Contacts of the helix formed by residues 187 - 210 (chain B) in PDB entry 3RFU
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 TYR 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 4.8 11.9 - - + +
162B TYR* 3.1 52.0 + + - -
163B SER* 3.8 6.8 - - - -
185B ALA* 4.6 5.1 - - + +
186B VAL* 1.3 72.6 - - - +
188B PHE* 1.3 66.4 + - - +
189B GLU* 3.1 3.4 - - - +
190B ALA* 2.8 23.3 + - + +
191B ALA* 3.0 11.0 + - - +
375B VAL* 6.2 0.2 - - + -
376B SER* 4.5 5.2 + - - -
379B ILE* 4.4 30.3 - - + -
708B LEU* 2.7 45.3 + - + +
709B SER 3.7 1.8 - - - -
710B PRO* 3.2 46.8 - - + +
713B ALA* 4.8 6.1 - - + -
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.5 0.9 - - + -
115B SER 3.9 2.0 - - - -
118B GLN* 3.8 13.2 - - + +
119B LEU* 3.3 40.6 - - + -
122B ALA* 3.7 25.8 - - + +
160B TRP* 3.6 31.9 - + + -
163B SER* 2.8 32.3 + - - -
164B MET* 3.2 31.6 - - + -
167B VAL* 3.8 9.2 - - + -
186B VAL* 3.2 21.9 - - + -
187B TYR* 1.3 76.5 - - - +
189B GLU* 1.3 64.4 + - - +
191B ALA* 3.0 7.7 + - + +
192B ALA* 2.9 24.3 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 3.9 14.4 - - + +
96B VAL* 4.0 37.2 - - + +
99B GLU* 3.9 34.9 - - + +
100B MET* 3.8 23.0 - - - +
118B GLN* 4.6 2.0 - - - +
186B VAL 4.8 1.1 + - - +
187B TYR* 3.1 1.5 - - - +
188B PHE* 1.3 78.3 - - - +
190B ALA* 1.3 65.4 + - - +
192B ALA* 3.5 0.9 + - - +
193B VAL* 3.0 26.7 + - + +
710B PRO* 4.6 9.1 - - + +
714B ALA* 3.9 18.8 - - - +
717B MET* 4.4 12.0 - - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 2.8 22.7 + - + +
189B GLU* 1.3 81.8 + - - +
191B ALA* 1.3 62.9 + - - +
193B VAL* 4.1 0.3 - - - +
194B ILE* 3.0 36.3 + - + +
379B ILE* 4.0 22.7 - - + -
710B PRO* 6.2 0.9 - - + +
713B ALA* 5.0 11.4 - - + -
717B MET* 4.2 15.9 - - - -
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 5.4 0.4 - - + -
126B VAL* 3.5 21.1 - - + -
156B ILE* 3.6 17.1 - - + +
159B ALA* 4.4 18.7 - - + +
160B TRP* 4.9 6.7 - - + +
187B TYR 3.0 9.7 + - - +
188B PHE* 3.4 13.9 - - + +
190B ALA* 1.3 76.5 - - - +
192B ALA* 1.3 64.1 - - - +
194B ILE* 4.9 0.2 - - - -
195B THR* 2.9 30.4 + - - +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.3 26.9 - - + +
95B VAL* 4.6 6.7 - - + -
122B ALA* 4.4 6.3 - - + -
125B VAL* 3.5 25.6 - - + -
126B VAL* 4.2 0.8 - - - +
188B PHE 2.9 15.8 + - - +
189B GLU 3.9 2.7 - - - +
191B ALA* 1.3 75.0 - - - +
193B VAL* 1.3 64.8 + - - +
195B THR* 2.8 18.9 + - - -
196B THR* 2.9 13.8 + - - +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 4.0 7.4 - - + -
96B VAL* 3.9 28.3 - - + -
189B GLU* 3.0 15.6 + - + +
192B ALA* 1.3 78.9 - - - +
194B ILE* 1.3 67.8 + - - +
196B THR* 3.4 5.9 + - - +
197B LEU* 3.0 47.2 + - + +
384B CYS* 4.5 2.0 - - + -
717B MET* 3.3 36.3 - - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 4.8 4.7 - - + -
156B ILE* 3.4 28.0 - - + -
190B ALA* 3.0 38.1 + - + +
193B VAL* 1.3 77.0 - - - +
195B THR* 1.3 58.3 + - - +
