Contacts of the helix formed by residues 240 - 266 (chain A) in PDB entry 5U3W
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 GLU 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.5 16.0 - - - -
239A LYS* 1.3 83.3 + - + +
241A ILE* 1.3 60.2 + - - +
242A SER* 4.1 7.9 + - - +
243A VAL* 3.3 23.2 + - + +
244A HIS* 2.8 28.2 + - - +
321A ARG* 2.6 50.9 + - - -
506A PGO 5.4 3.8 + - - +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 4.1 40.6 - - + -
219A LEU* 4.2 28.5 - - + -
238A TYR* 3.4 22.5 + - + +
240A GLU* 1.3 73.1 - - - +
242A SER* 1.3 63.4 + - - +
244A HIS* 3.3 7.0 + - + +
245A VAL* 3.0 23.4 + - + +
316A PHE* 4.5 6.3 - - + -
320A LEU* 4.3 17.7 - - + -
506A PGO 4.8 16.6 - - - +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU* 3.3 10.1 + - - +
241A ILE* 1.3 78.3 - - - +
243A VAL* 1.3 57.1 + - - +
245A VAL* 3.5 4.7 + - - +
246A PHE* 3.0 24.6 + - - +
320A LEU* 3.6 17.8 - - - +
321A ARG* 3.1 31.7 + - - +
324A PHE* 3.8 30.4 - - - +
506A PGO 3.3 15.3 + - - +
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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 LYS* 4.0 17.3 - - + +
240A GLU* 3.3 33.3 + - + +
241A ILE 3.3 0.2 - - - -
242A SER* 1.3 75.6 - - - +
244A HIS* 1.3 59.4 + - - +
246A PHE* 3.1 7.7 + - - +
247A TYR* 2.8 64.3 + - + +
321A ARG* 4.4 2.5 - - - +
324A PHE* 4.0 13.9 - - + -
427A THR* 3.6 24.7 - - + +
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Residues in contact with HIS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 4.2 24.2 - - + -
223A GLU* 2.5 38.4 + - + +
232A VAL* 4.1 9.2 - - + -
235A LEU* 3.5 29.1 - - + +
238A TYR* 4.2 25.8 - + + -
239A LYS 5.8 1.0 - - - +
240A GLU 2.8 17.9 + - - +
241A ILE* 3.5 7.6 - - + +
243A VAL* 1.3 77.4 - - - +
245A VAL* 1.3 64.1 + - - +
247A TYR* 3.2 13.7 + - - +
248A ARG* 3.2 25.0 + - + +
502A 7U1 5.8 0.7 - + - -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 4.5 10.3 - - + -
241A ILE 3.0 18.9 + - - +
242A SER 3.6 7.4 - - - +
244A HIS* 1.3 76.7 - - + +
246A PHE* 1.3 63.7 + - - +
248A ARG* 3.2 6.9 + - - +
249A CYS* 3.0 29.7 + - - -
316A PHE* 4.4 12.3 - - + -
317A LEU* 4.0 5.8 - - + -
320A LEU* 3.7 30.5 - - + -
328A ILE* 4.7 3.1 - - + -
502A 7U1 3.6 40.4 - - + -
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER 3.0 14.0 + - - +
243A VAL* 3.1 8.7 + - - +
245A VAL* 1.3 78.7 - - - +
247A TYR* 1.3 62.7 + + - +
249A CYS* 3.2 8.4 + - - +
250A GLN* 2.9 38.6 + - - +
324A PHE* 3.7 26.5 - + + -
327A ILE* 5.1 3.4 - - + -
328A ILE* 6.5 0.2 - - - -
417A MET* 3.7 32.5 - - + -
420A ILE* 4.3 10.5 - - + -
427A THR* 3.5 33.2 - - + -
428A SER 3.8 10.8 - - - -
429A LEU* 3.8 7.2 - - + -
502A 7U1 3.7 36.3 - - + -
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Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 4.3 12.3 - - + -
236A PRO* 3.6 47.9 - - + +
237A PRO 3.7 14.6 + - - -
238A TYR* 5.4 1.8 - - - -
239A LYS* 4.2 6.2 - - + +
243A VAL* 2.8 38.7 + - + +
244A HIS* 3.2 13.2 + - - +
246A PHE* 1.3 79.1 - + - +
248A ARG* 1.3 57.8 + - - +
250A GLN* 3.3 18.0 + - - +
251A CME 2.9 33.4 + - - -
426A GLU 3.7 5.4 + - - -
427A THR* 3.6 9.9 - - + -
428A SER* 2.8 46.3 + - - -
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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
----------------------------------------------------------
223A GLU* 2.7 42.4 + - - -
228A TRP* 3.7 48.6 - - - +
230A GLN* 3.2 29.7 + - - +
232A VAL* 3.5 21.4 - - - +
235A LEU* 3.9 21.1 - - + +
244A HIS* 3.2 21.7 + - + +
245A VAL* 3.7 7.4 - - - +
247A TYR* 1.3 74.1 - - - +
249A CYS* 1.3 65.8 + - - +
251A CME 3.5 6.7 + - - +
252A THR* 3.1 28.2 + - - -
502A 7U1 3.9 23.8 - - + -
