Contacts of the helix formed by residues 188 - 214 (chain D) in PDB entry 2FRV
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 VAL 188 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LEU* 3.9 23.1 - - + -
184D LEU* 3.8 22.4 - - + -
185D PRO* 3.0 19.3 + - + +
187D GLU* 1.3 73.7 - - - +
189D ASP* 1.3 66.7 + - - +
190D LEU 3.0 1.0 + - - -
191D ILE* 3.1 13.0 + - + +
192D ALA* 3.0 23.4 + - + +
263D ALA* 5.4 6.3 - - + -
264D VAL* 4.3 14.1 - - + +
267D PHE* 3.9 35.4 - - + -
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D TRP 4.9 0.2 - - - +
121D VAL* 3.4 15.0 - - + +
122D ASN* 3.0 45.7 + - - +
125D ASN* 2.8 30.3 + - - +
126D ALA* 3.8 8.6 - - - +
184D LEU* 3.3 22.6 - - - +
185D PRO 3.1 9.9 + - - +
186D ALA 3.6 8.1 - - - +
187D GLU 3.3 0.4 - - - -
188D VAL* 1.3 77.9 - - - +
190D LEU* 1.3 53.8 + - - +
192D ALA* 4.1 1.5 - - - +
193D THR* 2.7 32.1 + - - -
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA* 3.9 20.4 - - + +
129D ALA* 3.8 15.9 - - + -
131D PRO* 4.1 16.4 - - + -
134D ALA* 3.6 27.1 - - + -
151D LEU* 3.7 31.6 - - + +
154D VAL* 4.2 17.3 - - + -
155D GLN* 4.2 16.4 - - + +
186D ALA 3.1 15.6 + - - +
187D GLU 3.4 2.0 + - - +
188D VAL 3.0 0.8 - - - -
189D ASP* 1.3 78.3 - - - +
191D ILE* 1.3 59.2 - - - +
192D ALA 3.2 0.2 - - - -
193D THR* 3.8 1.2 - - - +
194D ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ALA* 3.6 28.7 - - + +
137D LEU* 3.8 27.4 - - + -
138D ALA* 3.8 18.6 - - + +
141D LEU* 5.1 9.6 - - + -
151D LEU* 4.6 6.7 - - + -
187D GLU 3.3 18.1 + - - +
188D VAL* 3.6 13.9 - - + +
190D LEU* 1.3 76.2 - - - +
192D ALA* 1.3 62.2 + - + +
194D ALA* 3.1 7.6 + - - +
195D HIS* 2.9 44.0 + - + -
260D ASP* 3.9 22.4 - - - +
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TYR* 4.7 6.1 - - + -
117D ALA* 5.9 4.1 - - + +
121D VAL* 4.0 28.9 - - + -
188D VAL* 3.0 18.2 + - + +
189D ASP 4.1 3.4 - - - +
191D ILE* 1.3 83.1 - - + +
193D THR* 1.3 57.1 + - - +
195D HIS* 3.9 6.3 - - - +
196D TYR* 3.0 26.5 + - - +
260D ASP* 4.6 7.0 - - + +
264D VAL* 5.2 9.9 - - + -
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Residues in contact with THR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 4.3 2.1 - - - +
123D VAL* 3.9 30.3 - - + +
126D ALA* 4.1 8.2 - - + +
154D VAL* 3.9 18.2 - - + -
158D VAL* 3.9 20.6 - - + -
189D ASP 2.7 24.1 + - - -
190D LEU* 3.8 6.3 - - - -
191D ILE 3.2 0.8 - - - -
192D ALA* 1.3 75.5 - - - +
194D ALA* 1.3 68.5 + - - +
195D HIS 3.1 0.4 - - - -
196D TYR* 3.5 7.5 + - + +
197D LEU* 3.3 33.8 + - + +
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Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 3.6 25.4 - - + -
154D VAL* 3.8 23.6 - - + +
190D LEU 3.0 18.0 + - - +
191D ILE 3.1 4.2 + - - +
193D THR* 1.3 80.6 - - - +
195D HIS* 1.3 66.3 + - + +
197D LEU* 3.6 4.4 + - - +
198D GLU* 3.3 22.0 + - - +
