Contacts of the helix formed by residues 316 - 341 (chain A) in PDB entry 5Q1B
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 316 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A THR 3.9 0.8 + - - -
315A LEU* 1.4 73.7 - - - +
317A HIS* 1.3 62.7 + - - +
318A GLU* 3.3 14.8 + - - +
319A ASP* 3.1 27.2 + - - +
320A GLN* 3.0 25.5 + - - +
403A LYS* 3.3 32.2 + - - -
404A ASP* 6.2 1.3 - - + -
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Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLN 5.7 2.2 - - - -
315A LEU 3.5 1.5 + - - -
316A ASP* 1.3 76.6 + - - +
318A GLU* 1.3 68.1 + - + +
320A GLN* 3.4 27.2 + - - +
321A ILE* 3.4 26.4 + - - +
750B ARG* 6.1 2.7 - - + +
753B LEU 5.8 0.7 - - - -
754B ASP* 3.5 32.1 + - - -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP* 3.3 13.1 + - - +
317A HIS* 1.3 80.6 - - + +
319A ASP* 1.4 61.0 + - - +
321A ILE* 3.3 12.1 + - - +
322A ALA* 3.1 26.7 + - - +
401A TYR 5.7 1.3 - - - -
403A LYS* 3.7 22.0 - - - +
746B HIS* 5.7 0.9 + - - -
750B ARG* 3.1 37.6 + - - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 5.0 7.3 - - + +
316A ASP* 3.1 30.3 + - + +
318A GLU* 1.4 72.3 - - - +
320A GLN* 1.3 58.5 + - - +
322A ALA* 3.4 5.9 + - - +
323A LEU* 2.9 40.0 + - + +
401A TYR 3.8 4.0 - - - +
402A ILE* 3.6 14.5 - - + +
403A LYS* 2.8 34.0 + - - +
404A ASP* 3.2 33.0 + - - +
408A VAL* 5.1 3.4 - - + +
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 2.9 63.5 + - + +
313A GLN* 3.6 19.0 + - - +
315A LEU* 3.1 22.7 + - + +
316A ASP 3.0 15.2 + - - +
317A HIS* 3.4 32.6 + - - +
319A ASP* 1.3 75.8 - - - +
321A ILE* 1.4 55.4 + - - +
323A LEU* 3.4 1.5 + - - +
324A LEU* 3.1 28.2 + - - +
753B LEU* 4.1 25.2 - - + +
754B ASP* 4.8 0.2 - - - +
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Residues in contact with ILE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A HIS 3.4 16.6 - - - +
318A GLU* 3.3 19.0 + - - +
320A GLN* 1.4 70.9 - - - +
322A ALA* 1.4 56.3 + - - +
324A LEU* 3.2 3.6 + - - +
325A LYS* 2.8 39.2 + - + +
746B HIS* 3.8 37.9 - - + +
749B LEU* 3.9 11.1 - - + +
750B ARG* 3.5 47.8 - - + +
753B LEU* 3.7 19.7 - - + -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU 3.1 16.4 + - - +
319A ASP 3.4 5.6 + - - +
321A ILE* 1.4 76.0 - - - +
323A LEU* 1.4 62.1 + - - +
325A LYS* 4.1 5.8 - - - +
326A GLY* 3.1 20.6 + - - -
399A ARG* 5.0 2.6 - - - -
400A GLN 4.1 16.3 - - - +
401A TYR* 4.1 18.6 - - + +
402A ILE* 3.8 19.2 - - + +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.8 17.0 - - + -
315A LEU* 3.7 30.1 - - + -
319A ASP 2.9 22.6 + - - +
320A GLN 3.7 4.5 - - - +
321A ILE 3.3 0.2 - - - -
322A ALA* 1.4 77.2 - - - +
324A LEU* 1.3 58.5 + - - +
326A GLY 3.6 1.0 + - - -
327A SER* 2.9 28.3 + - - -
394A ILE* 3.3 24.3 - - + +
395A LEU* 4.4 5.8 - - + -
396A SER 3.5 23.6 - - - +
399A ARG* 4.6 6.6 + - + +
402A ILE* 3.7 15.5 - - + -
408A VAL* 3.9 23.1 - - + -
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 4.7 3.4 - - + -
302A LEU* 4.5 16.8 - - + -
303A VAL* 3.8 33.0 - - + -
306A THR* 4.0 23.8 - - + +
312A PHE* 5.4 0.2 - - - -
320A GLN 3.1 14.1 + - - +
321A ILE* 3.2 5.4 + - - +
323A LEU* 1.3 74.6 - - - +
325A LYS* 1.3 63.4 + - - +
327A SER* 3.6 4.1 + - - +
328A ALA* 3.1 24.3 + - + +
394A ILE* 5.5 2.0 - - + +
472A ILE* 4.3 7.2 - - + -
749B LEU* 4.2 18.4 - - + -
