Contacts of the helix formed by residues 225 - 256 (chain A) in PDB entry 4OQB
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 LYS 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 1.3 77.2 - - - +
226A LYS* 1.3 64.9 - - + +
228A LYS* 4.3 1.0 - - - +
229A ASP* 3.1 39.1 + - - +
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER 4.7 0.4 - - - +
225A LYS* 1.3 81.7 - - + +
227A GLU* 1.3 66.3 + - + +
229A ASP* 4.2 4.7 - - + -
230A LYS* 3.1 62.2 + - + +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.5 32.6 + - - +
225A LYS 3.3 0.4 - - - -
226A LYS* 1.3 79.3 - - + +
228A LYS* 1.3 58.5 + - - +
230A LYS* 4.1 2.2 - - - +
231A ASP* 3.1 28.2 + - - +
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.1 20.2 + - - +
225A LYS* 4.3 1.1 - - - +
227A GLU* 1.3 77.5 - - - +
229A ASP* 1.3 58.9 + - - +
231A ASP* 3.6 11.6 - - - +
232A SER* 2.8 36.4 + - - -
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LYS* 3.1 31.0 + - + +
226A LYS* 3.9 6.7 - - + +
227A GLU 3.3 0.4 - - - -
228A LYS* 1.3 74.3 - - - +
230A LYS* 1.3 64.0 + - + +
232A SER* 3.3 4.0 + - - -
233A LYS* 2.7 45.6 + - - +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LYS* 3.1 49.6 + - + +
227A GLU* 4.3 2.5 - - - +
229A ASP* 1.3 82.0 + - + +
231A ASP* 1.3 57.5 + - - +
233A LYS* 4.0 5.5 - - + +
234A LEU* 3.0 32.1 + - - +
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU 3.1 21.1 + - - +
228A LYS* 3.6 13.0 - - - +
230A LYS* 1.3 79.3 - - - +
232A SER* 1.3 61.2 + - - +
234A LEU* 3.9 5.3 - - - +
235A GLU* 3.5 20.1 + - - +
359A PRO* 5.7 4.5 - - - +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS* 2.8 27.6 + - - -
229A ASP* 3.9 4.3 - - - -
231A ASP* 1.3 74.8 - - - +
233A LYS* 1.3 62.8 + - - +
235A GLU* 3.4 11.8 + - - +
236A LYS* 3.2 19.6 + - - +
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASP* 2.7 33.1 + - - +
230A LYS* 4.4 5.6 - - + +
232A SER* 1.3 70.7 - - - +
234A LEU* 1.3 64.1 + - - +
236A LYS* 3.4 22.9 - - + +
237A ALA* 3.2 20.4 + - - +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS 3.0 20.7 + - - +
231A ASP* 3.9 6.7 - - - +
232A SER 3.3 0.2 - - - -
233A LYS* 1.3 73.6 - - - +
235A GLU* 1.3 58.1 + - + +
236A LYS 3.1 1.8 - - - -
237A ALA* 3.0 8.6 + - + +
238A LEU* 2.7 55.9 + - + +
356A ILE* 4.7 15.0 - - + +
357A PHE 4.7 7.4 - - - +
359A PRO* 5.1 13.9 - - + -
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 3.8 25.6 - - + -
86A LYS* 5.0 9.5 + - - -
231A ASP 3.5 10.1 + - - +
232A SER* 3.4 12.7 + - - +
234A LEU* 1.3 81.9 - - + +
236A LYS* 1.3 61.8 + - - +
238A LEU* 3.7 9.5 - - + +
239A LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER 3.2 12.8 + - - +
233A LYS* 3.4 31.6 - - + +
235A GLU* 1.3 78.5 + - - +
237A ALA* 1.3 56.0 + - - +
239A LYS* 3.7 30.7 - - - +
240A ALA* 3.1 27.2 + - - +
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LYS 3.2 9.7 + - - +
234A LEU* 3.0 11.9 + - + +
236A LYS* 1.3 77.1 - - - +
238A LEU* 1.3 59.9 + - - +
239A LYS 3.4 0.2 - - - -
240A ALA* 3.5 10.0 - - + +
241A GLN* 3.1 27.2 + - - +
356A ILE* 3.6 21.4 - - + +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 3.8 24.5 - - + -
234A LEU* 2.7 28.8 + - + +
235A GLU* 3.8 10.1 - - + +
236A LYS 3.3 0.2 - - - -
237A ALA* 1.3 71.9 - - - +
239A LYS* 1.3 58.7 + - - +
241A GLN* 3.4 5.4 + - + +
