Contacts of the helix formed by residues 343 - 367 (chain A) in PDB entry 3QJQ
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 ASN 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLN* 4.3 24.7 + - - +
340A PRO* 3.1 21.5 + - + +
341A TRP 3.2 0.8 - - - -
342A ASP* 1.3 79.0 + - - +
344A PRO* 1.3 74.6 - - - +
345A ALA* 2.8 19.6 + - - +
346A PHE* 2.8 24.4 + - - +
347A VAL* 3.1 13.4 + - - +
402A TYR* 5.4 1.0 - - - +
418A ARG* 5.2 2.5 - - - +
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Residues in contact with PRO 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASP 3.5 9.2 - - - +
343A ASN* 1.3 89.4 - - - +
345A ALA* 1.3 56.8 - - - +
347A VAL* 3.8 8.5 - - + -
348A ALA* 2.9 35.2 + - - +
399A GLY* 4.0 2.5 - - - +
402A TYR* 3.8 38.4 - - + -
418A ARG* 3.7 26.2 - - + +
421A GLY* 4.7 4.0 - - - -
422A LEU* 4.4 23.7 - - + +
425A VAL* 4.7 7.2 - - + +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.2 3.7 - - - +
254A GLN* 3.7 14.5 - - - +
343A ASN* 2.8 16.4 + - - +
344A PRO* 1.3 77.1 - - - +
346A PHE* 1.3 62.4 + - - +
349A PRO* 3.2 19.2 - - - +
399A GLY 3.0 22.0 + - - +
400A SER* 5.3 0.5 + - - -
402A TYR* 4.6 8.9 - - + +
403A TRP* 3.6 25.6 + - + -
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Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.0 13.4 - - + +
254A GLN* 4.8 5.6 - - + +
255A ALA* 4.2 10.8 - - + -
320A LEU* 3.6 25.6 - - + -
339A LEU* 3.4 31.0 - - + -
340A PRO* 3.6 38.1 - - + +
341A TRP* 3.5 42.6 - + - -
343A ASN* 2.8 14.2 + - - +
345A ALA* 1.3 75.8 - - - +
347A VAL* 1.3 85.1 + - + +
349A PRO* 3.0 13.2 - - - +
350A VAL* 3.1 34.0 - - + +
801A HAS 6.1 0.4 - - + -
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TRP* 3.3 52.5 - - + +
343A ASN 3.1 13.2 + - - +
344A PRO* 4.0 4.3 - - + +
346A PHE* 1.3 82.5 - - + +
348A ALA* 1.3 65.8 + - - +
350A VAL* 2.8 14.0 + - - -
351A LEU* 2.9 39.0 + - + +
422A LEU* 4.0 10.3 - - + -
425A VAL* 4.2 8.7 - - + -
426A TRP* 3.9 13.9 - - + +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO 2.9 21.0 + - - +
347A VAL* 1.3 72.9 - - - +
349A PRO* 1.4 64.6 - - + +
351A LEU* 4.2 0.4 - - - +
352A GLY 3.0 18.7 + - - -
395A LEU* 3.2 43.3 - - + +
399A GLY* 3.4 13.2 - - - +
425A VAL* 3.8 24.4 - - + +
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Residues in contact with PRO 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 5.8 3.4 - - + -
247A ILE* 4.5 11.7 - - + -
251A LEU* 4.0 18.3 - - + +
345A ALA* 3.2 19.1 - - - +
346A PHE 3.0 21.5 - - - +
348A ALA* 1.4 86.7 - - + +
350A VAL* 1.3 58.2 + - - -
352A GLY* 3.5 3.3 - - - +
353A LEU* 3.0 30.2 + - - +
392A LEU* 3.8 2.4 - - - +
396A THR* 3.5 38.1 - - + +
399A GLY 5.2 1.6 - - - +
400A SER* 5.6 2.5 - - - +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.3 14.8 - - + -
320A LEU* 4.7 7.6 - - + -
341A TRP* 4.2 15.7 - - + -
346A PHE* 3.1 48.0 - - + +
347A VAL* 2.8 8.0 + - - +
349A PRO* 1.3 74.9 - - - +
351A LEU* 1.3 63.1 + - + +
352A GLY 3.0 1.1 - - - -
353A LEU* 3.1 10.4 + - + +
354A LEU* 2.9 28.1 + - + +
801A HAS 3.7 36.1 - - + -
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TRP* 4.3 15.0 - - + -
347A VAL* 2.9 36.8 + - + +
348A ALA 4.2 3.1 - - - +
350A VAL* 1.3 71.3 - - + +
