Contacts of the helix formed by residues 204 - 228 (chain A) in PDB entry 4JR8
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 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A THR* 4.6 1.8 - - - -
202A LEU 4.0 1.8 + - - -
203A VAL* 1.3 76.8 - - - +
205A ILE* 1.3 61.0 + - - -
206A GLY 3.2 3.9 + - - -
207A ILE* 3.4 9.2 + - - +
208A GLU* 2.9 30.5 + - - +
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Residues in contact with ILE 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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5A GLU* 4.8 6.1 - - - +
7A GLU* 3.2 30.5 - - + +
75A PRO* 4.7 16.4 - - + +
77A TYR* 3.8 29.6 - - + -
80A ARG* 6.2 0.2 - - - +
197A THR* 3.7 27.6 - - + +
204A GLY* 1.3 70.2 - - - -
206A GLY* 1.3 59.5 + - - +
208A GLU* 4.2 11.7 - - - +
209A THR* 2.7 63.1 + - - +
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 4.8 3.8 - - - -
7A GLU* 4.0 19.5 - - - -
10A TRP* 3.2 18.7 + - - -
204A GLY 3.2 1.4 - - - -
205A ILE* 1.3 83.6 - - - +
207A ILE* 1.3 60.5 + - - +
210A ALA 3.1 17.3 + - - -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TRP* 3.7 15.1 - - + -
203A VAL* 3.6 22.9 - - + -
204A GLY* 3.4 7.7 + - - +
206A GLY* 1.3 71.5 - - - +
208A GLU* 1.3 68.0 + - - +
210A ALA* 3.1 9.3 + - + +
211A GLY 2.9 18.9 + - - -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 5.2 0.9 + - - -
192A TRP* 2.9 38.3 + - + +
193A TRP* 5.4 0.3 - - - -
196A GLY* 4.0 10.3 - - - -
197A THR* 2.7 40.9 + - - +
198A GLU* 2.6 23.4 - - - +
203A VAL* 3.5 8.4 - - + +
204A GLY 2.9 18.2 + - - +
205A ILE* 3.7 9.9 - - - +
207A ILE* 1.3 77.2 - - - +
209A THR* 1.3 63.3 + - - +
211A GLY 3.1 0.9 + - - -
212A PHE* 3.0 38.8 + - + -
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Residues in contact with THR 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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7A GLU* 3.5 12.9 - - + +
10A TRP* 3.7 17.7 - - + -
11A LEU* 3.6 36.1 - - + +
55A TYR* 5.1 1.1 + - + -
77A TYR* 4.9 1.4 - - - -
80A ARG* 3.9 16.3 + - - +
205A ILE* 2.7 46.6 + - - +
206A GLY 3.8 3.8 - - - -
208A GLU* 1.3 73.4 - - - +
210A ALA* 1.3 63.0 + - - +
212A PHE* 3.3 3.2 + - - +
213A MET* 3.0 22.1 + - + +
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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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10A TRP* 3.6 41.4 - - + -
206A GLY 3.1 14.3 + - - +
207A ILE* 3.3 13.5 - - + +
209A THR* 1.3 75.9 - - - +
211A GLY* 1.3 63.8 + - - +
213A MET* 3.2 7.7 + - + +
214A VAL* 3.1 25.9 + - + +
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TRP* 3.6 20.9 - - - -
207A ILE 2.9 12.5 + - - -
208A GLU 3.1 3.3 + - - -
210A ALA* 1.3 74.6 - - - +
212A PHE* 1.3 65.8 + - - +
214A VAL* 2.9 19.1 + - - +
215A ILE* 3.1 17.6 + - - +
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Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.8 1.8 - - - -
80A ARG* 3.5 43.5 - - - +
84A TRP* 3.9 20.0 - + - -
189A TYR* 3.8 32.1 - + - -
192A TRP* 3.6 16.9 - + + +
193A TRP* 4.4 17.9 - + + -
198A GLU* 3.8 12.6 - - - -
208A GLU* 3.0 52.3 + - + -
209A THR* 3.8 2.0 - - - +
211A GLY* 1.3 74.2 - - - +
213A MET* 1.3 57.5 + - - +
215A ILE* 3.4 16.3 - - + +
216A ASP* 2.8 37.7 + - - +
301A RET 5.5 0.2 - - + -
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Residues in contact with MET 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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10A TRP* 3.6 51.1 - - + +
