Contacts of the helix formed by residues 239 - 261 (chain A) in PDB entry 5A86
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 LEU 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PRO* 3.7 29.4 - - + -
209A LEU 5.1 8.1 - - - +
210A LYS* 5.8 0.2 - - - -
211A VAL* 3.7 36.6 - - + +
213A LEU* 4.4 13.9 - - + -
225A TYR* 3.9 24.9 - - + +
227A PRO* 4.4 9.2 - - + -
236A ILE 5.1 1.8 + - - -
237A PHE 3.3 0.8 - - - -
238A SER* 1.3 75.8 - - - +
240A LEU* 1.3 61.4 + - + +
241A PRO 3.5 2.0 - - - -
242A HIS* 3.2 17.8 + - + +
243A MET* 2.9 27.6 + - - +
1433A D7E 4.2 7.5 - - - -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.2 15.7 - - + -
209A LEU* 4.5 8.3 - - + -
236A ILE 4.8 0.7 - - - +
237A PHE* 3.2 44.2 + - + +
239A LEU* 1.3 76.3 - - + +
241A PRO* 1.3 69.8 - - + +
243A MET* 3.1 19.0 + - - +
244A ALA* 2.8 24.3 + - - +
414A ILE* 3.6 21.8 - - + -
418A HIS* 4.2 6.5 - - + -
420A PHE* 3.6 41.7 - - + -
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Residues in contact with PRO 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 3.5 42.2 + - + +
174A LEU 6.1 1.8 - - - +
237A PHE 3.5 10.5 - - - +
238A SER* 3.8 8.5 - - - +
239A LEU 3.6 2.7 - - - -
240A LEU* 1.3 93.4 - - + +
242A HIS* 1.3 61.0 + - - +
244A ALA* 3.2 6.1 + - + +
245A ASP* 3.1 26.7 + - - -
418A HIS* 5.9 3.8 - - - +
420A PHE* 5.1 7.4 - - + +
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Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 4.2 8.4 - + - -
172A PHE* 3.6 30.9 - + - +
173A ARG 2.8 31.0 + - - +
174A LEU* 3.7 13.1 - - + +
175A PRO* 4.7 1.1 - - + -
213A LEU* 3.7 18.2 - - + +
238A SER 5.3 0.2 + - - -
239A LEU* 3.2 18.9 + - + +
241A PRO* 1.3 79.6 - - - +
243A MET* 1.3 57.5 + - - +
245A ASP* 3.1 6.5 + - - +
246A MET* 2.9 24.4 + - - +
304A LEU* 4.4 2.7 - - + -
306A TYR* 2.7 31.6 + + - -
1433A D7E 3.3 28.0 - - - -
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.6 10.3 - - + -
239A LEU 2.9 11.9 + - - +
240A LEU* 3.4 21.3 - - - +
242A HIS* 1.3 75.8 - - - +
244A ALA* 1.3 57.9 + - - +
246A MET* 3.3 0.7 + - - +
247A SER* 2.9 46.0 + - - +
407A HIS* 5.1 15.7 - - + +
411A LEU* 5.1 2.9 - - + -
420A PHE* 3.8 29.6 - - + -
425A MET* 4.7 9.0 - - + -
1433A D7E 3.2 64.8 - - + -
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 4.0 8.7 - - - +
240A LEU 2.8 13.1 + - - +
241A PRO 3.4 9.6 - - - +
243A MET* 1.3 77.7 - - - +
245A ASP* 1.3 54.4 + - - +
248A THR* 2.7 38.0 + - - -
420A PHE* 3.7 28.7 - - + +
422A THR* 4.0 3.8 - - + -
425A MET* 3.7 23.4 - - - +
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Residues in contact with ASP 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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169A PHE* 3.6 6.4 - - + -
171A ASN 4.9 0.8 - - - +
172A PHE* 3.6 20.1 - - + -
173A ARG* 2.8 63.6 + - - +
241A PRO 3.1 8.2 + - - +
242A HIS 3.1 7.6 + - - +
244A ALA* 1.3 75.6 - - - +
246A MET* 1.4 58.9 + - - +
248A THR* 3.5 5.1 + - - -
249A TYR* 3.0 29.3 + - - +
422A THR* 4.2 5.5 - - - +
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Residues in contact with MET 246 (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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166A PHE* 3.6 37.9 - - + -
169A PHE* 3.6 30.9 - - + -
242A HIS* 2.9 10.8 + - - +
243A MET 3.8 2.2 - - - +
245A ASP* 1.4 75.0 - - - +
247A SER* 1.3 58.7 + - - +
249A TYR* 3.2 8.0 + - - +
250A MET* 3.0 32.5 + - - +
288A PHE* 4.0 10.5 - - + -
301A CYS* 4.2 7.0 - - + -
304A LEU* 4.6 1.1 - - + -