352A GLY* 1.3 67.4 + - - +
354A LEU* 2.9 34.5 + - + +
355A GLY* 3.0 11.8 + - - -
395A LEU* 4.6 1.1 - - + -
425A VAL* 4.3 8.1 - - + -
426A TRP* 3.8 50.5 - - + -
429A PHE* 3.2 39.4 - - + -
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Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA 3.0 17.6 + - - -
349A PRO 3.6 5.2 - - - -
350A VAL 3.0 0.4 - - - -
351A LEU* 1.3 79.7 - - - +
353A LEU* 1.3 61.4 + - - +
355A GLY* 3.0 10.6 + - - -
356A PHE* 3.1 10.6 + - - +
391A SER* 4.0 3.2 + - - -
392A LEU* 3.3 33.1 - - - +
395A LEU* 4.0 7.7 - - - +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 5.7 2.5 - - + -
247A ILE* 4.3 23.6 - - + -
251A LEU* 5.3 1.8 - - + -
312A THR* 6.3 1.1 - - + -
316A VAL* 3.8 20.6 - - + -
320A LEU* 4.5 6.5 - - + -
349A PRO 3.0 20.1 + - - +
350A VAL* 3.1 10.3 + - - +
352A GLY* 1.3 73.4 - - - +
354A LEU* 1.3 62.8 + - - +
356A PHE* 2.9 17.5 + - + +
357A ILE* 3.1 16.8 + - - +
392A LEU* 3.2 22.0 - - + +
801A HAS 3.5 61.6 - - + +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TRP* 6.2 1.3 - - + -
350A VAL* 2.9 19.1 + - + +
351A LEU* 2.9 31.6 + - + +
353A LEU* 1.3 77.8 - - - +
355A GLY* 1.3 57.2 + - - +
356A PHE 3.2 0.5 + - - -
357A ILE* 3.3 18.7 - - + +
358A PRO* 3.1 21.5 - - - +
429A PHE* 4.0 16.4 - - + -
433A MET* 5.3 2.4 - - - +
801A HAS 4.0 41.3 - - + -
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU 3.0 12.0 + - - -
352A GLY 3.0 4.9 + - - -
354A LEU* 1.3 76.0 - - - +
356A PHE* 1.3 60.6 + - - +
357A ILE 3.4 0.2 - - - -
358A PRO* 3.3 8.0 - - - +
359A GLY 3.4 0.7 + - - -
387A LEU* 3.1 48.2 - - - +
391A SER* 4.5 4.9 - - - -
429A PHE* 3.9 2.8 - - - -
433A MET* 4.2 11.4 - - - -
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.8 26.5 - - + -
244A TYR* 3.5 25.1 - + - -
309A SER* 5.0 0.2 - - - -
352A GLY 3.1 9.1 + - - +
353A LEU* 2.9 17.6 + - + +
355A GLY* 1.3 77.8 - - - +
357A ILE* 1.3 68.5 + - - +
360A GLY* 2.9 23.4 + - - -
387A LEU 4.1 4.7 - - - -
388A GLN* 3.0 47.1 - - + +
392A LEU* 3.3 25.4 - - + -
801A HAS 3.5 56.5 - - + +
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU 3.1 7.7 + - - +
354A LEU* 3.3 36.8 - - + +
356A PHE* 1.3 79.0 - - - +
358A PRO* 1.4 67.2 - - + +
360A GLY* 3.5 5.4 + - - -
361A ALA* 3.7 9.2 + - - +
801A HAS 3.9 34.4 - - + +
11C VAL* 5.7 5.6 - - + -
14C VAL* 4.5 9.9 - - + -
15C LEU* 3.8 37.5 - - + +
18C THR* 4.1 22.1 - - + +
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Residues in contact with PRO 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU 3.1 25.8 - - - +
355A GLY* 3.3 13.5 - - - +
357A ILE* 1.4 84.1 - - + +
359A GLY* 1.3 62.2 + - - +
360A GLY 3.1 2.2 - - - -
361A ALA* 3.2 14.4 + - + +
362A GLY* 3.3 8.5 + - - -
387A LEU* 3.8 15.4 - - + +
433A MET* 5.1 10.8 - - + -
440A HIS* 5.0 0.9 + - - -
18C THR* 4.6 15.0 - - + -
22C PHE* 3.9 23.8 - - + -
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Residues in contact with GLY 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLY 3.4 5.9 + - - -
356A PHE 3.1 3.2 + - - -
358A PRO* 1.3 77.1 - - - +
360A GLY* 1.3 59.0 + - - +
362A GLY 3.4 2.6 + - - -
384A HIS* 3.0 34.0 + - - -
387A LEU* 3.5 16.7 - - - +
388A GLN* 3.0 30.4 - - - +
440A HIS* 5.7 0.2 - - - -