13A LEU* 3.7 24.5 - - + -
14A GLY* 4.0 10.1 - - - -
55A TYR* 3.4 14.7 + - + +
209A THR 3.0 13.9 + - - +
210A ALA* 3.2 20.2 - - + +
211A GLY 3.0 0.2 - - - -
212A PHE* 1.3 78.5 - - - +
214A VAL* 1.3 75.4 + - + +
216A ASP* 4.0 0.3 - - - +
217A LEU* 3.1 50.4 + - + +
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Residues in contact with VAL 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* 3.1 17.2 + - + +
211A GLY* 2.9 9.7 + - - +
213A MET* 1.3 90.2 - - + +
215A ILE* 1.3 66.0 + - + +
217A LEU* 3.4 5.1 + - - +
218A VAL* 3.0 43.3 + - + +
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 3.7 24.0 - - + +
188A VAL* 4.0 30.5 - - + -
189A TYR* 3.3 41.3 - - + +
192A TRP* 4.7 5.4 - - + -
211A GLY 3.1 11.3 + - - +
212A PHE* 3.4 25.8 - - + +
214A VAL* 1.3 77.4 - - + +
216A ASP* 1.3 59.9 + - - +
218A VAL* 3.7 5.1 - - + +
219A ALA* 2.7 37.8 + - - +
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Residues in contact with ASP 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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18A MET* 3.7 16.6 - - + -
55A TYR* 2.6 32.9 + - + +
80A ARG* 3.7 12.1 + - - -
83A ASP* 5.3 1.0 - - - +
84A TRP* 3.9 8.1 + - - -
189A TYR* 2.6 37.7 + - - -
212A PHE* 2.8 21.6 + - - +
213A MET 4.0 1.8 - - - +
215A ILE* 1.3 76.2 - - - +
217A LEU* 1.3 58.0 + - - +
219A ALA* 3.3 1.0 + - - -
220A LYS* 3.0 45.2 + - + +
301A RET 3.8 7.3 - - - +
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Residues in contact with LEU 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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13A LEU 5.0 3.8 - - - +
14A GLY* 4.6 6.3 - - - +
17A GLY* 4.1 22.4 - - - -
18A MET* 3.7 22.7 - - + +
55A TYR* 6.4 0.2 - - + -
213A MET* 3.1 46.7 + - + +
214A VAL* 3.8 5.4 - - - +
216A ASP* 1.3 80.0 - - - +
218A VAL* 1.3 57.9 + - + +
221A VAL* 2.9 29.6 + - + +
222A GLY 2.9 22.9 + - - -
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Residues in contact with VAL 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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181A LEU* 3.9 29.6 - - + +
185A VAL* 4.6 9.6 - - + -
214A VAL* 3.0 39.8 + - + +
215A ILE* 3.7 7.4 - - + +
217A LEU* 1.3 76.6 - - + +
219A ALA* 1.3 57.6 + - - +
222A GLY* 3.3 7.4 - - - +
223A PHE* 2.9 28.6 + - - +
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Residues in contact with ALA 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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91A LEU* 3.7 16.8 - - - +
181A LEU* 5.5 1.3 - - - -
185A VAL* 4.3 21.3 - - + -
186A TRP* 4.5 3.5 + - - +
189A TYR* 3.8 4.7 - - - +
215A ILE 2.7 21.8 + - - +
216A ASP* 3.8 4.0 - - - +
218A VAL* 1.3 74.5 - - - +
220A LYS* 1.3 58.9 + - - +
223A PHE* 3.1 18.9 - - - +
301A RET 3.8 27.6 - - + -
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Residues in contact with LYS 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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18A MET* 3.4 27.1 - - + -
25A PHE* 4.1 5.2 - - - -
44A THR* 4.9 2.6 - - - +
47A ILE* 3.6 23.5 - - + +
48A THR* 4.8 3.8 - - + -
51A ALA* 3.7 21.3 - - + -
83A ASP* 3.7 14.5 + - - -
84A TRP* 4.2 1.0 - - - +
87A THR* 3.7 13.3 + - - -
91A LEU* 4.3 3.7 - - + +
216A ASP* 3.0 24.1 + - - +
218A VAL 3.2 0.4 - - - -
219A ALA* 1.3 80.1 - - - +
221A VAL* 1.3 56.9 + - + +
222A GLY 3.4 0.2 - - - -
223A PHE* 3.8 2.1 - - - +
224A GLY* 2.6 32.2 + - - -
