Contacts of the helix formed by residues 241 - 266 (chain A) in PDB entry 3C6G
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 GLY 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 5.7 0.7 - - - -
240A PHE* 1.3 75.5 - - - +
242A LYS* 1.3 64.5 + - - -
243A HIS* 3.2 6.5 - - - -
244A GLN* 3.1 15.8 + - - +
245A GLN* 3.3 9.9 + - - +
1D GLC 4.9 2.2 - - - -
6D GLC 4.2 2.2 + - - -
7D GLC 3.6 25.5 + - - -
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Residues in contact with LYS 242 (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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2A UNX 3.9 11.5 - - - -
220A LEU* 3.5 33.2 - - + +
223A SER* 3.3 27.6 + - - +
225A SER* 3.8 23.6 + - - +
226A VAL* 5.5 2.2 - - + -
241A GLY* 1.3 70.5 - - - -
243A HIS* 1.3 58.1 + - - +
245A GLN* 3.6 14.0 + - - +
246A LEU* 3.1 26.5 + - - +
485A LEU* 6.3 1.0 - - - +
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Residues in contact with HIS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 4.7 10.0 - - - +
226A VAL* 5.1 9.2 - - + -
229A TYR* 4.1 21.3 - + + -
235A ILE* 3.0 46.0 + - + +
236A GLY* 4.0 7.0 - - - -
238A LEU* 3.2 16.9 + - + -
240A PHE 3.0 27.6 - - - -
241A GLY* 3.7 5.8 - - - -
242A LYS* 1.3 78.4 + - - +
244A GLN* 1.3 78.1 + - + +
246A LEU* 3.3 7.0 + - - +
247A PHE* 3.1 46.9 + + + -
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Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLY* 3.0 28.7 + - - -
238A LEU 3.3 15.4 + - - +
239A PRO* 3.3 28.5 - - - +
241A GLY 3.1 8.3 + - - +
243A HIS* 1.3 95.2 + - + +
245A GLN* 1.3 68.2 + - - +
247A PHE* 3.3 18.0 + - - +
248A ARG* 3.0 27.1 + - - +
117B LYS* 4.7 12.9 + - - +
6D GLC 4.9 8.7 - - - +
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Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLU* 2.6 33.5 + - - +
220A LEU* 3.8 28.0 - - + +
241A GLY 3.3 9.4 + - - +
242A LYS* 3.6 16.1 - - - +
244A GLN* 1.3 78.7 - - - +
246A LEU* 1.3 54.7 - - - +
248A ARG* 3.6 8.6 + - - +
249A ASN* 2.9 42.2 + - - +
6D GLC 5.5 2.5 + - - +
7D GLC 6.2 0.2 - - - +
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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
----------------------------------------------------------
114A LEU* 3.6 33.2 - - + -
118A MET* 3.9 17.0 - - + -
217A ASN* 3.3 37.5 + - + +
220A LEU* 3.8 22.6 - - + +
226A VAL* 3.8 28.5 - - + -
242A LYS 3.1 15.2 + - - +
243A HIS* 3.5 7.2 - - - +
244A GLN 3.2 0.6 - - - -
245A GLN* 1.3 77.5 - - - +
247A PHE* 1.3 59.6 + - + +
249A ASN 3.4 0.3 + - - -
250A ALA* 2.9 24.1 + - - +
701A VD3 4.3 7.0 - - + -
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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
----------------------------------------------------------
114A LEU* 3.7 24.2 - - + -
117A LYS* 3.3 41.3 - - + -
118A MET* 3.6 11.4 - - + +
229A TYR* 3.5 43.1 - + - -
236A GLY* 5.1 1.8 - - - -
243A HIS* 3.1 36.1 + + + +
244A GLN* 4.0 22.4 - - - +
246A LEU* 1.3 76.1 - - + +
248A ARG* 1.3 65.4 + - - +
250A ALA* 3.4 6.7 + - - +
251A ALA* 3.1 22.3 + - - +
248B ARG* 5.9 0.5 - - - +
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Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLN 3.0 18.7 + - - +
245A GLN* 3.8 7.6 - - - +
247A PHE* 1.3 75.1 - - - +