753B LEU* 3.7 36.3 - - + -
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 2.8 21.8 + - + +
322A ALA* 4.1 5.8 - - - +
324A LEU* 1.3 71.8 - - - +
326A GLY* 1.3 60.2 + - - +
327A SER 3.5 0.7 + - - -
328A ALA* 4.2 5.2 + - - +
329A VAL* 5.2 2.6 + - - +
448A ASN* 5.2 4.0 - - - +
470A CYS 5.6 0.6 + - - -
471A GLU* 3.3 25.4 + - - +
472A ILE* 4.0 31.2 + - + +
473A TRP 4.8 1.6 + - - -
474A ASP* 3.3 25.7 + - - -
746B HIS* 3.1 35.0 - - + +
749B LEU* 4.3 9.4 - - + +
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Residues in contact with GLY 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ALA 3.1 17.4 + - - -
323A LEU 3.6 0.6 + - - -
324A LEU 3.3 0.2 - - - -
325A LYS* 1.3 75.0 - - - +
327A SER* 1.3 56.1 + - - +
329A VAL 5.5 0.2 - - - -
330A GLU* 3.6 1.6 - - - +
399A ARG* 3.1 36.2 + - - -
448A ASN* 3.4 24.1 + - - -
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 4.7 2.6 - - - +
323A LEU 2.9 20.3 + - - -
324A LEU* 3.3 6.5 + - - +
326A GLY* 1.3 80.2 - - - +
328A ALA* 1.3 66.7 + - - +
329A VAL 3.4 2.0 - - - -
330A GLU* 3.3 4.9 + - - +
331A ALA* 2.9 25.7 + - - +
393A VAL* 3.8 6.2 - - - +
394A ILE* 3.6 34.9 - - - +
399A ARG* 3.7 17.7 - - - +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A HIS* 3.9 5.4 + - - -
299A VAL* 4.4 8.1 - - + -
302A LEU* 3.7 19.1 - - + -
324A LEU* 3.1 17.7 + - + +
325A LYS 4.2 4.1 + - - +
326A GLY 3.9 0.6 - - - -
327A SER* 1.3 77.3 + - - +
329A VAL* 1.3 62.3 + - + +
331A ALA* 3.4 2.4 + - - +
332A MET* 3.2 22.6 + - - +
472A ILE* 3.7 36.8 - - + -
473A TRP* 5.8 0.4 - - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS 5.2 2.8 + - - +
326A GLY 5.5 0.2 - - - -
327A SER 3.4 0.4 - - - -
328A ALA* 1.3 72.8 - - + +
330A GLU* 1.3 66.6 + - - +
332A MET* 3.3 8.5 + - - +
333A PHE* 3.1 41.0 + - + -
448A ASN* 3.8 27.6 - - - +
451A HIS* 3.7 37.5 - - + +
472A ILE 4.5 6.5 - - - +
473A TRP* 3.4 37.7 - - + +
501A 9N7 5.1 2.0 - - + -
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLY 3.9 1.6 - - - +
327A SER 3.3 7.0 + - - +
329A VAL* 1.3 75.2 - - - +
331A ALA* 1.4 57.5 + - - +
333A PHE* 3.4 2.3 + - - -
334A LEU* 2.9 27.3 + - - +
393A VAL* 3.9 14.6 - - + +
399A ARG* 2.8 41.2 + - - -
441A LEU* 4.6 2.1 - - - +
444A LEU* 3.2 44.5 - - + +
445A ARG* 3.5 25.4 + - - +
448A ASN* 3.0 34.3 + - + +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A HIS* 3.6 5.6 - - + +
302A LEU* 3.8 31.0 - - + -
327A SER 2.9 16.7 + - - +
328A ALA 3.7 5.2 - - - +
330A GLU* 1.4 74.2 - - - +
332A MET* 1.3 59.0 + - - +
334A LEU* 3.4 7.9 + - - +
335A ARG* 3.0 30.0 + - - +
390A THR* 4.4 15.8 + - + +
393A VAL* 4.5 8.9 - - + +
394A ILE* 5.3 1.8 - - + -
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.6 4.3 - - + -
295A ALA* 3.7 28.5 - - + -
298A HIS* 3.3 27.5 + - + +
328A ALA 3.2 9.3 + - - +
329A VAL* 3.3 9.6 + - - +
331A ALA* 1.3 74.2 - - - +
333A PHE* 1.3 61.2 + - - +
335A ARG* 3.4 2.6 + - - +
336A SER* 2.8 34.3 + - - +
473A TRP* 3.6 26.2 - - + +
501A 9N7 3.5 66.1 - - + -
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Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 3.1 37.6 + - + -
330A GLU* 3.7 7.9 - - - +
332A MET* 1.3 73.2 - - + +
334A LEU* 1.4 65.7 + - - +
336A SER* 3.3 4.8 + - - -
337A ALA* 3.0 22.5 + - - +
369A MET* 4.2 14.8 - - + -
372A PHE* 4.1 2.9 - - + -
