Contacts of the helix formed by residues 312 - 338 (chain A) in PDB entry 3DCT
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 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR 4.0 0.2 + - - -
311A LEU* 1.3 73.4 - - - +
313A HIS* 1.3 67.2 + - - +
314A GLU* 3.4 12.4 + - - +
315A ASP* 2.9 36.5 + - - +
316A GLN* 3.1 9.7 + - - +
399A LYS* 3.0 43.8 + - + +
400A ASP* 5.8 3.1 - - + -
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Residues in contact with HIS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN 6.3 0.6 - - - -
310A THR* 6.0 1.8 + - - -
311A LEU 3.7 11.8 + - - -
312A ASP* 1.3 79.3 + - - +
314A GLU* 1.3 60.3 + - - +
315A ASP 3.2 0.2 - - - -
316A GLN* 3.5 28.2 + - - +
317A ILE* 3.5 27.0 + - + +
754B ASP* 5.4 8.4 + - - -
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASP* 3.1 16.7 + - - +
313A HIS* 1.3 77.7 - - - +
315A ASP* 1.3 63.5 + - - +
316A GLN 3.4 0.2 - - - -
317A ILE* 3.8 9.4 + - - +
318A ALA* 3.4 19.1 + - - +
397A TYR 5.0 2.5 - - - +
399A LYS* 3.9 20.0 - - + +
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 4.7 9.2 - - + +
312A ASP* 2.9 31.5 + - + +
314A GLU* 1.3 77.9 - - - +
316A GLN* 1.3 62.4 + - - +
317A ILE 3.3 0.2 - - - -
318A ALA* 3.3 6.1 + - - +
319A LEU* 3.0 34.4 + - + +
397A TYR 4.3 1.2 - - - +
398A ILE* 3.9 12.4 - - + +
399A LYS* 3.0 34.9 + - - +
400A ASP* 3.2 34.0 + - - +
404A VAL* 5.4 2.4 - - + +
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Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.1 56.3 - - + +
309A GLN* 3.6 14.4 - - - +
310A THR 4.0 0.3 + - - -
311A LEU* 3.6 16.7 - - + +
312A ASP 3.1 9.9 + - - +
313A HIS* 3.6 32.8 + - - +
314A GLU 3.4 0.2 - - - -
315A ASP* 1.3 79.2 - - - +
317A ILE* 1.3 62.4 + - - +
319A LEU* 3.3 2.9 + - - +
320A LEU* 3.0 28.6 + - - +
753B LEU* 3.9 27.0 - - + +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 3.5 15.9 + - + +
314A GLU* 4.0 10.5 - - - +
315A ASP 3.3 0.4 - - - -
316A GLN* 1.3 79.8 - - - +
318A ALA* 1.3 55.9 + - - +
320A LEU* 3.2 6.0 + - - +
321A LYS* 2.7 63.6 + - + +
746B HIS* 3.9 35.7 - - + +
749B LEU* 4.2 15.0 - - + -
750B ARG* 4.8 8.7 - - + +
753B LEU* 3.9 23.6 - - + -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU 3.4 11.4 + - - +
315A ASP 3.3 8.9 + - - +
316A GLN 3.3 0.4 - - - -
317A ILE* 1.3 82.3 - - + +
319A LEU* 1.3 57.8 + - - +
321A LYS* 4.0 5.1 - - - +
322A GLY* 2.9 25.3 + - - -
395A ARG* 4.4 6.1 - - - +
396A GLN 4.0 14.6 - - - +
397A TYR* 4.1 14.1 - - + +
398A ILE* 3.6 20.4 - - + -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.6 28.0 - - + -
311A LEU* 3.9 20.4 - - + -
315A ASP* 3.0 20.7 + - + +
316A GLN 3.7 4.3 - - - +
317A ILE 3.2 0.2 - - - -
318A ALA* 1.3 74.5 - - - +
320A LEU* 1.3 57.0 + - - +
322A GLY 3.9 0.3 - - - -
323A SER* 2.7 39.0 + - - -
390A ILE* 3.7 22.4 - - + +
391A LEU* 4.5 6.7 - - + -
392A SER 3.3 28.7 - - - +
395A ARG* 4.2 6.7 + - + -
398A ILE* 3.7 17.9 - - + -
404A VAL* 4.2 13.2 - - + -
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.5 6.5 - - + +
299A VAL* 4.1 28.5 - - + +
302A THR* 3.8 32.1 - - + +
308A PHE* 4.5 6.7 - - + -
316A GLN 3.0 19.6 + - - +
317A ILE* 3.7 5.4 - - - +
319A LEU* 1.3 73.6 - - - +
321A LYS* 1.3 65.6 + - - +
323A SER* 3.9 2.8 + - - +
324A ALA* 3.3 21.5 + - - +
390A ILE* 5.1 2.5 - - + -
468A ILE* 3.5 20.3 - - + +
749B LEU* 4.6 9.6 - - + -
753B LEU* 4.1 35.7 - - + -