249A ASN* 1.3 72.2 + - - +
251A ALA* 3.1 6.1 + - - +
252A VAL* 3.1 27.8 + - + +
250B ALA 5.9 0.2 - - - -
251B ALA* 4.2 27.6 - - + +
254B TYR* 4.0 46.4 - - - +
5D GLC 5.7 2.8 + - - -
6D GLC 5.6 14.3 + - - -
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Residues in contact with ASN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 3.3 43.6 + - + +
216A GLU* 3.0 29.3 + - - +
217A ASN* 3.0 32.3 + - - +
220A LEU* 4.4 0.8 - - - +
245A GLN* 2.9 29.4 + - - +
246A LEU 3.6 0.2 - - - +
248A ARG* 1.3 80.3 - - - +
250A ALA* 1.3 56.4 + - - +
252A VAL* 3.3 3.1 + - - +
253A VAL* 2.9 34.6 + - - +
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A MET* 3.5 31.6 - - + -
217A ASN* 3.5 8.5 - - - +
246A LEU 2.9 17.8 + - - +
247A PHE 3.7 4.9 - - - +
248A ARG 3.2 0.4 - - - -
249A ASN* 1.3 77.1 - - - +
251A ALA* 1.3 58.2 + - - +
253A VAL* 4.4 0.9 - - - -
254A TYR* 2.9 20.4 + - - +
701A VD3 2.6 32.8 + - + +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE 3.1 13.3 + - - +
248A ARG* 3.1 9.6 + - - +
250A ALA* 1.3 73.9 - - - +
252A VAL* 1.3 67.9 + - - +
254A TYR* 3.1 7.8 + - - +
255A ASP 3.1 18.5 + - - -
248B ARG* 4.0 42.8 - - + +
251B ALA* 4.1 9.9 - - + -
252B VAL* 3.8 10.7 - - + +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A HIS* 5.0 1.6 - - + +
210A MET* 6.2 2.0 - - + -
213A LEU* 3.5 21.3 - - + -
248A ARG* 3.1 20.0 + - + +
249A ASN* 3.8 4.9 - - - +
251A ALA* 1.3 75.7 - - - +
253A VAL* 1.3 63.0 + - + +
255A ASP* 3.4 2.9 + - - +
256A PHE* 3.2 24.1 + - + +
251B ALA* 3.8 18.6 - - + +
252B VAL* 4.3 9.9 - - + -
255B ASP* 3.4 47.6 - - + +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.7 33.0 - - + +
213A LEU* 3.9 10.3 - - + -
214A PHE* 3.8 39.5 - - + +
217A ASN* 5.2 1.1 - - - +
249A ASN 2.9 21.9 + - - +
250A ALA* 4.4 0.7 - - - -
252A VAL* 1.3 76.4 - - - +
254A TYR* 1.3 56.8 + - - +
256A PHE* 3.3 2.6 + - - +
257A LEU* 2.9 50.0 + - + +
701A VD3 3.7 15.0 - - + +
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Residues in contact with TYR 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 ALA 2.9 19.3 + - - +
251A ALA* 3.1 7.2 + - - +
253A VAL* 1.3 76.0 - - - +
255A ASP* 1.3 68.1 + - + +
257A LEU 3.6 0.2 + - - -
258A SER* 3.2 21.7 + - - -
298A GLU* 3.9 22.2 - - - +
301A ILE* 3.4 47.0 - - + +
302A PHE* 3.5 35.0 - + - -
701A VD3 4.1 13.5 - - + +
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Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA 3.1 5.2 + - - +
252A VAL 3.8 4.9 - - - +
254A TYR* 1.3 79.5 - - + +
256A PHE* 1.3 67.2 + - - +
258A SER* 3.0 22.8 + - - -
259A ARG* 3.1 16.5 + - - +
209B HIS* 3.0 40.9 + - - -
213B LEU* 3.7 8.5 - - - +
252B VAL* 3.3 41.2 - - + +
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Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 3.8 24.2 - - + -
207A PHE* 3.7 35.7 - + + -
210A MET* 3.6 29.4 - - + -
252A VAL* 3.2 16.9 + - + +
253A VAL 3.7 4.0 - - - +
255A ASP* 1.3 79.6 - - - +
257A LEU* 1.3 61.9 - - - +
259A ARG* 3.1 12.2 + - + +
260A LEU* 3.1 54.0 + - + +
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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
----------------------------------------------------------
210A MET* 3.9 25.1 - - + -
214A PHE* 4.2 2.7 - - + -
253A VAL* 2.9 38.2 + - + +
255A ASP 3.3 0.2 - - - -
