Contacts of the helix formed by residues 233 - 260 (chain A) in PDB entry 4MBS
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 ASP 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.6 28.8 + - - +
229A LYS* 2.9 44.6 + - - +
230A ARG* 3.6 5.8 - - - +
231A HIS 3.3 0.6 - - - -
232A ARG* 1.4 73.1 - - - +
234A VAL* 1.3 62.7 + - - +
235A ARG 3.2 1.0 + - - -
236A LEU* 3.5 15.5 + - - +
237A ILE* 3.7 19.3 + - + +
302A GLU* 5.6 1.2 - - - +
303A GLU* 4.1 13.8 - - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.6 26.0 - - + +
130A VAL* 3.8 14.1 - - + -
214A TYR* 4.0 13.2 - - + -
217A ILE* 3.8 24.5 - - + -
221A LEU* 4.5 3.4 - - + -
230A ARG 3.8 7.9 - - - +
231A HIS* 3.3 20.0 - - - +
232A ARG 3.1 0.4 - - - -
233A ASP* 1.3 77.1 - - - +
235A ARG* 1.4 55.2 + - - +
237A ILE* 3.7 1.3 + - - +
238A PHE* 3.0 27.4 + - - +
1108A OLC 3.8 31.2 - - - +
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.3 15.3 + - - +
233A ASP 3.2 0.8 - - - -
234A VAL* 1.4 78.1 - - - +
236A LEU* 1.3 56.0 + - - +
238A PHE* 4.0 2.0 - - - +
239A THR* 2.6 37.1 + - - +
299A PHE 5.1 4.4 + - - -
300A VAL* 4.0 36.0 + - + +
302A GLU* 6.3 2.0 - - - +
1108A OLC 3.7 26.0 - - - +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 5.0 15.0 - - + -
232A ARG 4.7 0.4 + - - -
233A ASP* 3.5 11.0 + - - +
234A VAL 3.4 0.4 - - - -
235A ARG* 1.3 75.1 - - - +
237A ILE* 1.3 68.4 + - + +
239A THR* 3.2 4.7 + - - -
240A ILE* 3.0 39.4 + - + +
296A ILE* 3.8 19.1 - - + -
297A TYR* 3.7 34.5 - - + -
300A VAL* 4.0 11.4 + - + +
301A GLY* 4.0 30.5 - - - +
304A PHE* 5.5 5.6 - - + -
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 4.4 20.4 - - + -
69A LEU* 5.6 1.1 - - + -
119A ILE* 4.9 2.3 - - + +
122A LEU* 3.7 50.7 - - + +
123A THR* 3.8 8.7 - - - +
126A ARG* 3.7 28.5 - - + +
214A TYR* 3.5 15.2 + - - +
233A ASP* 3.7 22.7 + - + +
234A VAL 3.7 3.2 + - - +
235A ARG 3.6 0.2 - - - -
236A LEU* 1.3 86.6 - - + +
238A PHE* 1.4 61.1 + - - +
240A ILE* 3.3 13.4 + - + +
241A MET* 3.2 19.8 + - - +
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 4.7 12.3 - - + -
214A TYR* 3.3 48.0 + + + +
234A VAL* 3.0 21.4 + - + +
235A ARG 4.0 3.4 - - - +
237A ILE* 1.4 74.4 - - - +
239A THR* 1.4 58.7 + - - +
241A MET* 3.5 3.3 + - + +
242A ILE* 3.0 62.2 + - + +
1108A OLC 3.7 47.3 - - + +
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 2.6 27.8 + - - +
236A LEU 3.2 5.8 + - - -
238A PHE* 1.4 74.8 - - - +
240A ILE* 1.4 60.5 + - - +
242A ILE* 3.4 9.1 + - + +
243A VAL* 2.9 49.3 + - + +
296A ILE* 3.8 21.3 - - + -
300A VAL* 3.7 22.4 - - + +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.4 9.6 - - + -
72A LEU* 4.3 7.6 - - + -
119A ILE* 3.8 33.2 - - + -
122A LEU* 5.0 3.6 - - + -
236A LEU* 3.0 29.0 + - + +
237A ILE* 3.3 14.5 + - + +
239A THR* 1.4 74.2 - - - +
241A MET* 1.4 58.0 + - - +
243A VAL* 3.3 2.4 + - - +
244A TYR* 3.0 26.9 + - - +
289A HIS* 4.9 0.3 + - - -
293A ASN* 4.1 18.6 - - - +
296A ILE* 4.2 20.4 - - + -
297A TYR* 3.4 36.1 - - + +
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 5.0 2.7 - - + -
119A ILE* 3.8 31.6 - - + +
120A ILE* 4.0 25.1 - - + -
123A THR* 3.4 27.1 - - - +
206A PRO* 4.0 17.5 - - + +
209A VAL* 4.3 3.6 - - + -
210A MET* 3.7 37.2 - - + -
214A TYR* 4.5 4.9 - - + +
237A ILE 3.2 8.7 + - - +
238A PHE* 3.5 7.8 + - + +
239A THR 3.4 0.2 - - - -