197B LEU* 3.8 1.9 - - - +
198B VAL* 2.9 33.1 + - + +
379B ILE* 4.7 9.0 - - + +
382B CYS* 3.7 38.8 - - + +
383B PRO 4.7 2.0 - - - +
384B CYS* 3.7 33.4 - - + +
717B MET* 4.2 11.4 - - + -
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Residues in contact with THR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 5.1 0.3 - - - +
125B VAL* 3.2 25.8 + - - +
126B VAL* 4.0 8.3 - - + -
130B GLY* 4.7 9.9 - - - -
133B PHE* 3.6 7.8 - - + -
156B ILE* 3.5 35.0 - - + -
191B ALA 2.9 16.5 + - - +
192B ALA* 2.8 17.7 + - - -
194B ILE* 1.3 76.2 - - - +
196B THR* 1.3 56.3 + - - +
198B VAL* 3.0 12.1 - - - +
199B LEU* 3.0 34.6 + - - +
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.4 18.8 - - - -
88B ALA* 3.4 27.4 - - + -
89B LEU* 4.3 15.8 - - - +
92B THR* 3.1 28.2 - - - +
125B VAL* 3.7 3.4 - - + -
192B ALA 2.9 17.2 + - - +
193B VAL* 3.5 8.5 + - - +
195B THR* 1.3 75.6 - - - +
197B LEU* 1.3 71.4 + - - +
199B LEU* 3.6 8.2 - - - +
200B LEU* 3.0 21.1 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 6.6 0.2 - - + -
193B VAL* 3.0 39.2 + - + +
194B ILE 3.8 3.1 - - - +
196B THR* 1.3 86.0 + - - +
198B VAL* 1.3 59.7 + - - +
200B LEU* 3.2 14.3 - - + +
201B GLY 3.0 20.1 + - - -
384B CYS* 3.4 44.6 - - + +
385B ALA* 4.8 0.4 - - - +
387B GLY 4.9 0.2 - - - -
388B LEU* 3.5 27.1 - - + +
721B SER* 3.8 13.7 - - - +
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.1 37.0 - - + -
148B MET* 5.1 2.2 - - - -
149B PHE* 5.0 5.6 - - + -
152B ILE* 3.3 34.5 - - + -
194B ILE 2.9 21.2 + - - +
195B THR* 3.0 20.0 - - - +
197B LEU* 1.3 74.0 - - - +
199B LEU* 1.3 63.4 + - - +
201B GLY* 3.0 3.2 + - - +
202B GLN* 3.0 28.3 + - - +
384B CYS 4.3 8.4 + - - +
387B GLY* 4.6 12.1 - - - -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 3.9 19.4 - - + +
84B ARG* 3.9 38.6 - - + -
85B PHE* 4.0 21.5 - - + -
88B ALA* 4.2 16.8 - - + -
129B GLY 4.0 12.1 - - - +
130B GLY 4.2 6.7 - - - +
132B PRO* 5.4 1.1 - - + -
133B PHE* 3.5 22.2 - - + -
195B THR* 3.0 26.2 + - - +
196B THR* 3.6 6.1 - - - +
197B LEU 3.2 0.2 - - - -
198B VAL* 1.3 73.7 - - - +
200B LEU* 1.3 65.9 + - - +
202B GLN* 3.1 6.4 + - - +
203B VAL* 3.0 24.9 + - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.4 42.6 - - + -
196B THR 3.0 9.3 + - - +
197B LEU* 3.2 19.7 - - + +
199B LEU* 1.3 76.2 - - - +
201B GLY* 1.3 59.4 + - - +
203B VAL* 3.3 9.1 + - + +
204B LEU* 3.0 48.1 + - + +
388B LEU* 3.8 26.0 - - + -
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU 3.0 10.1 + - - -
198B VAL 3.0 7.2 + - - -
200B LEU* 1.3 78.2 - - - +
202B GLN* 1.3 60.5 + - - +
204B LEU* 3.5 2.2 + - - +
205B GLU* 3.0 30.8 + - - +
387B GLY* 2.9 32.1 - - - +
388B LEU* 3.7 5.6 - - - +
391B PRO* 4.2 4.4 - - - +
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 4.0 26.5 - - + +
133B PHE* 4.0 18.3 - - + -
136B ARG* 4.4 13.9 + - - -
148B MET* 4.4 8.1 - - - +
149B PHE* 3.8 33.5 - - - -