373A TYR* 3.7 29.1 - + - -
444A LEU* 3.8 14.1 - - + -
447A PHE* 3.8 36.1 - + + -
454A MET* 3.9 14.8 - - - -
501A 9N7 3.4 59.5 - + + -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 5.8 0.9 - - - +
330A GLU 2.9 17.4 + - - +
331A ALA* 3.7 7.6 - - - +
332A MET 3.3 0.2 - - - -
333A PHE* 1.4 75.2 - - - +
335A ARG* 1.3 61.7 + - - +
337A ALA* 3.3 8.9 + - - +
338A GLU* 3.2 19.2 + - - +
372A PHE* 4.6 3.1 - - + -
376A ILE* 4.5 19.1 - - + -
381A MET* 5.0 0.2 - - + -
386A TYR* 4.3 20.7 - - + +
389A LEU* 4.0 29.2 - - + +
390A THR* 3.5 41.5 - - + +
393A VAL* 4.6 2.9 - - + -
440A ARG* 6.3 0.4 - - + -
444A LEU* 3.9 24.4 - - + +
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 3.9 7.0 - - - +
267A GLN* 3.3 43.2 + - - +
268A ARG 2.7 30.3 + - - -
269A MET* 6.1 0.2 - - - +
270A PRO* 4.0 20.6 - - - +
273A ILE* 4.7 0.2 - - - +
298A HIS* 4.2 5.2 - - + -
331A ALA 3.0 18.3 + - - +
332A MET 3.6 4.9 - - - +
334A LEU* 1.3 74.2 - - - +
336A SER* 1.3 57.5 + - - +
338A GLU* 2.8 43.7 + - - +
339A ILE* 3.0 40.0 + - + +
342A LYS* 5.2 0.2 - - - +
501A 9N7 3.1 35.4 + - + +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A MET 2.8 22.6 + - - -
333A PHE* 3.3 5.8 + - - -
335A ARG* 1.3 75.2 - - - +
337A ALA* 1.4 57.2 + - - +
339A ILE* 3.8 8.0 - - - +
340A PHE* 2.9 30.0 + - - +
373A TYR* 3.5 12.8 - - - -
501A 9N7 3.2 61.6 + - - -
----------------------------------------------------------
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PHE 3.0 10.5 + - - +
334A LEU* 3.4 11.0 - - + +
336A SER* 1.4 72.2 - - - +
338A GLU* 1.4 63.3 + - - +
340A PHE* 3.4 2.1 + - - +
341A ASN* 2.8 32.9 + - - +
372A PHE* 4.1 4.0 - - + -
373A TYR* 3.6 27.1 - - + -
376A ILE* 3.7 34.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 2.7 35.0 + - - -
334A LEU 3.2 5.9 + - - +
335A ARG* 2.8 34.6 + - - +
337A ALA* 1.4 76.5 - - - +
339A ILE* 1.4 61.7 + - - +
341A ASN* 3.2 12.5 + - - +
342A LYS* 3.2 35.6 + - + +
383A GLN* 4.7 9.2 - - - +
386A TYR* 3.6 52.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PRO* 4.0 26.0 - - + +
273A ILE* 3.8 28.3 - - + -
274A THR* 3.7 21.9 - - + +
335A ARG* 3.0 47.5 + - + +
336A SER* 3.8 5.2 - - - +
338A GLU* 1.4 72.2 - - - +
340A PHE* 1.3 62.6 + - - +
342A LYS* 3.2 24.7 + - - +
344A LEU* 5.9 0.7 - - - +
352A LEU* 4.9 0.9 - - - +
501A 9N7 3.4 43.3 - - + -
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER 2.9 19.6 + - - +
337A ALA* 3.5 8.3 - - - +
338A GLU 3.3 0.2 - - - -
339A ILE* 1.3 76.8 - - - +
341A ASN* 1.3 72.9 + - - +
342A LYS 3.5 6.1 + - - +
344A LEU* 5.8 0.3 - - - +
349A SER* 5.0 11.3 + - - -
352A LEU* 4.4 13.6 - - + +
353A GLU* 3.8 38.8 - - + -
356A ILE* 4.3 4.7 - - + -
370A PHE* 3.4 30.3 - + - -
373A TYR* 3.8 33.2 - + + -
374A LYS* 5.1 4.0 - - + -
501A 9N7 3.2 23.0 - - + -
----------------------------------------------------------
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA 2.8 27.5 + - - +
338A GLU 3.2 4.9 + - - +
340A PHE* 1.3 85.6 - - - +
342A LYS* 1.3 61.6 + - - +
343A LYS* 3.5 6.1 + - - +
373A TYR 2.9 27.7 + - - +
374A LYS* 5.1 1.7 - - - +
376A ILE* 3.8 4.0 - - - +
377A GLY* 3.2 30.3 - - - +
386A TYR* 4.4 8.1 - - - +
----------------------------------------------------------
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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