242A ASN* 3.0 27.9 + - - +
356A ILE* 3.3 39.0 - - + +
357A PHE 3.7 15.5 - - - +
358A PRO* 4.6 17.5 - - + -
359A PRO* 5.0 4.9 - - + -
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 3.7 49.9 - - + +
235A GLU 3.2 14.6 + - - +
236A LYS* 3.7 23.8 - - - +
238A LEU* 1.3 76.9 - - - +
240A ALA* 1.3 65.4 + - - +
242A ASN 3.2 0.2 + - - -
243A ASP* 3.0 50.8 + - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LYS* 3.1 19.4 + - - +
237A ALA* 3.5 12.8 - - + +
238A LEU 3.3 0.2 - - - -
239A LYS* 1.3 78.2 - - - +
241A GLN* 1.3 56.0 + - - +
243A ASP* 3.5 6.5 - - - +
244A LEU* 3.1 27.8 + - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA 3.1 16.4 + - - +
238A LEU* 3.4 6.3 + - + +
240A ALA* 1.3 76.8 - - - +
242A ASN* 1.3 67.0 + - - +
244A LEU* 3.6 9.9 - - + +
245A ILE* 3.4 27.6 + - + +
288A VAL* 6.0 0.4 - - + -
289A PHE* 3.6 22.2 - - + -
353A GLN* 3.5 21.5 + - - +
354A ASP 3.4 20.6 + - - -
355A ARG* 3.5 11.7 - - - +
356A ILE* 2.7 46.8 + - + +
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Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER 3.7 9.9 + - - -
76A GLU 5.0 0.2 + - - -
77A LEU 3.0 20.4 + - - -
78A ARG* 3.5 4.2 - - - -
79A TRP* 2.7 44.9 + - + +
82A GLN* 3.3 12.9 - - - +
238A LEU 3.0 17.3 + - - +
239A LYS* 3.2 4.5 + - - +
241A GLN* 1.3 79.8 - - - +
243A ASP* 1.3 59.6 + - - +
245A ILE* 3.5 5.3 + - - +
246A TRP* 3.3 33.2 + - - +
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 5.1 4.7 - - + +
239A LYS* 3.0 51.1 + - - +
240A ALA* 3.5 8.1 - - - +
242A ASN* 1.3 80.8 - - - +
244A LEU* 1.3 61.2 + - - +
246A TRP* 3.9 12.8 - - + -
247A ASN* 3.0 36.4 + - - +
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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
----------------------------------------------------------
240A ALA 3.1 20.1 + - - +
241A GLN* 3.6 10.1 - - + +
242A ASN 3.2 0.8 - - - -
243A ASP* 1.3 80.2 + - - +
245A ILE* 1.3 66.1 - - + +
247A ASN* 3.4 8.2 + - + +
248A ILE* 3.0 46.9 + - + +
288A VAL* 4.6 15.3 - - + -
348A LEU* 4.5 19.3 - - + +
349A LYS 5.3 4.0 - - - +
350A VAL* 5.1 11.4 - - + -
353A GLN* 3.7 30.5 - - - +
----------------------------------------------------------
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN* 3.4 17.1 + - + +
242A ASN* 3.9 7.4 - - - +
244A LEU* 1.3 77.6 - - + +
246A TRP* 1.3 54.4 + - + +
248A ILE* 3.1 9.2 + - - +
249A LYS* 2.6 45.4 + - + +
281A ASP* 5.2 6.3 - - - +
284A ALA* 3.7 24.7 - - + +
285A ASP* 5.1 3.4 - - + +
288A VAL* 4.4 17.9 - - + -
289A PHE* 3.8 30.7 - - + -
355A ARG* 3.8 19.7 - - - +
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Residues in contact with TRP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.8 32.8 - + - -
76A GLU 3.3 28.4 + - - -
77A LEU 3.4 8.9 + - - -
78A ARG* 3.1 50.0 - - + +
242A ASN* 3.3 37.5 + - - +
243A ASP* 4.0 9.2 - - + -
244A LEU 3.3 0.2 - - - -
245A ILE* 1.3 78.7 - - + +
247A ASN* 1.3 64.9 + - - +
249A LYS* 3.7 42.8 - - + +
250A ASP* 3.0 34.5 + - + +
280A LEU* 6.0 0.7 - - + -
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Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 5.7 1.6 + - - -
243A ASP* 3.0 29.5 + - - +
244A LEU* 3.5 9.3 - - + +
246A TRP* 1.3 76.5 - - - +
248A ILE* 1.3 61.8 + - + +
250A ASP* 3.1 14.8 - - - +
