Contacts of the helix formed by residues 229 - 257 (chain A) in PDB entry 6B3I
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 SER 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU 5.5 0.2 - - - -
228A THR* 1.3 80.7 + - - +
230A GLY* 1.3 69.8 + - - +
232A LEU* 3.5 13.4 + - - +
233A GLN* 3.4 14.7 + - - -
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Residues in contact with GLY 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 1.3 75.7 - - - +
231A ASP* 1.3 65.6 + - - -
233A GLN* 3.3 16.5 + - - +
234A LYS* 3.4 10.7 + - - +
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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
----------------------------------------------------------
104A THR 5.3 1.6 - - - +
105A ASP* 4.5 5.1 - - - +
106A GLU* 3.4 35.0 + - - +
110A ILE* 3.4 15.0 - - + +
148A LEU* 3.7 22.4 - - + -
230A GLY* 1.3 74.0 - - - -
232A LEU* 1.3 59.6 + - - +
234A LYS* 3.2 18.7 + - - +
235A ALA* 2.9 25.8 + - - +
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 4.3 12.1 - - + +
148A LEU* 4.2 29.8 - - + +
151A ILE* 4.5 5.8 - - + -
190A GLU* 3.3 42.6 - - + +
194A ASN* 4.5 1.1 - - - +
228A THR* 4.4 8.5 - - + -
229A SER 3.5 11.0 + - - +
230A GLY 3.2 0.6 - - - -
231A ASP* 1.3 78.8 - - - +
233A GLN* 1.3 61.8 + - - +
235A ALA* 3.4 4.3 + - + +
236A TYR* 3.1 56.8 + - + +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ILE* 4.2 5.6 - - + -
225A GLU* 3.7 26.9 - - - +
228A THR* 3.2 39.6 + - - +
229A SER* 3.4 12.1 + - - +
230A GLY 3.3 12.1 + - - +
231A ASP 3.2 0.4 - - - -
232A LEU* 1.3 79.0 - - - +
234A LYS* 1.3 57.7 + - - +
236A TYR* 3.1 2.3 + - - +
237A LEU* 2.9 53.4 + - + +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.9 8.5 + - - -
106A GLU 4.9 0.2 - - - -
107A SER* 3.0 34.3 + - - +
110A ILE* 4.0 20.9 - - + -
230A GLY 3.4 8.7 + - - +
231A ASP* 3.2 23.3 + - - +
233A GLN* 1.3 81.9 - - - +
235A ALA* 1.3 53.5 + - - +
237A LEU* 4.3 6.0 - - - +
238A THR* 2.6 45.1 + - - +
249A TYR* 6.0 0.2 - - - +
253A ARG* 5.8 5.8 - - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.7 17.6 - - + +
114A CYS* 4.0 8.0 - - - -
148A LEU* 3.9 20.4 - - + -
151A ILE* 4.7 14.1 - - + -
152A LEU* 5.3 1.1 - - + -
231A ASP 2.9 15.9 + - - +
232A LEU* 3.7 6.1 - - - +
234A LYS* 1.3 77.7 - - - +
236A TYR* 1.3 66.0 + - + +
238A THR* 3.5 1.9 + - - -
239A LEU* 3.1 28.8 + - - +
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.8 8.1 - - + -
190A GLU* 3.0 20.6 + - + +
193A PHE* 3.5 30.7 - + + +
194A ASN* 2.3 34.4 + - - -
197A LEU* 3.6 18.5 - - + +
224A ILE* 3.7 22.7 - - + -
228A THR* 3.5 33.9 - - + -
232A LEU* 3.1 37.7 + - + +
233A GLN 3.1 6.0 + - - +
235A ALA* 1.3 76.0 - - + +
237A LEU* 1.3 60.2 - - - +
239A LEU* 3.1 9.9 + - + +
240A VAL* 2.9 31.2 + - - +
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Residues in contact with LEU 237 (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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221A GLU* 4.0 31.9 - - + +
224A ILE* 3.7 31.4 - - + -
225A GLU* 4.1 15.3 - - + +
233A GLN* 2.9 48.6 + - + +
234A LYS* 4.3 5.2 - - - +
236A TYR* 1.3 73.5 - - - +
238A THR* 1.3 57.5 + - - +
240A VAL* 3.9 3.0 - - - +
241A ARG* 2.9 43.0 + - + +
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.9 14.4 - - + +
111A GLU* 4.7 0.2 - - - -
114A CYS* 3.6 24.5 - - + +
115A THR* 4.3 4.3 - - + -
234A LYS* 2.6 30.5 + - - +
235A ALA 3.8 4.5 - - - -
237A LEU* 1.3 74.7 - - - +
239A LEU* 1.3 65.9 + - - +
241A ARG* 4.0 0.5 - - - +
242A CYS* 3.0 25.1 + - - +