240A ILE* 1.4 76.9 - - - +
242A ILE* 1.3 63.4 + - + +
244A TYR* 3.3 6.5 + - - +
245A PHE* 3.2 40.9 + - + -
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 4.2 20.4 - - + -
238A PHE* 3.0 50.8 + - + +
239A THR* 3.5 15.9 - - + +
241A MET* 1.3 76.2 - - - +
243A VAL* 1.4 71.1 + - + +
245A PHE* 3.4 11.2 + - + +
246A LEU* 3.3 31.7 + - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A THR* 2.9 31.7 + - + +
240A ILE 3.9 1.3 - - - +
242A ILE* 1.4 77.8 - - + +
244A TYR* 1.3 64.9 + - - +
246A LEU* 3.1 25.0 + - + +
247A PHE* 3.2 29.0 + - + -
289A HIS* 4.2 4.3 - - - +
292A ILE* 3.7 31.0 - - + -
296A ILE* 3.9 19.7 - - + -
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.5 27.0 - + - -
115A GLY 5.5 0.7 - - - -
116A ILE* 3.5 41.5 - - + +
119A ILE* 3.9 26.2 - - + -
202A GLY* 3.2 25.8 + - - -
240A ILE 3.0 13.6 + - - +
241A MET* 3.3 11.2 + - + +
243A VAL* 1.3 75.8 - - - +
245A PHE* 1.4 74.9 + + - +
247A PHE* 3.3 4.0 + - - +
248A TRP* 2.9 60.7 + + + +
289A HIS* 3.6 21.8 + + - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLY 4.6 0.9 - - - -
203A LEU* 4.2 23.6 - - + -
206A PRO* 3.7 28.0 - - + -
207A LEU* 3.6 45.8 - - + -
210A MET* 3.8 22.2 - - - -
241A MET* 3.2 34.3 + - + -
242A ILE* 3.7 12.8 - - + +
243A VAL 3.3 0.2 - - - -
244A TYR* 1.4 88.1 - + - +
246A LEU* 1.4 60.7 + - + +
249A ALA* 2.9 40.4 + - + +
250A PRO* 3.7 0.5 - - - +
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.3 23.7 + - + +
243A VAL* 3.1 23.8 + - + +
245A PHE* 1.4 76.8 - - + +
247A PHE* 1.3 66.7 + - + +
250A PRO* 3.5 19.1 - - - +
285A LEU* 4.2 5.5 - - - +
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Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 3.2 38.0 + - + -
244A TYR 3.9 2.2 - - - +
246A LEU* 1.3 86.9 - - + +
248A TRP* 1.4 61.0 + - + +
250A PRO* 4.0 2.9 - - - +
251A TYR 5.1 0.3 + - - -
282A THR 4.4 3.3 - - - +
285A LEU* 3.3 45.8 - - + +
286A GLY* 3.4 19.9 + - - -
288A THR* 3.7 23.3 - - + -
289A HIS* 3.7 36.6 - + + -
292A ILE* 3.5 27.8 - - + -
1107A OLC 5.2 3.1 - - + -
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Residues in contact with TRP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.9 17.0 - + - -
108A TYR* 4.2 9.6 - - - -
112A PHE* 3.8 21.6 - + - -
244A TYR* 2.9 60.4 + + + +
247A PHE* 1.4 78.1 - - - +
249A ALA* 1.4 60.4 + - - +
250A PRO* 3.3 2.9 - - - -
251A TYR* 3.1 41.8 + + + +
252A ASN* 2.7 31.0 + - - +
283A GLU* 4.2 6.7 - - + -
286A GLY* 3.4 42.7 + - - -
287A MET 3.8 3.4 - - - -
289A HIS* 4.2 12.6 + - + +
1101A MRV 3.7 33.4 - + - -
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 4.3 17.5 - - + -
244A TYR* 5.8 0.2 - - - -
245A PHE* 2.9 31.6 + - + +
248A TRP* 1.4 75.7 - - - +
250A PRO* 1.4 62.8 - - + +
252A ASN* 3.3 9.6 + - - +
253A ILE* 3.1 41.7 + - + +
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Residues in contact with PRO 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE 3.7 0.4 - - - +
246A LEU* 3.5 25.6 - - - +
247A PHE 4.0 1.8 - - - +
248A TRP 3.4 6.3 - - - +
249A ALA* 1.4 91.3 - - + +
251A TYR* 1.4 59.7 + - - +
253A ILE* 3.5 6.9 + - + +
254A VAL* 3.1 29.2 + - + +
282A THR* 3.9 18.8 - - + -
285A LEU* 4.0 16.6 - - + -
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 4.5 5.6 - - + -
247A PHE 5.1 0.2 + - - -
248A TRP* 3.1 33.6 + + + +