251A GLU* 3.0 26.9 - - + +
348A LEU* 6.3 4.0 - - + +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.0 34.7 + - + +
245A ILE* 3.4 7.0 - - - +
247A ASN* 1.3 77.3 - - + +
249A LYS* 1.3 66.7 + - - +
251A GLU* 3.5 7.1 - - - +
252A LEU* 3.2 21.2 + - + +
284A ALA* 4.1 13.9 - - + -
287A MET* 3.2 34.5 - - + -
288A VAL* 3.4 29.6 - - + -
345A LEU* 5.3 13.2 - - + +
348A LEU* 5.8 4.9 - - + -
350A VAL* 5.6 6.7 - - + -
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU 5.6 0.6 + - - -
245A ILE* 2.6 32.7 + - + +
246A TRP* 3.7 49.5 - - + +
247A ASN 3.4 0.2 - - - -
248A ILE* 1.3 73.1 - - - +
250A ASP* 1.3 59.1 + - - +
252A LEU* 3.1 9.9 + - - +
253A LYS 3.1 19.1 + - - -
277A SER* 4.0 9.5 + - - -
280A LEU* 3.2 44.4 - - + +
281A ASP* 3.3 36.8 + - - +
284A ALA* 3.8 18.8 - - + -
----------------------------------------------------------
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 2.8 36.1 + - - +
246A TRP* 3.0 18.0 - - + +
247A ASN* 3.1 13.0 - - - +
249A LYS* 1.3 73.9 - - + +
251A GLU* 1.3 59.1 + - - +
253A LYS* 3.7 15.7 - - + +
254A LYS* 3.2 27.9 + - - +
280A LEU* 5.0 0.7 - - - -
----------------------------------------------------------
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Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 3.0 22.8 + - + +
248A ILE* 3.5 9.9 - - + +
249A LYS 3.2 0.4 - - - -
250A ASP* 1.3 84.0 + - - +
252A LEU* 1.3 62.7 + - + +
254A LYS* 3.3 24.5 + - - +
255A VAL* 3.2 37.8 + - - +
344A TYR* 5.2 7.9 - - - +
345A LEU* 5.3 17.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.2 13.9 + - + +
249A LYS* 3.1 9.0 + - - +
251A GLU* 1.3 76.9 - - + +
253A LYS* 1.3 59.1 + - - +
255A VAL* 3.9 7.4 - - + -
256A CYS* 2.7 56.0 + - - +
261A LEU* 4.0 21.8 - - + +
264A LEU* 5.0 5.8 - - + -
280A LEU* 5.0 6.7 - - + +
283A VAL* 3.6 31.2 - - + -
284A ALA* 4.7 4.3 - - - +
287A MET* 3.7 27.6 - - + -
345A LEU* 5.9 7.0 - - + -
----------------------------------------------------------
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Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS 3.1 6.8 + - - +
250A ASP* 3.9 22.0 - - + +
251A GLU 3.3 0.2 - - - -
252A LEU* 1.3 76.5 - - - +
254A LYS* 1.3 60.9 + - - +
256A CYS 4.0 9.2 - - - +
261A LEU* 5.7 5.4 - - - -
276A GLU* 3.6 32.5 + - - +
277A SER* 4.9 4.8 - - - +
280A LEU* 3.6 35.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASP 3.2 16.2 + - - +
251A GLU* 3.5 28.3 + - - +
252A LEU 3.2 0.2 - - - -
253A LYS* 1.3 80.1 - - - +
255A VAL* 1.3 65.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 3.4 26.9 - - - +
252A LEU* 3.9 11.4 - - + -
254A LYS* 1.3 90.3 - - + +
256A CYS* 1.3 81.4 + - - +
257A SER 4.2 0.5 + - - -
260A ASP* 5.4 0.3 - - - +
341A GLU* 4.7 22.4 - - + -
----------------------------------------------------------
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Residues in contact with CYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 2.7 39.9 + - - +
253A LYS* 4.0 10.6 - - - +
255A VAL* 1.3 91.1 - - - +
257A SER* 1.3 67.6 + - - +
260A ASP* 4.1 22.4 - - + -
261A LEU* 4.2 16.9 - - + +
264A LEU* 5.0 6.7 - - - -
----------------------------------------------------------
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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