Contacts of the helix formed by residues 327 - 358 (chain B) in PDB entry 5EKD
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 327 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LYS 5.4 1.3 - - - +
324B LEU* 3.2 10.9 + - - +
325B LYS 3.2 0.4 - - - -
326B LEU* 1.3 81.0 - - + +
328B LYS* 1.3 60.2 + - - +
329B ASP* 3.3 12.3 + - - +
330B HIS* 3.2 39.9 + - + +
331B LEU* 3.4 14.1 + - - +
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Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLN* 3.4 34.4 + - - +
93B LEU* 4.0 18.2 - - + -
325B LYS 4.3 15.9 + - - +
326B LEU 3.9 2.1 + - - -
327B ASP* 1.3 73.4 + - - +
329B ASP* 1.3 63.6 + - - +
331B LEU* 3.3 12.5 + - + +
332B GLU* 3.0 38.2 + - - +
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Residues in contact with ASP 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASP* 3.2 9.5 + - - +
328B LYS* 1.3 78.4 - - - +
330B HIS* 1.3 62.7 + - - +
332B GLU* 3.5 14.1 + - - +
333B LYS* 3.1 24.9 + - - +
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Residues in contact with HIS 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.7 6.2 - - + +
324B LEU* 4.6 20.5 - - + +
327B ASP* 3.2 30.9 + - + +
328B LYS 3.2 0.6 - - - -
329B ASP* 1.3 80.4 - - - +
331B LEU* 1.3 68.9 + - + +
333B LYS* 3.4 9.8 + - - +
334B VAL* 3.0 47.0 + - + +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.6 33.7 - - + +
94B ASP* 6.0 0.2 - - - +
96B THR* 3.9 18.3 + - + +
97B ALA* 4.0 24.5 - - + +
100B LEU* 4.0 26.5 - - + -
324B LEU* 3.7 25.1 - - + +
325B LYS* 4.5 7.2 - - + +
327B ASP 3.6 11.7 - - - +
328B LYS* 3.3 14.5 + - + +
330B HIS* 1.3 81.6 - - + +
332B GLU* 1.3 62.7 + - - +
334B VAL* 3.5 4.6 + - - +
335B LEU* 3.4 18.9 + - - +
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.6 24.6 - - + +
328B LYS* 3.0 27.4 + - - +
329B ASP* 3.7 12.8 - - - +
331B LEU* 1.3 75.4 - - - +
333B LYS* 1.3 58.0 + - - +
335B LEU* 3.4 6.7 + - - +
336B GLN* 3.0 28.7 + - - +
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASP 3.1 18.0 + - - +
330B HIS* 3.8 10.1 - - - +
332B GLU* 1.3 74.9 - - - +
334B VAL* 1.3 63.4 + - + +
336B GLN* 3.3 22.3 + - - +
337B ILE* 3.1 43.3 + - + +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 4.7 3.6 - - + -
100B LEU* 4.4 12.8 - - + -
106B PRO* 4.2 31.7 - - + +
111B LEU* 3.9 26.2 - - + +
330B HIS* 3.0 43.4 + - + +
331B LEU* 3.8 5.8 - - - +
332B GLU 3.4 0.2 - - - -
333B LYS* 1.3 77.2 - - + +
335B LEU* 1.3 62.1 + - - +
337B ILE* 3.5 6.7 + - - +
338B GLY* 3.1 17.0 + - - -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 4.1 16.6 - - + -
92B ILE* 3.9 24.0 - - + -
96B THR* 3.6 24.7 - - + +
111B LEU* 3.7 26.4 - - + +
112B PHE* 3.8 19.3 - - - +
113B GLN* 3.9 27.8 - - + +
331B LEU 3.4 7.0 + - - +
332B GLU* 3.4 9.1 + - - +
333B LYS 3.3 0.4 - - - -
334B VAL* 1.3 75.3 - - - +
336B GLN* 1.3 61.8 + - - +
339B SER* 2.8 35.9 + - - -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLU 3.0 17.1 + - - +
333B LYS* 3.6 22.1 - - - +
334B VAL 3.3 0.2 - - - -
335B LEU* 1.3 75.9 - - - +
337B ILE* 1.3 77.4 + - - +
339B SER* 3.8 5.5 - - - -
340B ALA* 3.1 23.4 + - + +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 5.7 2.5 - - - +
333B LYS* 3.1 41.2 + - + +
334B VAL* 4.0 5.8 - - - +
336B GLN* 1.3 90.9 - - - +
338B GLY* 1.3 62.2 + - - +
340B ALA* 3.4 6.4 + - - +
341B LYS* 3.3 42.3 + - + +
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Residues in contact with GLY 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 3.5 15.5 - - - +
111B LEU 3.3 22.0 - - - -
