Contacts of the helix formed by residues 238 - 267 (chain A) in PDB entry 5HJS
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 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP* 3.1 13.8 + - - +
237A ARG* 1.3 76.4 - - - +
239A MET* 1.3 64.7 + - - +
240A PHE 3.4 0.9 - - - -
241A PRO* 3.3 6.5 - - + +
242A ARG* 3.0 34.6 + - + +
219B HIS* 3.6 56.8 - - + +
222B VAL* 4.1 20.0 - - + -
223B GLU* 3.8 31.1 + - + +
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Residues in contact with MET 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.4 39.3 - - + +
229A VAL* 3.8 15.9 - - + -
233A HIS* 3.7 36.3 - - + +
236A ASP* 3.3 32.7 + - - +
238A LEU* 1.3 77.6 - - - +
240A PHE* 1.3 62.1 + - - +
242A ARG* 3.4 29.9 + - - +
243A MET* 3.1 41.5 + - + +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL* 3.5 32.1 - - + -
225A LEU* 4.0 15.5 - - + -
226A HIS* 3.5 62.6 - + + +
229A VAL* 3.7 20.9 - - + +
236A ASP 4.9 0.2 + - - -
237A ARG 4.3 4.5 + - - +
239A MET* 1.3 75.1 - - - +
241A PRO* 1.4 73.0 - - + +
243A MET* 3.2 7.8 + - - +
244A LEU* 3.1 45.6 + - + +
226B HIS* 5.7 0.9 - + - -
240B PHE* 4.6 10.5 - + - -
241B PRO* 3.9 17.3 - - + -
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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
----------------------------------------------------------
237A ARG 3.4 16.2 - - - +
238A LEU* 3.3 22.0 - - + +
240A PHE* 1.4 100.0 - - + +
242A ARG* 1.3 54.0 + - - -
244A LEU* 3.3 4.7 + - + +
245A MET* 2.9 37.6 + - + +
222B VAL* 3.6 32.8 - - + -
226B HIS* 5.5 1.6 - - - +
240B PHE* 4.0 9.9 - - + -
244B LEU* 3.6 20.6 - - + -
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA 5.9 0.2 + - - -
184A GLU* 5.2 12.3 + - - +
185A LEU* 3.6 38.2 - - + +
236A ASP* 4.6 6.3 + - - -
238A LEU* 3.0 37.1 + - + +
239A MET* 3.6 24.2 - - - +
240A PHE 3.3 0.2 - - - -
241A PRO* 1.3 74.8 - - - +
243A MET* 1.3 62.6 + - - +
245A MET* 3.4 15.0 + - - +
246A LYS* 3.5 18.9 + - - +
215B GLU* 4.3 15.0 + - - -
219B HIS* 3.4 43.5 - - + +
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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
----------------------------------------------------------
185A LEU* 4.3 9.6 - - + -
187A LEU* 3.6 32.1 - - + -
191A GLU* 3.5 41.5 - - - +
195A LEU* 3.6 26.0 - - + +
225A LEU* 4.1 10.8 - - + -
229A VAL* 3.8 28.5 - - + -
233A HIS* 4.5 1.8 - - + +
239A MET* 3.1 32.9 + - + +
240A PHE 3.2 6.0 + - - +
242A ARG* 1.3 73.2 - - - +
244A LEU* 1.4 66.0 + - - +
246A LYS* 3.1 19.5 + - - +
247A LEU 4.1 0.9 + - - -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.5 0.7 - - + -
198A ILE* 4.0 26.9 - - + -
222A VAL* 4.5 6.1 - - + -
225A LEU* 4.1 9.0 - - + -
240A PHE* 3.1 31.8 + - + +
