 1.3 77.2 - - - +
227A ILE* 1.3 71.4 + - + +
229A ILE* 3.4 5.9 + - - +
230A LEU* 3.2 54.9 + - + +
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.2 26.9 - - + -
11A TRP* 3.9 29.4 - - + -
14A VAL* 3.9 9.6 - - + -
223A ARG* 2.9 32.1 + - + +
226A PHE* 1.3 78.4 - - + +
228A SER* 1.3 63.7 + - - +
230A LEU* 3.3 7.8 + - + +
231A ILE* 3.0 44.2 + - + +
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.0 8.5 - - - -
17A ALA* 3.7 15.3 - - - +
18A VAL* 3.7 19.3 - - - -
21A MET* 3.4 24.5 - - - +
203A GLY* 5.1 1.4 - - - -
207A ILE* 4.1 1.0 - - - +
224A ALA 2.8 23.5 + - - -
225A ILE* 3.3 7.8 + - - -
227A ILE* 1.3 77.8 - - - +
229A ILE* 1.3 65.0 + - - +
231A ILE* 3.6 0.9 + - - +
232A VAL* 3.2 27.9 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 4.7 5.6 - - - -
52A ALA* 4.0 11.9 - - + +
53A LEU* 3.9 19.1 - - + -
56A ALA* 3.8 27.8 - - + -
201A TYR* 3.8 24.2 - - + +
203A GLY* 6.4 0.4 - - - -
204A PHE* 4.0 14.8 - - + -
225A ILE* 3.2 25.8 + - + +
226A PHE* 3.8 4.0 - - - +
227A ILE 3.3 0.2 - - - -
228A SER* 1.3 80.8 + - - +
230A LEU* 1.3 57.0 + - - +
232A VAL* 3.3 9.4 - - - +
233A MET* 2.9 48.8 + - + +
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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
----------------------------------------------------------
53A LEU* 4.5 17.9 - - + -
226A PHE* 3.2 46.4 + - + +
227A ILE* 3.3 8.5 + - + +
229A ILE* 1.3 73.1 - - - +
231A ILE* 1.3 66.8 + - + +
233A MET* 3.5 22.1 + - + +
234A PHE* 3.1 42.7 + - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 4.6 7.4 - - + -
14A VAL* 3.8 18.2 - - + -
18A VAL* 4.2 21.8 - - + -
159A LEU* 4.8 9.9 - - + -
227A ILE* 3.0 39.4 + - + +
228A SER 3.9 3.8 - - - +
229A ILE 3.4 0.2 - - - -
230A LEU* 1.3 78.7 - - + +
232A VAL* 1.3 59.8 + - - +
234A PHE* 3.2 5.8 + - - +
235A VAL* 3.0 36.9 + - + +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.9 26.9 - - + -
21A MET* 3.9 20.4 - - + -
22A ILE* 4.0 17.0 - - + -
201A TYR* 3.7 21.8 - - + -
228A SER 3.2 18.3 + - - +
229A ILE* 3.3 9.2 - - - +
231A ILE* 1.3 72.9 - - + +
233A MET* 1.3 59.7 + - - +
235A VAL* 4.2 5.8 - - - -
236A TYR* 2.8 58.4 + - + +
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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
----------------------------------------------------------
45A PHE 4.6 3.6 - - - +
46A ILE* 4.5 22.0 - - + +
49A GLY* 3.8 19.7 - - - -
50A ILE* 5.5 3.1 - - - -
53A LEU* 3.8 24.2 - - + -
201A TYR* 3.6 19.1 - - + +
229A ILE* 2.9 39.3 + - + +
230A LEU* 3.7 15.3 - - + +
231A ILE 3.3 0.2 - - - -
232A VAL* 1.3 77.9 - - - +
234A PHE* 1.3 67.6 + - + +
236A TYR* 3.6 1.5 + - - +
237A VAL* 3.2 35.4 + - + +
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.8 1.6 - - - +
230A LEU* 3.1 34.9 + - + -
231A ILE* 3.2 9.9 + - - +
233A MET* 1.3 81.3 - - + +
235A VAL* 1.3 64.9 + - + +
237A VAL* 3.6 3.7 + - - +
238A GLY* 3.0 21.1 + - - -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.3 14.4 - - + -
26A ILE* 4.7 1.1 - - + -
159A LEU* 4.0 22.4 - - + -
162A LEU* 4.0 30.3 - - + -
166A ILE* 3.7 11.8 - - + +
231A ILE* 3.0 27.1 + - + +
232A VAL* 3.8 7.4 - - - +
234A PHE* 1.3 76.4 - - + +
236A TYR* 1.3 60.1 - - + +
238A GLY 3.4 1.0 + - - -
239A VAL* 2.9 36.5 + - + +
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.1 24.9 + - - +
22A ILE* 4.3 9.6 - - + -
25A SER* 3.1 18.6 + - - -
26A ILE* 3.6 31.4 - - + -
45A PHE* 3.5 32.5 - + + -
200A SER* 2.7 34.4 + - - -
201A TYR* 3.4 29.2 - + - -
232A VAL* 2.8 41.1 + - + +