256A PHE* 1.3 75.9 - - - +
258A SER* 1.3 61.7 + - - +
260A LEU* 3.3 10.6 + - + +
261A ILE* 3.0 32.8 + - + +
301A ILE* 3.8 20.9 - - + +
304A VAL* 4.1 9.4 - - + -
305A GLY* 3.5 27.8 - - - +
308A ILE* 3.9 22.7 - - + -
701A VD3 4.3 9.4 - - + -
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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 TYR* 3.2 13.5 + - - -
255A ASP* 3.0 17.5 + - - -
257A LEU* 1.3 76.3 - - - +
259A ARG* 1.3 64.7 + - - +
261A ILE* 3.8 4.5 - - - +
262A GLU* 3.1 33.9 + - - +
297A LYS* 5.4 9.0 - - - -
301A ILE* 3.5 32.6 - - - +
209B HIS* 5.3 2.9 + - - -
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP* 3.1 24.7 + - - +
256A PHE* 3.4 13.5 - - + +
258A SER* 1.3 81.6 + - - +
260A LEU* 1.3 60.6 + - + +
262A GLU* 3.3 24.5 + - - +
263A LYS* 3.1 46.3 + - - +
205B THR* 2.9 42.8 + - - -
206B ASP* 3.2 26.1 + - - +
209B HIS* 3.8 37.4 + - + +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.8 32.2 - - + -
200A PHE* 4.4 20.0 - - + -
207A PHE* 3.8 21.3 - - + -
210A MET* 4.5 4.9 - - + -
256A PHE* 3.1 46.9 + - + +
257A LEU* 3.6 10.8 - - + +
259A ARG* 1.3 73.9 - - + +
261A ILE* 1.3 61.6 + - - +
263A LYS* 3.4 16.9 + - + +
264A ALA* 2.9 30.8 + - - +
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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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196A PHE* 4.3 6.7 - - + -
257A LEU* 3.0 22.5 + - + +
258A SER* 3.8 5.6 - - - +
259A ARG 3.3 0.2 - - - -
260A LEU* 1.3 77.1 - - - +
262A GLU* 1.3 55.4 + - + +
264A ALA* 3.5 5.8 + - - -
265A SER* 2.7 33.8 + - - +
277A VAL* 3.9 24.8 - - + +
281A LEU* 5.7 1.1 - - + -
297A LYS* 6.5 1.3 - - + -
300A LEU* 3.7 35.7 - - + +
301A ILE* 3.7 40.2 - - + +
304A VAL* 3.9 15.0 - - + -
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 3.1 22.8 + - - +
259A ARG* 3.7 23.1 + - - +
260A LEU 3.1 0.2 - - - -
261A ILE* 1.3 78.2 - - + +
263A LYS* 1.3 64.7 + - + +
265A SER* 3.2 21.9 + - - -
266A VAL* 3.4 13.8 + - - +
297A LYS* 4.6 21.1 - - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 3.1 35.3 + - - +
260A LEU* 3.8 16.3 - - + +
262A GLU* 1.3 75.6 - - - +
264A ALA* 1.3 59.9 + - - +
265A SER 3.5 0.5 + - - -
266A VAL* 3.6 22.3 + - + +
267A ASN* 5.3 0.7 + - - -
205B THR* 4.7 5.2 - - - +
206B ASP* 2.8 42.7 + - - -
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 4.0 30.3 - - + +
198A GLU* 6.1 2.0 - - - +
260A LEU 2.9 17.9 + - - +
261A ILE* 3.9 5.4 - - - +
262A GLU 3.2 0.2 - - - -
263A LYS* 1.3 75.7 - - - +
265A SER* 1.3 58.6 + - - +
266A VAL 3.5 0.8 + - - -
267A ASN 5.1 1.6 + - - -
268A ARG 5.4 0.5 + - - -
275A HIS* 3.2 38.1 + - + +
277A VAL* 4.6 3.8 - - + -
278A ASP* 3.7 2.4 - - - +
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ILE* 2.7 23.1 + - - +
262A GLU* 3.2 19.9 + - - -
264A ALA* 1.3 77.3 - - - +
266A VAL* 1.3 68.4 + - - +
267A ASN 3.5 1.6 - - - -
268A ARG* 3.1 17.7 - - - +
277A VAL* 4.2 3.1 - - - -
278A ASP* 4.1 7.4 - - - -
281A LEU* 3.4 33.5 - - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU 3.4 16.3 + - - +
263A LYS* 3.6 18.8 - - + +
264A ALA 3.5 1.6 - - - -
265A SER* 1.3 80.3 - - - +
267A ASN* 1.3 75.3 + - - +
268A ARG* 3.0 5.7 + - - +
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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