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Residues in contact with HIS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D TYR* 3.6 15.9 - - + +
138D ALA* 5.8 5.4 - - + +
144D LYS* 5.1 5.1 - - - -
146D THR* 5.3 8.3 + - - +
191D ILE* 2.9 29.1 + - + +
192D ALA 4.0 2.2 - - - +
194D ALA* 1.3 81.6 - - + +
196D TYR* 1.3 54.1 + - - +
198D GLU* 3.1 19.0 + - - +
199D ALA* 2.6 36.6 + - - +
252D PHE* 4.2 2.1 - - - -
256D VAL* 3.4 27.0 - - + +
259D THR* 5.5 0.4 - - - -
260D ASP* 2.2 47.5 + - - +
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Residues in contact with TYR 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 4.8 7.6 + - - +
113D TYR* 2.9 42.5 - - + -
114D HIS* 3.2 48.6 + + - +
117D ALA* 5.1 3.6 - - + -
118D LEU* 4.3 28.7 - - + +
123D VAL* 6.1 1.6 - - + -
169D ILE* 4.0 22.8 - - + +
170D PHE* 5.3 8.7 - + - -
192D ALA 3.0 18.1 + - - +
193D THR* 3.8 9.6 - - + +
194D ALA 3.4 0.2 - - - -
195D HIS* 1.3 73.8 - - - +
197D LEU* 1.3 78.3 + - + +
200D LEU* 3.4 20.7 + - + +
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASP* 4.6 11.7 - - + +
37C LEU* 4.5 21.1 - - + -
154D VAL* 3.9 25.1 - - + -
157D LYS* 4.3 28.5 - - + +
158D VAL* 5.9 1.3 - - + -
193D THR* 3.3 23.7 + - + +
194D ALA* 4.0 5.2 - - - +
195D HIS 3.3 0.4 - - - -
196D TYR* 1.3 91.4 - - + +
198D GLU* 1.3 63.0 + - - +
200D LEU* 3.1 31.4 + - + +
201D ARG* 3.7 9.0 + - - +
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Residues in contact with GLU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LYS* 2.5 34.2 + - - -
194D ALA 3.3 11.7 + - - +
195D HIS* 3.1 27.7 + - - +
197D LEU* 1.3 76.1 - - - +
199D ALA* 1.3 63.8 - - - +
201D ARG* 3.1 19.9 + - + +
202D VAL* 3.2 19.4 + - + +
252D PHE* 3.7 16.2 - - + -
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 4.6 6.4 - - + +
113D TYR* 3.5 31.2 - - + -
114D HIS* 3.7 20.5 - - + +
195D HIS 2.6 19.2 + - - +
196D TYR 3.9 0.2 - - - +
198D GLU* 1.3 71.0 - - - +
200D LEU* 1.3 58.6 + - - +
201D ARG 3.2 0.2 - - - -
202D VAL* 3.8 5.8 - - - -
203D GLN* 2.9 31.9 + - - +
252D PHE* 4.1 11.8 - - + -
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 5.3 8.5 - - + -
31C TYR* 5.7 0.2 - - - -
32C VAL* 3.8 32.0 - - + +
33C ASP* 4.3 25.1 - - + +
36C ILE* 6.3 2.2 - - + -
48C LEU* 6.5 1.3 - - + -
114D HIS* 3.5 24.7 - - + +
196D TYR* 3.4 31.1 + - + +
197D LEU* 3.1 20.1 + - + +
198D GLU 3.1 0.6 - - - -
199D ALA* 1.3 78.1 - - - +
201D ARG* 1.3 58.8 + - - +
203D GLN* 2.9 33.8 + - + +
204D VAL* 3.7 4.9 - - - +
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Residues in contact with ARG 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 3.5 47.0 - - + +
33C ASP* 2.7 40.7 + - - +
34C GLU* 3.9 14.5 + - - +
197D LEU 4.1 10.3 - - - +
198D GLU* 3.1 10.6 + - + +
200D LEU* 1.3 77.0 - - - +
202D VAL* 1.3 66.3 + - + +