249A TYR* 3.3 47.4 + - + +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A CYS* 3.7 36.6 - - + +
151A ILE* 4.3 24.9 - - + -
155A LEU* 4.1 7.0 - - + -
160A ARG* 3.6 25.6 - - - +
197A LEU* 3.8 38.8 - - + +
198A ALA 4.8 0.2 - - - +
202A TYR* 5.2 3.4 - - + +
205A LEU* 5.0 3.0 - - - +
235A ALA 3.1 23.2 + - - +
236A TYR* 3.5 8.5 - - + +
238A THR* 1.3 77.5 - - - +
240A VAL* 1.3 61.6 + - - +
242A CYS* 4.4 0.3 - - - +
243A ALA* 3.1 26.0 + - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.1 11.4 - - + -
209A PHE* 3.6 38.3 - - + -
220A ILE* 3.7 19.1 - - + -
221A GLU* 3.9 21.3 - - + +
224A ILE* 3.7 22.4 - - + -
236A TYR 2.9 18.8 + - - +
237A LEU* 3.9 6.5 - - - +
239A LEU* 1.3 77.7 - - - +
241A ARG* 1.3 57.0 + - - +
243A ALA* 3.4 2.8 + - - +
244A GLN* 2.8 31.6 + - + +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 3.4 27.8 + - - +
237A LEU* 2.9 26.8 + - + +
238A THR 4.2 0.2 - - - +
240A VAL* 1.3 76.9 - - - +
242A CYS* 1.3 54.5 + - - +
244A GLN* 4.4 4.3 - - - -
245A ASP* 2.7 39.9 + - - +
248A ASP* 2.6 42.4 + - - -
249A TYR* 3.9 32.1 - - + +
252A GLU* 2.6 41.2 + - - +
290A LYS* 4.4 3.6 - - - +
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Residues in contact with CYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A CYS 3.8 10.3 - - - +
115A THR* 3.8 27.6 - - + -
202A TYR* 4.4 18.8 - - + +
238A THR 3.0 18.5 + - - +
239A LEU 4.4 0.9 - - - +
241A ARG* 1.3 74.5 - - - +
243A ALA* 1.3 66.5 + - - +
245A ASP 3.8 0.2 + - - -
246A CYS* 2.0 65.9 + - - +
249A TYR* 4.7 4.0 - - + +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.7 36.6 - - + +
205A LEU* 3.8 27.8 - - + -
206A ARG* 3.3 26.2 + - - +
209A PHE* 4.4 4.0 - - + -
239A LEU 3.1 20.6 + - - +
240A VAL 3.7 2.9 - - - +
242A CYS* 1.3 77.6 - - - +
244A GLN* 1.3 60.9 + - - +
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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
----------------------------------------------------------
206A ARG* 4.1 30.2 + - - +
209A PHE* 3.4 33.9 - - + +
210A GLN* 6.0 3.7 - - - +
221A GLU* 5.8 2.7 - - - +
240A VAL* 2.8 20.9 + - + +
241A ARG* 3.9 5.2 - - - +
242A CYS 4.2 0.2 - - - -
243A ALA* 1.3 79.8 - - - +
245A ASP* 1.3 65.8 + - + +
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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
----------------------------------------------------------
241A ARG* 2.7 19.7 + - - +
244A GLN* 1.3 81.7 - - + +
246A CYS* 1.3 61.7 + - - +
247A GLU* 3.4 14.4 - - - +
248A ASP* 3.2 30.6 + - + +
249A TYR 3.1 16.5 + - - -
286A LYS* 3.2 28.1 + - - +
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Residues in contact with CYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 3.9 4.5 - - - -
242A CYS* 2.0 59.3 + - - +
245A ASP* 1.3 71.5 + - - +
247A GLU* 1.3 71.5 + - - +
249A TYR* 3.3 4.3 + - - +
250A PHE* 3.2 53.6 + - - -
275A ARG* 4.3 11.2 - - - +
279A ASP* 4.6 2.5 - - - +
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Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 3.4 13.7 - - - +
246A CYS* 1.3 82.2 + - - +
248A ASP* 1.3 56.8 + - - +
250A PHE 3.8 0.3 + - - -
251A ALA* 3.2 24.9 + - - +
279A ASP* 3.4 30.2 - - + +
282A GLY* 3.7 37.5 - - - +
283A ILE* 4.0 15.0 - - - +
286A LYS* 3.9 15.2 + - + +
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Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 2.6 34.8 + - - -
245A ASP* 3.2 34.3 + - + +
246A CYS 3.2 0.2 - - - -
247A GLU* 1.3 74.0 - - - +
249A TYR* 1.3 65.7 + - - +
251A ALA* 3.3 6.2 + - - +
252A GLU* 3.1 17.7 + - - +
286A LYS* 4.3 12.8 - - + +
290A LYS* 3.0 35.3 + - - +