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 2.7 34.1 + - + +
318A ALA* 4.0 5.6 - - - +
320A LEU* 1.3 76.2 - - - +
322A GLY* 1.3 59.2 + - - +
323A SER 3.8 0.2 + - - -
324A ALA* 4.4 3.3 + - - +
325A VAL* 5.5 0.5 + - - +
444A ASN* 6.0 0.2 + - - -
467A GLU 3.6 7.2 - - - +
468A ILE* 3.3 43.4 - - + +
469A TRP* 4.6 8.8 + - - -
470A ASP* 2.4 44.1 + - - +
746B HIS* 2.9 38.8 + - + -
749B LEU* 4.1 4.9 - - + -
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Residues in contact with GLY 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA 2.9 19.0 + - - -
319A LEU 3.5 0.6 + - - -
320A LEU 3.3 0.2 - - - -
321A LYS* 1.3 78.6 - - - +
323A SER* 1.3 58.1 + - - +
324A ALA 3.7 0.2 - - - -
325A VAL 5.3 0.4 - - - -
326A GLU* 4.1 3.8 - - - +
395A ARG* 3.2 35.6 + - - -
444A ASN* 4.2 13.4 + - - -
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 5.9 1.6 - - - +
319A LEU 2.7 22.7 + - - -
320A LEU* 3.9 4.9 + - - +
321A LYS 3.5 0.2 - - - -
322A GLY* 1.3 76.2 - - - +
324A ALA* 1.3 59.3 + - - +
325A VAL 3.3 2.7 - - - -
326A GLU* 3.0 5.3 + - - -
327A ALA* 2.7 35.4 + - - +
389A VAL* 3.7 13.2 - - - -
390A ILE* 3.7 27.4 - - - +
395A ARG* 3.5 20.2 - - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 5.3 1.8 - - + -
298A LEU* 3.9 19.2 - - + +
320A LEU 3.3 18.4 + - - +
321A LYS 4.4 2.2 + - - +
322A GLY 3.7 1.2 - - - -
323A SER* 1.3 76.0 + - - +
325A VAL* 1.3 63.1 + - - +
327A ALA* 3.8 1.2 - - - +
328A MET* 3.0 37.6 + - + +
468A ILE* 3.9 14.6 - - + -
469A TRP* 3.8 20.9 - - + +
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 064 4.1 13.0 - - + -
321A LYS 5.5 0.8 + - - +
322A GLY 5.2 0.6 + - - -
323A SER 3.3 0.6 - - - -
324A ALA* 1.3 75.6 - - - +
326A GLU* 1.3 63.9 + - + +
328A MET* 3.2 4.3 + - - +
329A PHE* 3.0 43.9 + - + -
443A PHE* 4.9 6.1 - - + +
444A ASN* 3.8 23.3 - - - +
447A HIS* 3.5 35.9 - - + +
469A TRP* 3.4 29.6 - - + +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLY 4.1 1.5 - - - +
323A SER 3.0 7.2 + - - +
325A VAL* 1.3 78.9 - - + +
327A ALA* 1.3 65.8 + - - +
329A PHE* 3.1 9.2 + - + +
330A LEU* 3.1 25.3 + - - +
389A VAL* 3.6 22.2 - - + +
395A ARG* 2.6 43.0 + - - -
437A LEU* 4.5 4.3 - - - +
440A LEU* 3.5 42.4 - - + +
441A ARG* 3.8 11.9 + - - -
444A ASN* 2.8 23.4 - - - +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A HIS* 4.2 3.1 + - - -
298A LEU* 3.4 38.4 - - + -
323A SER* 2.7 21.8 + - - +
326A GLU* 1.3 72.6 - - - +
328A MET* 1.3 56.3 - - - +
330A LEU* 3.4 8.6 + - - +
331A ARG* 3.0 28.6 + - - +
386A THR* 4.5 15.8 + - + +
389A VAL* 4.3 5.5 - - + +
390A ILE* 4.9 6.7 - - + -
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Residues in contact with MET 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 064 3.6 63.1 - - + +
291A ALA* 3.4 18.2 - - + +
294A HIS* 3.8 13.2 - - + -
295A VAL* 3.3 39.3 - - + +
298A LEU* 4.6 2.5 - - + -
324A ALA* 3.0 28.0 + - + +
325A VAL 3.4 6.1 - - - +
326A GLU 3.1 0.2 - - - -
327A ALA* 1.3 77.5 - - - +
329A PHE* 1.3 52.4 + - - +
331A ARG* 4.1 0.9 - - - +
332A SER* 2.7 35.9 + - - -
469A TRP* 3.9 18.8 - - + -
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 064 3.3 27.1 - + - -
325A VAL* 3.0 32.0 + - + +
326A GLU* 3.1 9.8 + - + +
328A MET* 1.3 74.7 - - - +
330A LEU* 1.3 59.3 + - - +
332A SER* 3.0 6.3 + - - -
333A ALA* 2.9 32.1 + - - +
365A MET* 3.7 35.9 - - + -
368A PHE* 3.7 22.8 - + + -
369A TYR* 3.7 7.7 - + - -