241A PRO* 3.7 8.3 - - + +
243A MET* 1.4 78.7 - - - +
245A MET* 1.3 57.5 + - - +
247A LEU* 3.1 35.6 + - + +
248A VAL* 4.1 3.7 + - - +
241B PRO* 3.5 36.8 - - + +
244B LEU* 4.6 14.1 - - + -
245B MET* 4.1 28.6 - - - +
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Residues in contact with MET 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO* 2.9 30.6 + - + +
242A ARG* 3.8 9.0 - - - +
243A MET 3.3 0.6 - - - -
244A LEU* 1.3 71.5 - - - +
246A LYS* 1.3 65.8 + - - +
247A LEU 3.2 0.7 - - - -
248A VAL* 3.1 35.8 + - + +
249A SER* 3.6 6.9 + - - -
198B ILE* 3.6 16.6 - - + -
218B GLN* 3.2 40.4 - - - +
219B HIS* 6.3 1.3 - - + +
222B VAL* 4.9 5.6 - - + -
244B LEU* 4.1 25.8 - - + +
247B LEU* 3.8 19.7 - - + -
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.7 0.9 - - + -
178A PHE* 3.7 21.3 - - + -
181A ALA* 3.9 37.3 + - - +
182A MET* 3.6 28.5 - - + +
185A LEU* 3.7 24.2 - - + +
195A LEU* 5.0 4.7 - - + -
242A ARG 3.5 14.1 + - - +
243A MET* 3.1 11.9 + - - +
244A LEU 3.1 0.8 - - - -
245A MET* 1.3 78.8 - - - +
247A LEU* 1.4 58.9 + - + +
249A SER* 3.3 14.1 + - - +
250A LEU* 3.1 24.6 + - - +
215B GLU* 4.7 12.1 + - - -
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 5.0 2.7 - - - +
136A LEU* 4.9 0.9 - - + -
195A LEU* 3.9 43.7 - - + +
198A ILE* 3.5 32.1 - - + -
199A SER* 4.8 10.8 - - - +
243A MET 4.6 0.9 - - - +
244A LEU* 3.1 20.7 + - + +
246A LYS* 1.4 76.0 - - + +
248A VAL* 1.4 62.8 + - - +
250A LEU* 3.5 25.8 + - + +
251A ARG* 3.4 16.3 + - - +
245B MET* 3.8 14.4 - - + -
248B VAL* 3.7 25.2 - - + +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 4.4 0.7 - - - +
245A MET* 3.1 39.7 - - + +
247A LEU* 1.4 76.2 - - - +
249A SER* 1.3 59.5 + - - +
251A ARG* 3.2 18.9 + - - +
252A THR 3.7 1.9 + - - -
244B LEU 4.8 1.6 - - - +
247B LEU* 3.5 31.2 - - + +
248B VAL* 3.7 29.6 - - + +
251B ARG* 3.5 39.0 + - + +
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 3.9 21.3 - - - -
245A MET 3.6 7.7 + - - -
246A LYS* 3.3 18.3 + - - +
248A VAL* 1.3 77.5 - - - +
250A LEU* 1.4 60.5 + - - +
252A THR* 3.3 6.6 + - - -
253A LEU* 3.1 22.6 + - - +
204B ASP* 2.9 33.9 + - - +
251B ARG* 4.4 1.8 - - - +
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.4 49.7 - - + +
135A LEU* 4.0 11.6 - - + +
136A LEU* 3.6 32.1 - - + -
178A PHE* 3.7 26.4 - - + -
199A SER* 4.8 1.8 - - - +
246A LYS 3.1 13.6 + - - +
247A LEU* 3.7 29.8 - - + +
248A VAL 3.3 0.6 - - - -
249A SER* 1.4 73.4 - - - +
251A ARG* 1.4 59.0 + - - +
253A LEU* 3.3 8.5 + - + +
254A SER* 3.0 28.6 + - - -
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.2 18.6 + - - -
202A SER* 3.6 15.0 + - - -
204A ASP* 2.8 43.4 + - - -
205A ARG* 3.2 26.3 - - - +
247A LEU 3.4 2.3 + - - +
248A VAL 3.2 10.7 + - - +