112B PHE* 3.5 7.9 - - - +
334B VAL 3.1 11.0 + - - -
337B ILE* 1.3 76.6 - - - +
339B SER* 1.3 61.6 + - - +
341B LYS* 3.3 10.5 + - - +
342B ALA 3.1 18.5 + - - -
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.5 9.3 - - - +
113B GLN* 3.1 31.4 + - - +
116B GLN* 3.7 25.6 - - - +
117B VAL* 4.0 3.7 - - - +
335B LEU 2.8 26.0 + - - -
336B GLN* 3.8 6.3 - - - -
338B GLY* 1.3 73.2 - - - +
340B ALA* 1.3 56.4 + - - +
342B ALA* 3.3 2.7 + - - +
343B LYS* 2.8 30.4 + - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 3.1 17.0 + - + +
337B ILE* 3.8 7.0 - - - +
338B GLY 3.3 0.2 - - - -
339B SER* 1.3 75.6 - - - +
341B LYS* 1.3 62.2 + - + +
343B LYS* 3.4 7.4 + - - +
344B GLU* 3.4 26.9 + - - +
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO 4.6 13.2 + - - -
107B GLU* 4.4 16.8 + - - +
109B SER 5.5 0.2 - - - -
110B ILE* 4.2 26.2 - - + +
337B ILE* 3.3 32.1 + - + +
338B GLY* 3.3 13.2 + - - +
339B SER 3.2 0.6 - - - -
340B ALA* 1.3 75.4 - - + +
342B ALA* 1.3 65.3 + - - +
344B GLU* 3.5 6.5 + - - +
345B LEU* 3.4 24.8 + - - +
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.8 0.7 - - + -
110B ILE* 4.2 6.0 - - + +
112B PHE* 3.7 29.4 - - + -
117B VAL* 4.2 1.6 - - + -
171B TYR* 3.7 26.4 - - + +
338B GLY 3.1 13.5 + - - +
339B SER 3.8 2.7 - - - +
341B LYS* 1.3 76.5 - - - +
343B LYS* 1.3 66.2 + - - +
345B LEU* 3.1 10.1 + - - +
346B ALA* 3.0 22.9 + - - +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 5.1 0.6 + - - -
343A LYS* 6.1 0.6 - - - +
116B GLN 4.4 11.6 + - - +
117B VAL* 4.1 16.1 - - + +
118B SER* 3.1 21.8 + - - +
119B GLU* 2.9 35.6 + - - +
339B SER 2.8 18.5 + - - +
340B ALA* 3.6 9.4 - - - +
341B LYS 3.2 0.4 - - - -
342B ALA* 1.3 77.3 - - - +
344B GLU* 1.3 58.7 + - - +
346B ALA* 3.7 0.9 - - - +
347B TYR* 2.9 30.5 + - - +
406B GOL 3.7 30.3 - - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA 3.4 13.4 + - - +
341B LYS* 3.9 7.9 - - - +
342B ALA 3.2 0.2 - - - -
343B LYS* 1.3 82.0 - - - +
345B LEU* 1.3 61.8 + - + +
347B TYR* 4.0 4.7 - - - +
348B THR* 3.2 23.2 + - - -
406B GOL 2.4 45.5 + - - -
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 4.1 31.0 - - - +
70B LEU* 4.1 18.4 - - + -
110B ILE* 3.7 29.6 - - + -
171B TYR* 4.1 9.9 - - + -
341B LYS 3.5 10.8 - - - +
342B ALA* 3.1 7.3 + - - +
344B GLU* 1.3 81.6 - - + +
346B ALA* 1.3 61.4 + - - +
348B THR* 3.5 11.3 + - - -
349B VAL* 3.5 18.5 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.7 24.0 - - + -
119B GLU* 4.0 5.6 - - + -
170B LEU* 3.8 30.3 - - + +
171B TYR* 3.9 8.3 - - + -
342B ALA 3.0 16.1 + - - +
343B LYS 3.7 3.4 - - - +
345B LEU* 1.3 75.9 - - - +
347B TYR* 1.3 66.2 + - - +
348B THR 3.3 0.2 + - - -
349B VAL 3.3 1.2 + - - -
350B CYS* 3.0 23.9 + - - +
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Residues in contact with TYR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 3.8 22.0 - - - +
343B LYS* 2.9 20.3 + - - +
344B GLU* 4.0 6.5 - - - +
345B LEU 3.4 0.2 - - - -
346B ALA* 1.3 75.3 - - - +
348B THR* 1.3 71.5 + - - +
350B CYS* 3.3 1.7 + - + +
351B GLN* 3.1 66.1 + - + +
406B GOL 3.3 50.2 + - - +
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Residues in contact with THR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU 3.2 13.1 + - - -
345B LEU* 3.5 9.1 + - - -
346B ALA 3.1 0.6 - - - -
347B TYR* 1.3 88.4 - - - +
349B VAL* 1.3 63.0 + - + +
351B GLN* 3.6 5.6 + - - +
352B GLU* 3.5 29.4 + - + +
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Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 6.2 1.6 - - - +
169B LEU 4.7 0.4 - - - +