203D GLN 3.3 1.1 - - - -
204D VAL* 3.4 17.1 + - - +
205D LYS* 3.6 15.9 + - - +
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 3.8 23.3 - - + -
198D GLU* 3.2 19.7 + - + +
199D ALA* 3.5 4.7 + - - +
201D ARG* 1.3 74.3 - - + +
203D GLN* 1.3 69.1 + - - +
205D LYS* 2.8 25.2 + - + +
206D ALA* 3.3 8.7 + - - +
248D GLU 5.1 0.7 - - - +
249D VAL* 3.9 28.0 - - + -
252D PHE* 3.7 39.0 - - + -
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Residues in contact with GLN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 2.8 37.4 + - - +
26C ARG* 3.1 27.7 + - - +
32C VAL* 5.4 0.4 - - - +
106D HIS* 3.1 36.7 + - + +
109D LEU* 4.4 8.9 - - + +
110D VAL* 3.5 29.3 - - + +
114D HIS* 4.5 3.4 - - + -
199D ALA 2.9 18.3 + - - +
200D LEU* 2.9 33.1 + - + +
202D VAL* 1.3 76.7 - - - +
204D VAL* 1.3 68.1 + - - +
206D ALA* 3.4 3.5 + - - -
207D ALA* 3.2 8.5 + - - +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU 3.7 10.5 - - - +
26C ARG* 4.4 11.8 - - + +
27C THR 4.4 9.2 - - - +
28C VAL* 3.9 15.3 - - + -
31C TYR* 4.5 14.8 - - + -
234C ASN* 5.2 1.4 + - - -
235C GLN* 4.7 1.7 + - - +
200D LEU 3.7 7.0 - - - +
201D ARG* 3.4 10.1 + - - +
202D VAL 2.8 0.6 + - - -
203D GLN* 1.3 96.5 - - - +
205D LYS* 1.3 59.2 + - + +
207D ALA* 3.6 5.9 + - - +
208D ARG* 3.2 51.5 + - - +
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Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ARG* 3.8 15.8 + - - +
202D VAL* 2.8 16.4 + - + +
204D VAL* 1.3 78.1 - - + +
206D ALA* 1.3 56.6 + - - +
207D ALA 3.3 0.2 - - - -
208D ARG* 3.4 18.9 + - - +
209D ALA* 3.2 26.7 + - - +
245D LEU* 4.0 22.0 - - + +
248D GLU* 2.7 42.7 + - + +
249D VAL* 3.8 13.7 - - + -
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ALA* 4.3 10.4 - - - +
105D MET* 5.3 1.3 - - + -
106D HIS* 3.6 38.3 - - + +
109D LEU* 5.3 1.3 - - + -
202D VAL 3.3 8.0 + - - +
203D GLN* 3.4 4.0 + - - +
205D LYS* 1.3 74.1 - - - +
207D ALA* 1.3 63.3 + - - +
209D ALA* 3.9 6.0 - - - +
210D MET* 3.3 20.6 + - - +
249D VAL* 4.0 25.0 - - + +
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.3 36.1 - - - +
234C ASN* 3.9 8.3 - - - +
106D HIS* 3.8 8.7 - - - +
203D GLN 3.2 14.6 + - - +
204D VAL 3.7 4.5 - - - +
206D ALA* 1.3 79.6 - - - +
208D ARG* 1.3 59.5 + - - +
210D MET* 3.3 5.6 + - - +
211D ALA* 3.1 26.3 + - - +
217D ASN* 3.7 16.4 - - - +
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 4.1 4.9 - - - +
31C TYR* 5.7 0.6 + - - -
234C ASN* 2.8 32.6 + - + +
235C GLN* 2.4 42.5 - - - +
236C VAL* 3.6 19.7 - - + +
204D VAL* 3.2 33.6 + - - +
205D LYS* 3.7 25.3 - - - +
206D ALA 3.4 0.4 - - - -
207D ALA* 1.3 74.5 - - - +
209D ALA* 1.3 62.5 + - - +
211D ALA* 3.2 4.5 + - - +
212D ILE* 3.2 18.5 + - - +
241D GLU* 5.5 0.7 - - - -
245D LEU* 3.7 26.9 - - + +