250A LEU* 1.4 76.8 - - - +
252A THR* 1.3 62.7 + - - +
254A SER* 3.4 5.6 - - - -
255A SER* 3.2 20.8 + - - -
248B VAL* 3.4 43.2 + - + +
251B ARG* 3.7 15.6 - - + +
252B THR* 2.7 41.0 + - - +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL 3.7 0.8 + - - -
249A SER* 3.3 9.5 + - - -
251A ARG* 1.3 72.9 - - - +
253A LEU* 1.3 60.9 + - - +
255A SER* 3.0 10.9 + - - -
256A VAL* 2.9 43.4 + - + +
204B ASP* 5.4 2.2 - - - +
206B PRO* 6.5 1.3 - - + -
251B ARG* 3.1 42.5 + - - +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.7 31.2 - - + -
171A PHE* 4.0 16.2 - - + -
174A PRO* 3.7 37.2 - - + +
175A ILE* 3.9 8.7 - - - +
178A PHE* 3.6 44.2 - - + -
249A SER 3.1 12.0 + - - +
250A LEU* 3.3 11.9 + - + +
252A THR* 1.3 75.4 - - - +
254A SER* 1.3 56.3 + - - +
256A VAL* 3.3 7.2 + - + +
257A HIS* 2.9 29.2 + - - +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR 4.6 3.8 + - - -
131A ILE* 3.6 29.2 - - - +
132A GLU* 3.8 17.0 + - - -
135A LEU* 5.0 0.8 - - - +
205A ARG* 5.6 0.3 + - - -
250A LEU 3.0 13.5 + - - -
251A ARG* 3.4 12.3 - - - -
253A LEU* 1.3 75.7 - - - +
255A SER* 1.3 56.7 + - - +
257A HIS* 3.3 6.2 + - - +
258A SER* 3.0 29.5 + - - -
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Residues in contact with SER 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ARG 3.2 11.8 + - - -
252A THR* 3.0 14.2 + - - -
254A SER* 1.3 73.9 - - - +
256A VAL* 1.3 63.7 + - - +
258A SER* 3.3 16.1 + - - -
259A GLU* 3.4 22.0 + - - +
251B ARG 5.8 0.4 - - - -
255B SER* 2.7 35.6 + - - -
258B SER* 5.6 0.3 + - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN* 5.1 1.3 - - - +
170A GLU* 3.4 27.6 - - + +
171A PHE* 3.7 21.0 - - + +
174A PRO* 4.4 13.2 - - + -
252A THR* 2.9 30.3 + - + +
253A LEU* 3.6 11.0 - - + +
255A SER* 1.3 73.8 - - - +
257A HIS* 1.4 63.0 + - - +
259A GLU* 3.3 21.5 + - - +
260A GLN* 3.1 18.9 + - - +
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Residues in contact with HIS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 3.6 27.7 - - + +
171A PHE* 3.7 31.2 - + + -
253A LEU 2.9 17.3 + - - +
254A SER 3.6 4.8 + - - +
255A SER 3.3 0.2 - - - -
256A VAL* 1.4 76.9 - - - +
258A SER* 1.3 61.3 + - - +
260A GLN* 3.0 6.3 + - + +
261A VAL* 2.9 44.3 + - + +
279A TRP* 3.4 46.2 + + + -
301A 668 2.8 31.0 + - - -
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER* 3.0 15.7 + - - -
255A SER* 3.5 12.4 - - - -
256A VAL 3.3 0.4 - - - -
257A HIS* 1.3 79.9 + - - +
259A GLU* 1.4 57.2 + - - +
261A VAL* 3.3 9.5 + - - +
262A PHE* 3.0 27.4 + - - +
259B GLU* 6.0 1.6 - - - -
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN* 4.1 8.2 - - - +
255A SER* 3.5 14.8 - - - +
256A VAL* 3.3 29.2 + - - +
257A HIS 3.2 0.2 - - - -