306A TYR* 3.4 33.4 - - + +
1433A D7E 3.6 38.6 - - + -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET* 2.9 33.0 + - - +
244A ALA* 4.0 3.6 - - - -
246A MET* 1.3 76.5 - - - +
248A THR* 1.3 58.4 + - - +
250A MET* 3.2 7.2 + - - +
251A PHE* 2.8 58.2 + - - -
284A CYS* 6.0 0.2 - - - -
288A PHE* 5.9 1.1 - - - -
425A MET* 4.5 10.5 - - - +
1433A D7E 4.5 10.2 - - - -
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Residues in contact with THR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ALA 2.7 24.1 + - - -
245A ASP* 3.8 4.9 - - - -
247A SER* 1.3 75.4 - - - +
249A TYR* 1.3 63.2 + - - +
251A PHE* 3.3 9.2 + - - +
252A LYS* 3.0 38.1 + - + +
422A THR* 2.7 34.5 + - + +
424A LEU* 4.2 20.8 - - + +
425A MET* 3.7 5.2 - - - +
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Residues in contact with TYR 249 (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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163A ASP* 2.6 38.3 + - + +
166A PHE* 4.2 20.2 - + - -
168A HIS* 3.4 29.0 - - + +
169A PHE* 3.6 40.6 - + + -
245A ASP 3.0 14.0 + - - +
246A MET* 3.3 10.1 - - - +
248A THR* 1.3 78.5 - - - +
250A MET* 1.3 70.1 + - - +
252A LYS* 3.4 12.9 + - + +
253A GLY* 3.3 16.3 + - - -
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Residues in contact with MET 250 (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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162A PHE* 4.6 6.7 - - + -
166A PHE* 3.6 31.2 - - + -
246A MET* 3.0 19.6 + - - +
247A SER* 3.2 9.4 + - - +
249A TYR* 1.3 84.0 - - - +
251A PHE* 1.3 61.9 + - - +
253A GLY* 3.1 5.0 + - - -
254A ILE* 3.0 25.5 + - - +
284A CYS* 3.6 28.7 - - + +
287A ARG* 3.8 39.0 + - + +
288A PHE* 3.4 33.7 - - + +
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Residues in contact with PHE 251 (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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247A SER* 2.8 43.0 + - - +
248A THR* 3.7 8.7 - - - +
250A MET* 1.3 75.5 - - - +
252A LYS* 1.3 56.8 + - - +
254A ILE* 3.1 6.8 + - - +
255A ILE* 2.9 34.6 + - + +
280A ALA* 3.6 26.0 - - + +
281A PHE* 3.9 7.4 - + + -
284A CYS* 3.1 30.7 - - + -
424A LEU* 4.2 6.3 - - + -
425A MET* 4.1 10.5 - - + -
428A LEU* 3.5 26.9 - - + -
429A PHE* 3.4 39.7 - + - -
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Residues in contact with LYS 252 (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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248A THR* 3.0 35.1 + - + +
249A TYR* 3.7 12.3 - - + +
250A MET 3.3 0.2 - - - -
251A PHE* 1.3 74.5 - - - +
253A GLY* 1.3 57.7 + - - +
255A ILE* 3.4 10.0 + - - +
256A SER* 3.0 32.1 + - - +
424A LEU* 3.9 15.3 - - + -
689C ILE* 5.8 1.6 - - - +
693C LEU* 3.7 32.0 - - + +
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Residues in contact with GLY 253 (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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161A THR* 3.7 16.9 - - - -
249A TYR 3.3 7.2 + - - -
250A MET* 3.1 9.0 + - - -
252A LYS* 1.3 78.7 - - - +
254A ILE* 1.3 57.3 + - - +
256A SER* 3.5 7.3 + - - -
257A PHE* 3.0 23.0 + - - +
287A ARG* 3.4 17.7 + - - -
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Residues in contact with ILE 254 (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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250A MET 3.0 17.5 + - - +
251A PHE* 3.1 9.6 + - - +
253A GLY* 1.3 74.5 - - - +
255A ILE* 1.3 63.8 + - + +
257A PHE* 3.3 6.2 + - + +