170B LEU* 3.3 38.8 - - + +
171B TYR* 5.0 2.9 - - - -
172B LYS* 4.3 21.1 - - + +
203B PHE* 4.2 20.2 - - + -
204B PHE* 4.6 4.7 - - + -
345B LEU 3.7 11.0 - - - +
346B ALA 3.3 5.2 + - - +
348B THR* 1.3 79.5 - - + +
350B CYS* 1.3 65.1 + - - +
352B GLU* 3.1 14.6 + - - +
353B VAL* 3.0 25.6 + - + +
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Residues in contact with CYS 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 3.6 28.3 - - + +
122B GLN* 4.1 23.6 - - - -
123B LEU* 4.9 7.0 - - - -
126B ILE* 5.8 2.7 - - - -
170B LEU* 4.4 5.8 - - + +
346B ALA 3.0 16.7 + - - +
347B TYR* 3.9 2.7 - - + +
349B VAL* 1.3 77.7 - - - +
351B GLN* 1.3 63.3 + - + +
353B VAL* 3.2 13.1 + - - +
354B LYS* 3.0 45.1 + - - +
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Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 4.6 5.3 + - - +
347B TYR* 3.1 58.6 + - + +
348B THR* 3.8 6.1 - - - +
350B CYS* 1.3 77.4 - - - +
352B GLU* 1.3 61.1 + - - +
354B LYS* 3.3 27.1 + - - +
355B LYS* 3.2 42.4 + - - +
360B LEU* 3.6 23.4 - - - +
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LYS* 3.2 25.7 + - - -
203B PHE* 3.5 19.5 - - + -
348B THR* 3.5 20.8 + - + +
349B VAL* 3.1 16.1 + - - +
351B GLN* 1.3 73.5 - - - +
353B VAL* 1.3 66.2 + - - +
355B LYS* 3.3 20.9 + - - +
356B LEU* 3.1 27.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.3 12.3 - - + -
126B ILE* 3.8 27.4 - - + -
170B LEU* 6.3 0.2 - - + -
196B PHE* 4.1 13.9 - - + -
203B PHE* 3.6 23.6 - - + -
204B PHE* 4.1 13.9 - - + -
349B VAL* 3.0 22.4 + - + +
350B CYS* 3.5 13.2 - - - +
352B GLU* 1.3 76.6 - - - +
354B LYS* 1.3 64.3 + - + +
356B LEU* 3.2 10.1 + - - +
357B VAL* 3.1 27.9 + - + +
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.1 31.7 + - - -
116A GLN* 3.2 22.1 + - - +
118A SER* 6.2 1.4 - - - -
122B GLN* 4.2 13.6 - - - +
126B ILE* 5.6 2.9 - - + -
350B CYS* 3.0 32.4 + - - +
351B GLN* 3.5 28.0 + - - +
352B GLU 3.2 0.2 - - - -
353B VAL* 1.3 78.5 - - + +
355B LYS* 1.3 62.9 + - - +
357B VAL* 3.4 1.9 + - - +
358B GLY 3.1 4.9 + - - -
359B PHE* 3.1 51.2 + - + +
360B LEU* 3.4 14.3 + - + -
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG* 2.6 29.4 + - - +
351B GLN* 3.2 34.1 + - - +
352B GLU* 3.6 18.6 - - + +
353B VAL 3.3 0.2 - - - -
354B LYS* 1.3 80.5 - - - +
356B LEU* 1.3 60.4 + - + +
358B GLY 3.5 1.6 + - - -
360B LEU* 3.5 34.5 - - + +
----------------------------------------------------------
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.5 12.0 - - - +
196B PHE* 4.2 17.3 - - + -
200B TYR* 3.3 48.1 - - + +
203B PHE* 3.8 37.9 - - + -
352B GLU* 3.1 15.8 + - + +
353B VAL* 3.2 7.4 + - - +
355B LYS* 1.3 79.2 - - + +
357B VAL* 1.3 61.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 4.1 19.1 - - + -
83A GLN 5.1 1.9 - - - +
84A ASP 5.0 0.2 - - - -
85A PRO* 3.5 16.3 - - - +
88A LEU* 3.5 7.6 - - - +
126B ILE* 4.4 17.0 - - + -
196B PHE* 4.5 2.0 - - + -
200B TYR* 3.8 32.4 + - + +
353B VAL* 3.1 30.1 + - + +
354B LYS 3.9 3.6 - - - +
355B LYS 3.3 0.4 - - - -
356B LEU* 1.3 76.4 - - - +
358B GLY* 1.3 56.7 - - - +
359B PHE* 3.8 33.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.6 18.4 - - - -
88A LEU* 4.1 7.6 - - - -
89A ARG* 3.5 34.3 + - - +
92A ILE* 3.8 5.2 - - - +
354B LYS 3.1 3.8 + - - -
355B LYS 3.5 6.7 + - - -
356B LEU 3.3 2.6 - - - -
357B VAL* 1.3 79.0 - - - +
359B PHE* 1.3 64.5 - - - +
360B LEU 3.2 3.6 - - - -
----------------------------------------------------------
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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