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Residues in contact with CYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 3.0 28.8 + - - -
246A PHE* 3.2 10.1 + - - +
248A ARG* 1.3 77.8 - - - +
250A GLN* 1.3 53.5 + - - +
252A THR* 3.4 2.6 + - - -
253A THR* 2.7 37.6 + - - -
328A ILE* 4.7 9.2 - - - -
502A 7U1 3.4 78.3 - - + +
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PHE* 2.9 26.1 + - + +
247A TYR* 3.6 20.6 - - - +
248A ARG 3.2 0.2 - - - -
249A CYS* 1.3 75.5 - - - +
251A CME 1.3 64.7 + - - +
253A THR* 3.3 2.1 + - - -
254A VAL* 3.1 24.8 + - - +
417A MET* 5.6 0.5 - - - +
428A SER 3.3 19.6 + - - +
429A LEU* 3.3 9.4 - - - +
430A HIS* 2.8 36.2 + - + +
433A LEU* 3.6 20.9 - - + +
502A 7U1 4.0 15.8 - - + +
507A PGO 3.5 16.9 + - + +
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Residues in contact with CME 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN* 3.2 42.3 + - + +
234A GLY 5.2 4.0 - - - +
235A LEU* 3.4 30.3 - - + -
236A PRO* 5.3 0.9 - - - -
247A TYR 2.9 15.2 + - - +
248A ARG* 4.0 5.6 - - - +
249A CYS 3.4 0.2 - - - -
250A GLN* 1.3 75.1 + - - +
252A THR* 1.3 57.9 + - - +
254A VAL* 3.4 26.9 + - - +
255A GLU* 3.0 27.7 + - - +
258A ARG* 3.4 27.1 + - - -
430A HIS* 4.1 14.7 + - + -
507A PGO 3.4 33.0 - - + -
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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 ARG 3.1 18.8 + - - -
249A CYS 3.8 4.3 - - - -
251A CME 1.3 74.0 + - - +
253A THR* 1.3 63.8 + - - +
255A GLU* 3.3 7.7 + - + +
256A THR* 2.8 30.8 + - - +
502A 7U1 3.3 44.3 - - + +
504A PGO 4.0 14.8 - - - +
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A CYS 2.7 21.6 + - - -
250A GLN 3.3 5.8 + - - -
252A THR* 1.3 77.1 - - - +
254A VAL* 1.3 56.9 + - - +
256A THR* 3.2 6.0 + - - -
257A VAL* 2.9 28.7 + - + +
287A HIS* 4.1 6.1 - - + +
290A ILE* 4.0 20.7 - - + +
291A PHE* 6.0 0.8 - - + -
433A LEU* 3.9 21.8 - - + -
502A 7U1 3.7 50.0 - - + +
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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 GLN 3.1 16.8 + - - +
251A CME 3.8 11.4 - - - +
253A THR* 1.3 75.0 - - - +
255A GLU* 1.3 63.4 + - - +
257A VAL* 3.3 10.0 + - - +
258A ARG* 3.1 39.0 + - - +
430A HIS* 3.8 43.1 - - + +
432A LEU* 4.3 4.7 - - + -
433A LEU* 3.9 19.5 - - + -
274B PHE* 3.8 19.1 - - + -
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS* 3.8 38.7 + - + -
251A CME 3.0 17.9 + - - +
252A THR* 3.3 9.6 + - + +
254A VAL* 1.3 78.8 - - - +
256A THR* 1.3 57.9 + - - +
258A ARG* 3.2 33.6 + - - +
259A GLU* 3.2 41.1 + - + +
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Residues in contact with THR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 5.2 0.7 - - + -
252A THR* 2.8 18.4 + - - +
253A THR* 3.2 5.8 + - - -
255A GLU* 1.3 76.7 - - - +
257A VAL* 1.3 64.8 + - - +
258A ARG 3.2 0.2 - - - -
259A GLU* 3.1 16.5 + - - +
260A LEU* 2.9 24.4 + - + +
290A ILE* 3.7 19.5 - - + -
293A MET* 3.7 29.8 - - + -
502A 7U1 4.8 0.2 - - - -
504A PGO 3.8 30.1 + - - +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 2.9 22.4 + - + +
254A VAL* 3.5 10.1 - - - +
256A THR* 1.3 75.4 - - - +
258A ARG* 1.3 56.8 + - - +
260A LEU* 3.4 8.7 + - - +
261A THR* 3.0 38.4 + - - +
286A VAL* 4.1 27.5 - - + +
287A HIS* 6.0 0.2 - - + -
290A ILE* 4.1 8.7 - - + +
432A LEU* 4.0 21.5 - - + -
433A LEU* 4.7 7.9 - - + -
436A ILE* 4.6 9.4 - - + -
503A B7G 4.1 24.5 - - + -
274B PHE* 4.7 0.9 - - + -
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A CME 3.4 24.0 + - - -
254A VAL* 3.1 23.5 + - - +
255A GLU* 3.2 40.3 + - - +
256A THR 3.2 0.2 - - - -
257A VAL* 1.3 76.6 - - - +
259A GLU* 1.3 62.8 + - + +
261A THR* 3.4 6.5 + - - -