440A LEU* 3.6 17.0 - - + -
443A PHE* 3.4 52.9 - + + -
447A HIS* 5.6 2.5 - + + -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A TYR* 5.7 0.9 - - - -
326A GLU 3.1 8.2 + - - +
327A ALA* 3.6 9.2 - - - +
329A PHE* 1.3 78.6 - - - +
331A ARG* 1.3 56.8 + - - +
333A ALA* 3.7 3.0 - - - +
334A GLU* 2.9 29.3 + - - +
368A PHE* 5.1 2.5 - - + -
372A ILE* 4.1 25.4 - - + -
377A MET* 5.4 0.2 - - - -
382A TYR* 4.0 20.7 - - + +
385A LEU* 3.8 26.9 - - + +
386A THR* 3.6 44.4 - - - +
389A VAL* 4.2 4.5 - - + -
436A ARG* 5.7 0.2 - - + -
440A LEU* 3.9 25.8 - - + -
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Residues in contact with ARG 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 064 2.8 58.5 + - + +
260A TYR* 4.1 17.0 + - - +
264A ARG* 5.5 2.8 - - - +
294A HIS* 3.6 29.5 - - + +
327A ALA 3.0 17.6 + - - +
328A MET 4.1 0.4 - - - +
329A PHE 3.4 0.2 - - - -
330A LEU* 1.3 77.0 - - - +
332A SER* 1.3 57.8 + - - +
334A GLU* 2.8 47.8 + - - +
335A ILE* 3.0 37.2 + - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 064 4.2 23.9 - - - +
328A MET 2.7 23.7 + - - -
329A PHE* 3.0 11.8 + - - -
331A ARG* 1.3 71.5 - - - +
333A ALA* 1.3 63.2 + - - +
335A ILE* 2.9 20.8 + - - +
336A PHE* 2.9 26.8 + - - -
348A LEU* 5.9 2.5 - - - -
352A ILE* 5.8 2.5 - - - -
369A TYR* 2.6 28.5 + - - -
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PHE 2.9 20.5 + - - +
330A LEU* 3.7 5.8 - - - +
332A SER* 1.3 75.1 + - - +
334A GLU* 1.3 57.8 + - - +
336A PHE* 4.5 1.1 - - - -
337A ASN* 2.8 38.4 + - - +
368A PHE* 4.0 5.8 - - + -
369A TYR* 3.4 26.2 - - + -
372A ILE* 3.9 26.9 - - + -
382A TYR* 4.9 0.4 - - + -
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A TYR* 2.6 35.2 + - - -
330A LEU 2.9 14.3 + - - +
331A ARG* 2.8 32.9 + - - +
333A ALA* 1.3 76.6 - - - +
335A ILE* 1.3 56.6 + - - +
337A ASN* 3.7 0.2 - - - +
338A LYS* 2.8 37.7 + - + +
379A GLN* 4.1 13.9 - - - +
382A TYR* 3.7 46.3 - - + +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 064 3.7 45.3 - - + -
331A ARG* 3.0 35.5 + - - +
332A SER* 2.9 12.6 + - - +
334A GLU* 1.3 77.1 - - - +
336A PHE* 1.3 63.9 + - + +
339A LYS* 3.2 3.3 + - - -
340A LEU* 3.2 41.2 + - + -
343A GLY* 3.8 25.6 - - - +
345A SER* 3.7 4.1 + - - +
348A LEU* 4.2 18.4 - - + -
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Residues in contact with PHE 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A SER* 2.9 29.8 + - - +
333A ALA* 4.0 3.1 - - - +
335A ILE* 1.3 78.6 - - + +
337A ASN* 1.3 68.9 + - - +
339A LYS* 3.3 13.0 + - - +
345A SER* 3.5 44.8 + - - -
348A LEU* 3.9 24.2 - - + -
349A GLU* 3.9 20.0 - - + -
352A ILE* 4.0 14.8 - - + -
366A PHE* 4.4 4.7 - + - -
369A TYR* 3.5 47.3 - + + -
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Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA 2.8 23.9 + - - +
334A GLU 3.7 1.1 - - - +
336A PHE* 1.3 84.0 - - - +
338A LYS* 1.3 56.3 + - + +
339A LYS* 3.2 3.9 + - - +
369A TYR* 3.1 24.0 + - - +
372A ILE* 3.4 11.4 - - - +
373A GLY* 3.1 32.4 + - - +
382A TYR* 2.8 28.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 2.8 27.5 + - + +
337A ASN* 1.3 71.5 - - + +
339A LYS* 1.3 69.6 + - - +
340A LEU* 2.8 12.7 + - + +
382A TYR* 6.1 2.0 - - + -
----------------------------------------------------------
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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