198B VAL* 3.0 23.6 + - - +
199B LEU* 3.4 7.9 - - - +
201B GLY* 1.3 76.5 - - - +
203B VAL* 1.3 66.1 + - - +
205B GLU* 3.8 24.0 + - - +
206B LEU* 3.0 36.2 + - + +
387B GLY* 5.6 1.8 + - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.5 26.8 - - + +
81B MET* 3.9 8.5 - - + -
82B ARG* 3.9 36.6 - - + +
85B PHE* 4.3 15.5 - - + -
199B LEU 3.0 17.4 + - - +
200B LEU* 3.5 14.8 - - + +
202B GLN* 1.3 76.0 - - - +
204B LEU* 1.3 69.1 + - + +
207B LYS* 3.0 30.9 + - + +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.0 31.9 + - + +
201B GLY 3.9 1.1 - - - +
203B VAL* 1.3 85.9 - - + +
205B GLU* 1.3 64.2 + - - +
207B LYS* 3.4 25.5 + - - +
208B ALA* 3.0 24.9 + - - +
388B LEU* 4.5 14.4 - - + -
391B PRO* 3.9 17.1 - - + +
392B MET* 4.5 19.3 - - + -
395B MET* 4.4 25.4 - - - +
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 5.4 4.7 - - - +
201B GLY 3.0 17.8 + - - +
202B GLN* 3.8 25.6 + - - +
204B LEU* 1.3 75.8 - - - +
206B LEU* 1.3 76.0 + - + +
208B ALA* 3.2 3.3 + - - +
209B ARG* 3.0 55.9 + - - +
334B ARG* 3.5 32.9 + - - -
391B PRO* 4.0 12.0 - - + +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 5.2 0.7 - - - +
77B GLU* 4.2 24.2 - - + +
78B TYR* 3.2 52.3 - - + +
81B MET* 4.3 14.1 - - + -
202B GLN* 3.0 28.3 + - + +
205B GLU* 1.3 91.2 - - + +
207B LYS* 1.3 54.6 + - - +
209B ARG* 3.0 4.3 + - + +
210B GLU* 2.6 41.4 + - + +
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.8 22.3 - - + +
203B VAL* 3.0 21.0 + - + +
204B LEU* 3.9 26.3 - - - +
206B LEU* 1.3 76.1 - - - +
208B ALA* 1.3 59.3 + - - +
210B GLU* 3.9 21.5 + - - +
211B GLN* 4.3 6.2 + - - +
395B MET* 6.0 6.2 - - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU 3.0 17.7 + - - +
205B GLU* 3.5 6.7 - - - +
206B LEU 3.0 1.0 - - - -
207B LYS* 1.3 79.6 - - - +
209B ARG* 1.3 65.3 + - + +
210B GLU 3.5 0.7 - - - -
211B GLN* 5.6 0.4 - - - -
391B PRO* 5.3 4.5 - - + +
394B ILE* 4.5 21.8 - - + +
395B MET* 5.3 9.9 - - + -
398B VAL* 6.5 0.7 - - + -
409B LYS 5.7 0.5 - - - -
410B ASN* 4.8 9.7 - - - -
411B ALA* 4.8 1.9 + - - +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B GLU* 3.0 46.9 + - - +
206B LEU* 3.0 6.0 + - + +
208B ALA* 1.3 84.2 - - + +
210B GLU* 1.3 63.7 + - - +
211B GLN 3.8 4.6 - - - +
212B THR* 5.0 4.5 - - - +
334B ARG* 3.0 34.6 - - - +
390B THR* 4.1 14.6 - - - +
391B PRO* 4.9 6.1 - - - +
394B ILE* 4.2 9.1 - - - +
410B ASN* 5.5 5.8 - - + +
411B ALA* 3.5 31.6 - - + +
412B GLU* 4.1 17.8 + - - +
415B GLU* 3.3 24.2 + - - -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.2 9.6 + - - +
75B SER* 3.6 38.7 + - - +
78B TYR* 4.3 22.6 - - + -
79B LEU* 5.3 0.7 - - - +
206B LEU* 2.6 21.4 + - + +
207B LYS* 3.9 19.1 - - - +
208B ALA 3.5 2.0 - - - -
209B ARG* 1.3 76.2 - - - +
211B GLN* 1.3 88.5 + - - +
212B THR* 3.1 14.2 + - - +
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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