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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
----------------------------------------------------------
110A ILE* 5.6 0.2 - - - +
111A GLU* 4.1 12.9 - - + +
115A THR* 4.0 25.4 - - + -
234A LYS* 6.0 0.3 - - - +
237A LEU 5.7 0.2 - - - -
238A THR* 3.3 37.7 + - + +
241A ARG* 3.9 43.2 - - + +
242A CYS 4.7 3.1 - - - +
245A ASP 3.1 12.1 + - - +
246A CYS* 3.3 11.6 + - - +
248A ASP* 1.3 77.1 + - - +
250A PHE* 1.3 76.2 + + - +
252A GLU* 3.2 5.9 + - - +
253A ARG* 3.0 64.6 + - + +
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 4.2 20.6 - - + -
115A THR* 3.7 27.1 - - + -
116A ARG* 4.3 4.0 - - - -
246A CYS* 3.2 38.2 + - - +
249A TYR* 1.3 92.2 - + - +
251A ALA* 1.3 60.5 + - - +
252A GLU 3.3 0.2 - - - -
253A ARG* 3.9 3.3 - - + +
254A LEU* 3.0 33.4 + - - +
271A ILE* 3.8 27.5 - - + +
275A ARG* 3.5 43.7 - - + -
279A ASP* 4.6 0.4 - - - -
283A ILE* 3.6 30.1 - - + -
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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 GLU 3.2 19.5 + - - +
248A ASP* 3.5 10.3 - - - +
249A TYR 3.2 0.8 - - - -
250A PHE* 1.3 78.0 - - - +
252A GLU* 1.3 57.6 + - - +
254A LEU* 3.9 0.6 - - - +
255A TYR* 3.1 22.2 + - - +
283A ILE* 4.1 7.6 - - - +
286A LYS 4.4 2.5 - - - -
287A PHE* 3.4 47.6 - - + +
290A LYS* 4.4 8.7 - - + -
291A TYR* 3.6 2.4 - - - -
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 2.6 36.6 + - - +
248A ASP 3.1 11.8 + - - +
249A TYR* 3.2 7.4 + - - +
251A ALA* 1.3 75.5 - - - +
253A ARG* 1.3 63.2 + - + +
255A TYR* 2.9 2.1 + - - +
256A LYS* 2.8 69.7 + - + +
290A LYS* 4.3 10.0 + - - +
291A TYR* 3.3 19.5 + - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 5.0 18.0 + - - -
111A GLU* 3.2 26.3 + - - +
234A LYS* 5.8 5.7 - - - +
249A TYR* 3.0 60.1 + - + +
250A PHE* 4.1 2.7 - - - +
252A GLU* 1.3 79.3 - - + +
254A LEU* 1.3 61.0 + - - +
256A LYS* 4.6 4.4 - - - +
257A SER* 3.1 26.7 + - - -
264A ASP* 4.9 1.8 + - - -
267A THR* 3.5 33.6 + - - +
270A ARG* 4.2 2.2 - - - +
271A ILE* 3.9 13.9 - - + -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE 3.0 21.7 + - - +
251A ALA* 3.9 5.6 - - - +
253A ARG* 1.3 75.6 - - - +
255A TYR* 1.3 62.0 + - - +
257A SER* 2.7 16.4 + - - -
258A MET* 3.2 18.9 - - - +
268A LEU* 4.1 31.9 - - + +
271A ILE* 3.8 37.5 - - + -
272A ILE* 4.4 9.4 - - + -
280A LEU* 5.4 1.6 - - + -
283A ILE* 3.8 18.8 - - + -
287A PHE* 4.7 0.4 - - - -
295A LEU* 3.7 39.5 - - + -
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Residues in contact with TYR 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 15.1 + - - +
252A GLU 2.9 7.0 + - - +
254A LEU* 1.3 77.0 - - - +
256A LYS* 1.3 75.5 + - + +
258A MET* 3.1 15.3 + - - +
259A LYS* 3.3 47.9 + - + -
287A PHE* 3.8 6.5 - + + -
291A TYR* 3.4 54.6 - + + -
293A LYS* 4.3 13.4 + - - -
298A MET* 3.5 36.0 - - + +
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A GLU* 2.8 54.0 + - + +
253A ARG* 4.6 4.0 - - - +
255A TYR* 1.3 86.2 - - + +
257A SER* 1.3 59.2 + - - +
258A MET 3.1 1.9 + - - -
259A LYS* 3.7 15.0 + - + +
401A EDO 4.0 15.8 + - - -
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 3.1 18.5 + - - -
254A LEU* 2.7 24.3 + - - -
256A LYS* 1.3 75.8 - - - +
258A MET* 1.3 61.3 + - - +
263A THR* 3.4 3.5 - - - +
264A ASP* 2.8 54.1 + - - +
267A THR* 4.2 17.7 - - - +
268A LEU* 4.5 7.4 + - - +
401A EDO 4.4 4.5 - - - -
----------------------------------------------------------
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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