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Residues in contact with ALA 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ALA* 5.2 3.8 - - + -
205D LYS 3.2 17.1 + - - +
206D ALA* 3.9 8.5 - - - +
208D ARG* 1.3 71.8 - - - +
210D MET* 1.3 65.8 + - - +
212D ILE* 3.0 19.4 + - - +
213D PHE 3.8 1.0 + - - -
242D PHE* 3.2 43.2 - - + +
245D LEU* 4.0 17.5 - - + -
246D TYR* 4.8 5.2 - - - +
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Residues in contact with MET 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D THR* 3.8 9.4 - - + -
70D TYR* 3.4 33.7 - - + -
99D THR* 4.0 20.6 - - + +
102D ALA* 4.0 14.5 - - + +
103D GLN* 3.5 38.8 - - + +
106D HIS* 5.8 2.0 - - - -
206D ALA 3.3 11.9 + - - +
207D ALA* 3.3 10.3 + - - +
208D ARG 3.2 0.6 - - - -
209D ALA* 1.3 81.3 - - - +
211D ALA* 1.3 48.8 + - - +
212D ILE 3.3 0.2 + - - -
213D PHE* 3.4 3.9 + - - +
214D GLY* 2.7 31.4 + - - -
217D ASN* 3.4 21.3 - - + +
220D THR* 3.5 16.6 - - + -
242D PHE* 5.0 1.1 - - - -
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Residues in contact with ALA 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PHE 4.7 0.2 - - - +
234C ASN* 3.4 28.5 - - + +
236C VAL* 3.6 14.4 - - + -
237C ASN* 3.1 21.5 + - - +
207D ALA 3.1 10.0 + - - +
208D ARG 3.4 10.1 - - - +
209D ALA 3.2 0.2 - - - -
210D MET* 1.3 74.4 - - - +
212D ILE* 1.3 63.4 + - - +
214D GLY* 3.8 3.1 - - - +
215D ALA 3.2 12.7 + - - +
216D LYS* 4.0 15.5 - - - +
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Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C VAL* 3.9 15.0 - - + -
237C ASN* 3.1 21.2 + - - +
208D ARG 3.2 14.3 + - - +
209D ALA* 3.0 11.3 + - - +
211D ALA* 1.3 75.8 - - - +
213D PHE* 1.3 63.1 + - + +
230D ASN* 3.3 7.1 + - - -
233D SER* 3.6 10.8 - - - -
238D ARG* 3.4 45.1 + - + +
241D GLU* 3.8 17.3 - - + +
242D PHE* 3.7 37.0 - - + +
245D LEU* 3.9 15.5 - - + -
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Residues in contact with PHE 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D MET* 4.1 26.5 - - + -
98D LEU* 3.8 33.0 - - + -
99D THR* 3.3 21.8 - - - +
209D ALA 4.4 0.4 - - - -
210D MET* 3.4 4.0 + - - +
212D ILE* 1.3 80.9 - - + +
214D GLY* 1.3 57.0 - - - +
222D PHE* 3.2 19.1 - - - +
230D ASN* 2.7 22.5 + - - +
233D SER* 3.4 34.8 - - - -
239D ILE* 4.6 7.6 - - + -
242D PHE* 3.2 53.2 - + + -
429D LEU* 4.3 8.1 - - + -
432D LEU* 4.4 6.5 - - + -
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Residues in contact with GLY 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D THR* 4.4 1.3 + - - -
210D MET 2.7 22.2 + - - -
211D ALA 4.1 0.2 - - - -
213D PHE* 1.3 71.5 - - - +
215D ALA* 1.3 62.5 + - - +
216D LYS 2.9 11.6 + - - -
220D THR* 3.3 15.1 - - - -
221D GLN 3.0 19.4 + - - -
222D PHE* 3.7 18.4 - - - -
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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