250A PRO* 1.4 75.9 - - - +
252A ASN* 1.4 62.2 + - - +
254A VAL* 3.2 2.3 + - - -
255A LEU* 2.8 58.3 + - + +
279A MET* 3.4 39.0 - - + +
282A THR* 3.4 36.8 + - - +
283A GLU* 3.8 23.3 - - + -
1101A MRV 3.0 48.0 + + - +
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Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 5.3 2.7 - - - -
198A ILE* 3.3 32.2 - - - +
199A VAL* 3.7 17.6 - - + +
202A GLY* 4.0 10.5 + - - -
203A LEU* 3.8 31.4 - - + +
244A TYR* 5.3 0.6 + - - -
248A TRP* 2.7 39.8 + - - +
249A ALA* 3.3 7.1 + - - +
251A TYR* 1.4 80.7 - - - +
253A ILE* 1.3 57.4 + - - +
255A LEU* 3.7 7.3 - - - +
256A LEU* 3.1 28.5 + - - +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 4.6 14.8 - - + -
249A ALA* 3.1 31.8 + - + +
250A PRO* 3.9 6.3 - - + +
252A ASN* 1.3 74.4 - - - +
254A VAL* 1.4 66.0 + - + +
256A LEU* 3.3 10.8 + - + +
257A LEU* 3.1 41.9 + - + +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 3.1 18.7 + - + +
251A TYR 3.2 3.6 + - - +
253A ILE* 1.4 75.2 - - + +
255A LEU* 1.4 52.3 + - - +
257A LEU* 3.2 14.0 + - + +
258A ASN* 2.8 33.4 + - - +
275A LEU* 3.8 18.6 - - + +
278A ALA* 3.9 13.9 - - + -
279A MET* 3.7 34.1 - - + +
282A THR* 4.0 18.6 - - + +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 3.8 21.2 - - + +
198A ILE* 4.0 30.3 - - + -
199A VAL* 4.5 5.4 - - + -
251A TYR* 2.8 59.5 + - + +
252A ASN* 3.7 5.4 - - - +
254A VAL* 1.4 72.0 - - - +
256A LEU* 1.3 60.5 + - - +
258A ASN* 4.1 3.8 - - - +
259A THR* 3.2 31.5 + - - +
279A MET* 3.9 12.7 - - + +
1101A MRV 3.7 34.1 - - + -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 4.3 6.3 - - + +
196A LEU* 4.7 7.4 - - + -
199A VAL* 3.8 35.9 - - + -
203A LEU* 5.7 5.8 - - + -
252A ASN 3.1 16.9 + - - +
253A ILE* 3.3 12.8 + - + +
255A LEU* 1.3 76.1 - - - +
257A LEU* 1.3 62.9 + - + +
260A PHE* 3.2 47.5 + - + +
261A GLN* 3.3 11.6 + - + +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 3.1 35.8 + - + +
254A VAL* 3.4 17.0 - - + +
256A LEU* 1.3 79.7 - - + +
258A ASN* 1.3 57.5 + - - +
261A GLN* 3.2 30.5 + - + +
262A GLU* 2.9 31.7 + - - -
275A LEU* 3.7 23.9 - - + +
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A VAL 2.8 19.8 + - - +
255A LEU 4.1 3.6 - - - +
257A LEU* 1.3 71.4 - - - +
259A THR* 1.3 68.0 + - - +
262A GLU* 3.3 15.2 - - - +
272A SER 4.8 2.1 - - - +
275A LEU* 3.7 38.9 - - + +
276A ASP* 3.9 7.8 + - - +
279A MET* 3.7 28.8 - - + +
1101A MRV 5.3 5.3 - - - +
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLN* 4.3 11.8 + - - +
191A LYS* 3.8 16.2 - - + +
192A ASN* 3.6 23.5 - - - +
195A THR* 2.7 32.1 + - - +
255A LEU* 3.2 18.6 + - - +
258A ASN* 1.3 81.6 + - - +
260A PHE* 1.3 75.0 + - + +
262A GLU* 4.1 5.2 - - - +
263A PHE* 5.9 0.5 - - - +
1101A MRV 3.4 13.3 - - - -
----------------------------------------------------------
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Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 3.5 51.6 - - + -
195A THR* 3.7 24.5 - - + -
196A LEU* 3.7 29.2 - - + -
256A LEU* 3.2 22.3 + - + +
259A THR* 1.3 81.7 - - + +
261A GLN* 1.4 59.1 + - - +
262A GLU* 2.6 17.2 + - - -
263A PHE* 2.8 20.8 + - - +
264A PHE* 3.6 26.9 + + + -
----------------------------------------------------------
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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