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE 2.9 13.1 + - - -
357A ILE 4.0 1.6 - - - -
358A PRO 3.1 0.2 - - - -
359A GLY* 1.3 73.4 - - - +
361A ALA* 1.3 55.9 + - - +
362A GLY 3.0 5.4 - - - -
363A GLY* 3.3 1.9 + - - -
364A ILE* 3.2 36.7 + - - +
388A GLN* 3.4 3.3 + - - -
801A HAS 3.7 35.4 - - - +
15C LEU* 6.1 0.2 - - - -
19C ILE* 5.8 0.7 - - - -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ILE 3.7 10.8 + - - +
358A PRO* 3.2 6.9 + - + +
360A GLY* 1.3 73.6 - - - +
362A GLY* 1.3 59.7 + - - +
364A ILE* 4.2 9.1 - - - +
365A VAL* 3.2 21.7 + - - +
15C LEU* 5.8 0.2 - - - +
18C THR 3.5 26.5 - - - +
19C ILE* 3.7 18.7 - - + +
22C PHE* 3.0 31.4 - - + +
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Residues in contact with GLY 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PRO 3.3 8.1 + - - -
359A GLY 3.4 4.7 + - - -
360A GLY 3.0 0.8 - - - -
361A ALA* 1.3 79.7 - - - +
363A GLY* 1.3 51.8 + - - +
365A VAL* 3.1 7.6 + - - +
366A ASN* 2.7 38.4 + - - +
380A TRP* 4.0 10.6 + - - -
384A HIS* 3.9 10.1 - - - -
440A HIS* 5.0 1.8 - - - -
22C PHE* 3.9 15.7 - - - -
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Residues in contact with GLY 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLY 3.5 1.4 + - - -
360A GLY 3.3 5.3 + - - -
362A GLY* 1.3 74.8 - - - +
364A ILE* 1.3 54.4 + - - +
365A VAL 3.2 0.2 - - - -
366A ASN* 3.6 7.4 - - - -
367A ALA* 2.7 34.7 + - - +
384A HIS* 3.3 27.4 + - - -
801A HAS 3.2 23.2 - - - +
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Residues in contact with ILE 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 3.8 19.6 - - + +
306A ALA* 4.6 23.3 - - + -
310A LEU* 5.4 1.1 - - + -
360A GLY 3.2 18.2 + - - +
361A ALA* 4.7 4.3 - - - +
362A GLY 3.3 0.2 - - - -
363A GLY* 1.3 74.0 - - - +
365A VAL* 1.3 55.4 - - - +
367A ALA* 3.3 10.5 + - - +
368A SER* 2.1 33.6 + - - -
801A HAS 4.6 13.7 - - + -
26B LEU* 4.9 7.2 - - + -
29B PHE* 4.1 13.0 - - + -
19C ILE* 3.7 40.2 - - + -
23C TRP* 3.6 20.4 - - + +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ALA 3.2 16.8 - - - +
362A GLY* 3.1 11.0 + - - +
364A ILE* 1.3 74.8 - - + +
366A ASN* 1.3 67.4 + - - +
368A SER* 3.1 18.0 + - - -
371A LEU* 3.8 18.5 - - + +
375A VAL* 5.0 4.3 - - + -
380A TRP* 4.1 12.8 - - + +
22C PHE* 3.5 8.5 - - + +
23C TRP* 3.4 44.0 - - + +
26C VAL* 3.8 33.9 - - + -
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Residues in contact with ASN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 4.2 1.0 - - - -
362A GLY 2.7 13.5 + - - +
363A GLY* 3.2 9.5 - - - +
365A VAL* 1.3 75.5 - - - +
367A ALA* 1.3 58.7 + - - +
368A SER 3.0 5.7 + - - -
372A ASP* 3.3 26.7 - - - +
375A VAL* 3.7 9.4 - - - +
380A TRP* 3.5 22.2 + - - -
381A VAL* 4.8 0.6 - - - +
384A HIS* 3.5 28.7 + - - +
801A HAS 3.2 62.2 + - - +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 3.4 11.0 - - - -
299A SER* 3.2 20.3 + - - +
302A THR* 3.4 23.5 - - + -
303A LEU* 4.5 9.4 - - + -
363A GLY 2.7 22.1 + - - +
364A ILE* 3.5 11.0 - - - +
365A VAL 3.1 1.4 - - - -
366A ASN* 1.3 72.6 - - - +
368A SER* 1.3 57.2 + - - +
369A PHE 3.4 3.3 + - - -
801A HAS 2.8 20.2 - - + +
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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