301A RET 1.4 72.2 - - + +
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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
----------------------------------------------------------
17A GLY 4.0 14.6 - - - +
18A MET* 4.4 11.2 - - - -
21A GLY* 4.4 17.0 - - - -
24A TYR* 6.0 0.9 - - + -
25A PHE* 3.5 13.8 - - + -
48A THR* 4.4 5.2 - - + -
217A LEU* 2.9 34.9 + - + +
220A LYS* 1.3 72.2 - - - +
222A GLY* 1.3 55.2 + - - +
224A GLY* 3.0 1.6 + - - -
225A ILE* 2.6 57.6 + - + +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.7 1.6 - - - -
217A LEU 2.9 11.6 + - - -
218A VAL* 3.3 13.2 - - - -
221A VAL* 1.3 77.5 - - - +
223A PHE* 1.3 61.7 + - - +
225A ILE* 3.3 11.2 + - - +
226A ILE* 3.1 33.1 + - - +
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Residues in contact with PHE 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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44A THR* 5.7 1.6 - - + -
91A LEU* 3.5 42.6 - - + -
94A ASP* 3.8 26.0 - - + -
95A LEU* 4.3 10.5 - - + -
178A LEU* 3.7 34.8 - - + +
181A LEU* 4.1 15.7 - - + +
182A VAL* 3.7 31.0 - - + -
218A VAL 2.9 7.8 + - - +
219A ALA* 3.1 28.0 - - - +
220A LYS 3.8 1.8 - - - +
222A GLY* 1.3 75.6 - - - +
224A GLY* 1.3 63.1 + - - +
226A ILE 3.4 0.3 + - - -
227A LEU* 2.9 39.5 + - + +
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Residues in contact with GLY 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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25A PHE* 3.5 17.5 - - - -
44A THR* 3.9 14.1 - - - -
220A LYS 2.6 22.5 + - - -
221A VAL 3.3 1.1 - - - -
223A PHE* 1.3 75.3 - - - +
225A ILE* 1.3 65.7 + - - +
227A LEU* 3.3 3.3 + - - +
228A LEU* 3.1 29.6 + - - +
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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
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24A TYR* 4.5 20.9 - - + +
25A PHE* 3.6 10.0 - - + -
28A ARG* 5.8 1.0 - - - +
221A VAL* 2.6 44.7 + - + +
222A GLY* 3.7 9.0 - - - +
224A GLY* 1.3 73.4 - - - +
226A ILE* 1.3 67.6 + - + +
228A LEU* 3.9 1.9 - - - -
229A ARG* 3.4 37.2 + - - +
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 4.1 16.6 - - + +
177A THR* 4.6 22.2 - - + -
178A LEU* 3.6 19.5 - - + -
181A LEU* 4.2 22.0 - - + -
222A GLY* 3.1 18.2 + - - +
223A PHE 3.8 3.4 - - - +
225A ILE* 1.3 81.4 - - + +
227A LEU* 1.3 62.7 + - - +
228A LEU 3.5 0.2 + - - -
229A ARG* 3.6 13.4 + - - +
230A SER 5.1 0.7 + - - -
233A VAL* 5.4 0.9 - - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.9 13.9 - - + -
44A THR* 3.8 5.4 - - + +
94A ASP* 3.4 43.5 - - + +
98A LEU* 4.0 26.7 - - + -
174A THR* 4.7 2.0 - - + -
178A LEU* 3.7 26.5 - - + -
223A PHE* 2.9 25.4 + - + +
224A GLY 3.3 3.3 + - - +
226A ILE* 1.3 79.5 - - - +
228A LEU* 1.3 77.5 + - + +
229A ARG 3.7 0.7 + - - -
230A SER 4.5 0.9 - - - +
233A VAL* 4.0 18.0 - - - +
234A LEU* 4.6 5.2 - - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.9 23.8 - - + -
28A ARG* 2.7 32.0 + - + +
40A PHE* 3.9 19.7 - - + -
41A TYR* 3.5 41.1 + - + +
44A THR* 4.0 19.5 - - + +
224A GLY 3.1 19.7 + - - +
225A ILE* 3.9 2.9 - - - +
227A LEU* 1.3 103.2 - - + +
229A ARG* 1.3 60.0 + - - +
230A SER 3.4 4.8 - - - -
231A HIS* 5.2 1.5 - - - -
234A LEU* 4.3 10.3 - - + -
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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
------------------------------------------------------------
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