262A GLU* 3.2 27.8 + - + +
430A HIS* 5.5 0.8 + - - -
274B PHE* 3.4 47.5 - - + -
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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
----------------------------------------------------------
189A ASN* 3.7 16.3 - - - +
190A PHE* 3.5 26.6 - - + -
191A ASN* 2.9 43.9 + - - +
255A GLU* 3.2 29.9 + - - +
256A THR* 3.1 17.1 + - - +
258A ARG* 1.3 76.1 - - - +
260A LEU* 1.3 59.1 + - - +
262A GLU* 3.2 6.6 + - - +
263A PHE* 2.8 28.8 + - - +
504A PGO 5.4 3.3 + - - -
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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
----------------------------------------------------------
190A PHE* 3.7 20.0 - - + -
256A THR 2.9 21.0 + - - +
257A VAL 3.8 3.8 - - - +
259A GLU* 1.3 76.9 - - - +
261A THR* 1.3 56.6 + - - +
263A PHE* 3.4 9.3 + - + +
264A ALA* 2.9 30.7 + - - +
282A LEU* 4.3 4.4 - - + +
286A VAL* 3.8 31.4 - - + +
289A ALA* 3.8 9.9 - - + -
290A ILE* 3.8 26.9 - - + -
293A MET* 3.8 17.0 - - + -
352A ILE* 3.7 24.9 - - + -
356A ILE* 4.6 6.3 - - + +
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Residues in contact with THR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 3.0 23.5 + - - +
258A ARG* 3.6 8.0 - - - -
259A GLU 3.2 0.2 - - - -
260A LEU* 1.3 78.2 - - - +
262A GLU* 1.3 61.0 - - - +
264A ALA* 3.4 2.1 + - - +
265A LYS* 2.9 48.0 + - + +
282A LEU* 3.6 33.3 - - + +
503A B7G 3.6 16.2 - - + +
274B PHE* 5.7 0.2 - - - -
275B LEU* 4.4 16.6 - - + +
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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
----------------------------------------------------------
189A ASN* 3.2 22.4 - - + +
258A ARG 3.2 14.9 + - - +
259A GLU* 3.8 7.4 - - - +
261A THR* 1.3 77.4 - - - +
263A PHE* 1.3 66.3 + - - +
265A LYS* 3.4 32.1 + - - +
266A SER* 3.0 27.9 + - - -
271B SER 5.1 3.8 - - - +
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Residues in contact with PHE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 3.7 15.0 - - + -
185A ALA* 3.7 7.4 - - + -
186A TYR* 3.6 39.0 - - + -
189A ASN* 3.7 11.1 - - + +
190A PHE* 3.7 23.6 - + + -
259A GLU 2.8 17.2 + - - +
260A LEU* 3.5 9.2 - - + +
262A GLU* 1.3 75.4 - - - +
264A ALA* 1.3 67.3 + - + +
266A SER* 3.0 13.9 + - - -
267A ILE* 3.4 32.0 + - + +
349A ALA* 3.5 25.6 - - - -
352A ILE* 3.8 25.4 - - + -
353A ALA* 4.1 7.6 - - + -
356A ILE* 5.4 3.8 - - + -
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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
----------------------------------------------------------
260A LEU 2.9 17.5 + - - +
261A THR 3.7 3.4 - - - +
263A PHE* 1.3 78.9 - - + +
265A LYS* 1.3 58.9 + - - +
267A ILE* 3.0 34.7 + - + +
270A PHE* 3.3 48.0 - - + +
282A LEU* 4.3 9.0 - - + -
356A ILE* 4.5 8.5 - - + -
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 2.9 39.8 + - + +
262A GLU* 3.6 30.7 + - - +
264A ALA* 1.3 77.1 - - - +
266A SER* 1.3 58.7 + - - +
267A ILE 3.1 2.0 + - - +
268A PRO* 5.4 0.2 - - - +
270A PHE* 4.1 5.4 - - + -
271A SER* 2.7 28.5 + - - +
278A GLN* 4.2 16.4 - - - +
265B LYS* 3.9 26.7 - - - +
271B SER* 4.4 18.4 + - - -
275B LEU* 4.4 10.6 - - + +
278B GLN* 4.7 2.0 - - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A HIS* 3.3 24.9 + - - -
185A ALA* 3.7 15.2 - - - +
188A LYS* 4.3 13.7 + - - +
189A ASN* 3.0 26.4 + - - -
262A GLU* 3.0 14.9 + - - -
263A PHE 3.0 8.9 + - - -
265A LYS* 1.3 75.8 - - - +
267A ILE* 1.3 59.3 + - - +
268A PRO* 3.7 0.7 - - - +
----------------------------------------------------------
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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