258A ALA* 3.1 22.3 + - - +
276A LEU* 4.1 15.0 - - + +
279A ALA 5.3 0.2 - - - -
280A ALA* 4.4 13.9 - - + -
283A LEU* 3.6 46.7 - - + +
284A CYS* 3.7 20.6 - - - +
287A ARG* 3.4 38.8 - - - +
348A LEU* 5.9 0.9 - - + -
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Residues in contact with ILE 255 (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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251A PHE* 2.9 24.3 + - + +
252A LYS* 3.4 6.5 + - - +
254A ILE* 1.3 75.7 - - + +
256A SER* 1.3 56.8 + - - +
258A ALA* 3.3 3.5 + - - +
259A LYS* 3.0 37.0 + - + +
276A LEU* 4.1 18.8 - - + -
280A ALA* 6.5 0.4 - - + -
424A LEU* 4.1 18.8 - - + -
428A LEU* 5.1 6.1 - - + -
690C LEU* 3.9 23.1 - - + -
693C LEU* 3.9 37.5 - - + -
694C LEU* 4.0 23.0 - - + +
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Residues in contact with SER 256 (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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161A THR* 3.5 20.4 - - - -
252A LYS 3.0 17.6 + - - -
253A GLY* 3.6 6.6 - - - -
255A ILE* 1.3 72.5 - - - +
257A PHE* 1.3 66.2 + - - +
259A LYS* 3.3 17.9 + - - +
260A VAL* 3.2 26.8 + - - +
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Residues in contact with PHE 257 (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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154A LEU* 3.8 7.2 - - + -
157A ALA* 3.7 23.8 - - + -
158A GLN* 3.8 6.7 - - - -
161A THR* 3.5 15.0 - - - +
253A GLY 3.0 11.8 + - - +
254A ILE* 3.3 12.8 - - + +
256A SER* 1.3 76.9 - - - +
258A ALA* 1.3 66.3 + - - +
260A VAL* 3.1 19.9 - - - +
261A ILE* 3.3 21.7 - - + +
283A LEU* 4.0 24.0 - - + -
287A ARG* 3.6 19.1 - - - +
341A VAL* 3.7 27.1 - - + -
344A GLN* 3.4 31.4 - - + -
345A ALA* 4.8 1.8 - - - -
348A LEU* 4.5 13.7 - - + -
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Residues in contact with ALA 258 (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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254A ILE 3.1 9.8 + - - +
255A ILE 3.7 6.5 - - - +
257A PHE* 1.3 79.3 - - + +
259A LYS* 1.3 62.7 + - - +
261A ILE* 3.0 14.0 + - - +
264A PHE* 3.3 45.6 - - + +
276A LEU* 3.9 11.2 - - + -
348A LEU* 3.8 27.1 - - + -
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ILE* 3.0 26.6 + - + +
256A SER* 3.5 16.1 + - - +
257A PHE 3.3 0.2 - - - -
258A ALA* 1.3 76.2 - - - +
260A VAL* 1.3 60.4 + - + +
264A PHE* 4.4 5.4 - - - -
265A ARG* 3.1 34.5 + - + +
272A GLN* 5.6 1.1 - - - +
693C LEU 2.8 30.8 + - - +
694C LEU* 3.7 33.2 - - + +
696C GLU* 3.0 36.5 + - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 3.8 9.0 - - - +
156A ASP* 5.9 1.3 - - - +
157A ALA* 3.2 34.0 - - + +
160A LYS* 5.1 14.1 - - + -
161A THR* 4.5 8.7 - - + -
256A SER* 3.2 13.2 + - - +
257A PHE* 3.1 18.6 - - - +
259A LYS* 1.3 78.3 - - + +
261A ILE* 1.3 62.7 + - - +
262A SER 3.4 2.9 + - - -
265A ARG* 4.0 10.1 + - - +
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Residues in contact with ILE 261 (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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153A GLU* 3.9 13.2 - - + +
154A LEU* 3.8 27.4 - - + -
157A ALA* 3.2 35.0 - - + -
257A PHE* 3.3 23.3 - - + +
258A ALA* 3.0 11.7 + - - +
260A VAL* 1.3 75.7 - - - +
262A SER* 1.3 65.8 + - - +
263A TYR* 3.7 28.3 - - + +
264A PHE* 2.9 23.4 + - + +
265A ARG* 3.0 13.9 + - - +
348A LEU* 5.4 3.1 - - + -
349A PHE* 4.3 11.7 - - + -
369A PHE* 5.0 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