258A SER* 1.4 75.1 - - - +
260A GLN* 1.4 58.6 + - - +
262A PHE* 3.4 9.9 + - - +
263A ALA* 3.0 28.2 + - - +
258B SER* 5.6 1.7 + - - -
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Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY 4.3 3.0 + - - -
167A LEU* 3.4 11.4 - - - +
168A GLN* 2.9 52.9 + - - +
171A PHE* 3.8 21.1 - - + +
256A VAL 3.1 11.5 + - - +
257A HIS* 3.2 15.3 - - + +
259A GLU* 1.4 73.5 - - - +
261A VAL* 1.4 63.0 + - - +
263A ALA* 3.3 5.6 + - - +
264A LEU* 3.1 33.4 + - - +
267A GLN* 5.3 2.2 + - - -
301A 668 3.1 27.8 - - - -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS* 2.9 46.4 + - + +
258A SER* 3.3 11.0 + - - +
260A GLN* 1.4 74.2 - - - +
262A PHE* 1.4 62.2 + - - +
264A LEU* 3.3 18.7 + - - +
265A ARG* 3.3 14.5 + - + +
271A LEU* 4.5 9.9 - - + -
279A TRP* 3.8 32.5 - - + +
280A ASP* 3.6 23.3 - - - +
281A VAL* 5.6 2.9 - - + +
301A 668 4.9 4.3 - - - +
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Residues in contact with PHE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER 3.0 13.4 + - - +
259A GLU* 3.6 11.4 - - - +
260A GLN 3.3 0.2 - - - -
261A VAL* 1.4 74.3 - - - +
263A ALA* 1.4 63.2 + - - +
265A ARG* 3.2 22.9 + - + +
266A LEU* 3.3 51.5 + - + +
281A VAL* 6.5 1.1 - - + -
262B PHE* 6.6 0.4 - + - -
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN* 3.6 27.4 - - - +
259A GLU 3.0 14.3 + - - +
260A GLN* 3.3 13.2 + - - +
262A PHE* 1.4 76.7 - - - +
264A LEU* 1.4 57.2 + - - +
266A LEU* 3.2 15.2 + - + +
267A GLN* 3.1 38.8 + - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.8 22.9 - - + -
166A GLY 4.2 4.9 - - - +
260A GLN* 3.1 27.5 + - - +
261A VAL* 3.3 13.0 + - + +
263A ALA* 1.4 71.5 - - - +
265A ARG* 1.4 61.9 + - - +
267A GLN* 3.5 24.6 + - - +
268A ASP 3.2 3.3 + - - -
269A LYS* 2.8 47.1 + - + +
271A LEU* 4.1 19.7 - - + -
301A 668 3.4 39.9 - - + +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 3.3 10.4 + - + +
262A PHE* 3.2 23.0 + - + +
264A LEU* 1.4 76.3 - - - +
266A LEU* 1.4 59.3 + - + +
268A ASP* 3.1 23.5 + - - +
269A LYS 5.0 2.0 - - - -
280A ASP* 3.7 37.6 + - - +
281A VAL* 2.8 34.1 + - - +
282A HIS* 4.2 8.7 + - - -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.3 53.8 + - + +
263A ALA* 3.2 13.6 + - - +
265A ARG* 1.4 75.0 - - + +
267A GLN* 1.3 56.1 + - - +
268A ASP* 3.1 9.3 + - - +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY* 4.1 10.5 + - - -
168A GLN* 5.6 0.7 + - - -
260A GLN* 5.3 1.0 + - - -
263A ALA* 3.1 31.2 + - - +
264A LEU* 3.6 24.2 - - - +
265A ARG 3.4 0.2 - - - -
266A LEU* 1.3 72.6 - - - +
268A ASP* 1.4 66.0 + - - +
269A LYS* 3.1 40.2 + - + +
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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