233A MET 3.9 3.1 - - - +
235A VAL* 1.3 73.8 - - + +
237A VAL* 1.3 58.3 + - - +
239A VAL* 3.3 1.4 + - - +
240A ALA* 2.9 32.2 + - - +
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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
----------------------------------------------------------
42A PRO* 3.8 17.0 - - + +
45A PHE* 4.4 7.0 - - + -
46A ILE* 3.7 35.9 - - + +
233A MET* 3.2 20.5 + - + +
234A PHE* 4.1 4.7 - - - +
236A TYR* 1.3 76.5 - - - +
238A GLY* 1.3 63.8 + - - +
240A ALA* 3.5 4.7 + - - +
241A ILE* 3.0 50.7 + - + +
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Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.5 28.8 - - - +
170A LEU* 5.0 1.5 - - - +
234A PHE 3.0 15.2 + - - -
235A VAL 3.7 2.9 - - - -
237A VAL* 1.3 78.8 - - - +
239A VAL* 1.3 55.4 + - - +
241A ILE* 4.1 5.1 - - - +
242A SER* 3.1 30.1 + - - -
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.9 15.9 - - + -
30A PHE* 4.0 4.3 - - + -
162A LEU* 4.0 22.0 - - + -
165A PHE* 3.6 10.7 - - + -
166A ILE* 3.8 19.5 - - + -
235A VAL* 2.9 29.3 + - + +
236A TYR 3.8 3.6 - - - +
238A GLY* 1.3 73.3 - - - +
240A ALA* 1.3 61.4 + - - +
243A ALA* 2.9 29.3 + - - +
260A LEU* 3.5 37.0 - - + -
----------------------------------------------------------
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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
----------------------------------------------------------
30A PHE* 3.8 11.2 - - - -
41A LEU* 4.0 17.9 - - + -
42A PRO* 3.8 29.8 - - + -
45A PHE* 4.1 7.0 - - + -
236A TYR 2.9 17.9 + - - +
237A VAL 4.0 1.8 - - - +
239A VAL* 1.3 75.1 - - - +
241A ILE* 1.3 59.6 + - - +
243A ALA* 4.1 0.2 - - - +
244A ILE* 2.9 36.7 + - - +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 3.9 21.1 - - + -
170A LEU* 3.8 23.1 - - + -
173A ILE* 4.0 3.0 - - + +
178A VAL* 3.7 36.0 - - + +
237A VAL* 3.0 40.7 + - + +
238A GLY* 4.1 4.5 - - - +
240A ALA* 1.3 75.1 - - - +
242A SER* 1.3 52.9 + - - +
244A ILE* 3.3 3.0 + - - +
245A GLY* 2.7 34.8 + - - -
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 2.7 39.6 + - - -
166A ILE* 3.9 12.1 - - - -
169A GLY* 3.2 13.4 - - - -
170A LEU* 4.6 2.5 - - - -
173A ILE* 4.1 9.6 - - - -
238A GLY 3.1 18.0 + - - -
241A ILE* 1.3 80.9 - - - +
243A ALA* 1.3 61.2 + - - +
246A ASN* 2.7 30.7 + - - +
267A PHE* 3.9 2.1 - - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.1 14.1 - - + -
165A PHE* 3.7 11.8 - - + -
239A VAL 2.9 18.7 + - - +
240A ALA 4.1 0.2 - - - +
242A SER* 1.3 75.4 + - - +
244A ILE* 1.3 62.8 + - - +
246A ASN* 3.2 3.4 + - - +
247A LEU* 3.1 29.1 + - - +
252A LEU* 4.4 6.1 - - + +
260A LEU* 3.7 25.1 - - + -
263A ALA* 4.0 11.8 - - + +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 5.6 0.2 - - + -
34A ALA* 6.1 0.2 - - - -
38A GLY 3.4 22.4 - - - +
39A ARG* 4.2 9.9 - - + +
41A LEU* 3.8 16.2 - - + -
42A PRO* 3.8 23.1 - - + -
177A TYR* 3.1 47.6 - - + +
178A VAL* 5.0 3.1 - - - -
240A ALA* 2.9 22.3 + - - +
241A ILE* 3.9 4.3 - - - +
243A ALA* 1.3 77.4 - - + +
245A GLY* 1.3 60.7 + - - +
246A ASN 3.2 1.3 + - - -
247A LEU 3.5 12.7 + - - +
249A ILE* 3.7 17.5 - - + -
252A LEU* 3.8 14.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 3.2 17.8 - - - -
174A HIS* 3.0 44.1 + - - -
177A TYR* 4.5 2.7 - - - -
178A VAL* 4.3 6.1 - - - -
241A ILE 2.7 21.5 + - - -
243A ALA 3.3 0.2 - - - -
244A ILE* 1.3 72.5 - - - +
246A ASN* 1.3 61.8 + - - +
247A LEU 3.9 0.2 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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