Contacts of the strand formed by residues 340 - 367 (chain A) in PDB entry 1QFG
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 TYR 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A VAL* 2.8 28.4 - - - +
318A CYS* 3.0 14.6 + - - -
332A LEU* 4.1 40.6 - - + +
336A ASP* 3.4 31.2 + - + +
337A LYS 3.7 0.6 + - - +
339A HIS* 1.3 97.8 - + - +
341A LEU* 1.3 60.4 + - - +
399A LEU* 4.4 14.8 - - + -
400A LEU* 3.2 17.7 - - - -
401A ASN* 3.0 33.5 + - + -
402A LEU* 4.0 0.7 - - - -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PRO* 4.2 22.7 - - + -
266A PHE* 4.9 4.3 - - + -
268A GLU* 4.0 32.5 - - + -
314A GLY* 4.5 4.0 - - - -
315A TYR 4.1 1.8 - - - +
316A GLY* 2.9 43.1 - - - +
317A VAL 4.0 0.9 - - - +
340A TYR* 1.3 75.7 - - - +
342A ALA* 1.3 71.3 + - - +
343A ARG* 3.7 6.8 + - + -
398A PRO 4.3 0.3 - - - +
399A LEU* 3.3 13.7 - - - -
400A LEU* 2.8 36.4 + - + +
402A LEU* 3.8 24.7 - - + -
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR* 2.7 34.7 + - + +
316A GLY 2.7 7.0 + - - +
318A CYS* 4.6 1.2 - - - -
323A ASN* 3.4 39.7 - - - +
326A SER* 5.2 2.9 - - - +
328A GLN* 6.0 1.1 - - - +
329A CYS* 4.2 12.1 - - - -
340A TYR 4.2 0.6 + - - -
341A LEU* 1.3 80.0 - - - +
343A ARG* 1.3 54.8 + - - +
344A LYS* 6.1 1.3 - - + -
394A ASP* 5.9 3.4 - - - +
399A LEU* 4.3 9.8 - - + +
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Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU 3.1 24.8 + - - +
269A GLY 4.2 8.5 + - - -
270A ALA* 4.6 3.6 - - - +
312A VAL* 3.6 12.6 - - + +
313A TYR 3.2 17.9 - - - +
314A GLY* 4.3 4.0 - - - -
315A TYR 4.3 0.4 - - - +
341A LEU* 3.7 11.1 + - + +
342A ALA* 1.3 77.5 - - - +
344A LYS* 1.4 65.2 + - - +
393A TYR 4.9 1.0 - - - +
394A ASP 4.9 4.5 - - - +
396A SER* 4.3 1.0 + - - -
397A VAL* 2.8 46.3 + - + +
398A PRO* 3.4 39.7 + - - +
399A LEU 3.7 0.6 + - - -
400A LEU* 3.2 41.4 - - - +
418A ASN* 4.2 10.3 - - - +
419A THR* 5.1 3.0 + - - +
420A ASP 5.7 1.0 + - - -
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Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 3.2 9.5 - - - +
313A TYR* 2.8 50.9 + - + +
315A TYR* 3.4 48.0 + - + -
323A ASN* 5.3 0.4 - - - -
342A ALA* 6.1 1.1 - - + -
343A ARG* 1.4 78.5 - - - +
345A TYR* 1.3 70.8 + - - +
392A GLY 3.6 19.7 - - - +
393A TYR* 3.8 16.1 - - - +
394A ASP* 3.5 29.0 + - - +
396A SER* 4.0 2.5 - - - -
397A VAL* 3.2 7.6 - - - -
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Residues in contact with TYR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER 3.0 14.6 - - - +
312A VAL* 3.6 11.9 - - + -
313A TYR* 3.5 10.1 - - - -
344A LYS* 1.3 85.6 - - - +
346A VAL* 1.3 73.6 + - - +
347A VAL* 4.5 10.5 - - + -
390A TRP* 3.3 37.6 + + - -
391A PHE* 3.5 4.9 - - - +
392A GLY* 3.0 42.4 + - - +
396A SER* 3.9 17.3 - - - -
397A VAL* 4.3 0.4 - - + -
421A PHE* 3.1 35.2 - + - -
422A ASP 5.3 0.2 - - - -
423A PHE* 4.2 15.1 + + + -
425A ALA 4.2 5.8 + - - -
426A LYS* 4.1 11.6 - - - +
427A ASP 4.9 0.3 + - - -
430A ASN* 5.0 1.5 + - - -
431A SER* 3.3 9.8 + - - -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 4.1 16.2 - - + +
309A GLN* 3.7 25.6 - - - +
310A ASN* 3.4 2.6 - - - -
311A SER* 2.6 45.2 + - - +
313A TYR* 4.9 2.0 - - + -
345A TYR* 1.3 78.7 - - - +
347A VAL* 1.3 84.3 + - - +
348A ASP* 4.5 5.2 - - + -
389A ALA* 4.3 1.8 - - + -
390A TRP 3.3 14.4 - - - +
391A PHE* 3.4 34.3 - - + -
423A PHE* 4.1 0.9 - - - -
1108A GOL 4.7 7.0 - - - +
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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
----------------------------------------------------------
309A GLN 3.2 4.5 - - - +
310A ASN* 3.4 26.7 - - - +
345A TYR* 4.5 7.6 - - + -
346A VAL* 1.3 78.7 - - - +
348A ASP* 1.3 70.0 + - - +
349A ASP* 6.3 0.2 - - + -
388A ASN 5.5 2.2 - - - +
389A ALA* 2.9 23.3 - - - +
390A TRP* 3.0 25.3 + - + -
423A PHE* 3.8 32.5 - - + +
426A LYS* 5.7 5.6 - - + -
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Residues in contact with ASP 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 4.2 0.9 - - - -
116A TYR* 3.7 17.8 - - + +
307A THR* 4.1 9.0 - - - +
308A SER* 3.2 6.8 - - - -
309A GLN* 2.8 46.5 + - + +
346A VAL* 4.5 6.5 - - + -
347A VAL* 1.3 81.1 - - - +
349A ASP* 1.3 67.9 + - - +
350A GLU* 2.4 41.5 - - - +
387A ILE* 3.7 7.1 - - - +
388A ASN 3.9 1.6 - - - -
389A ALA* 3.7 17.8 - - + +
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A THR 3.5 5.3 - - - +
308A SER* 3.7 13.4 + - - +
347A VAL* 6.3 0.2 - - + -
348A ASP* 1.3 77.5 + - - +
350A GLU* 1.3 71.1 + - - +
351A LYS* 5.5 1.9 - - - +
386A ASP 3.6 1.7 - - - +
388A ASN* 3.0 46.6 + - + +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN 3.5 9.5 - - - +
115A PHE* 3.4 6.3 - - - +
116A TYR* 3.2 22.1 + - - +
117A ASN* 3.7 10.9 + - - +
306A LYS* 3.4 6.2 - - - +
307A THR* 2.9 37.0 + - + +
348A ASP* 2.4 41.5 - - - +
349A ASP* 1.3 80.8 + - - +
351A LYS* 1.3 65.8 + - - +
385A ASN* 2.9 28.9 + - - +
386A ASP 3.2 7.6 - - - +
387A ILE* 3.2 16.3 - - + +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 3.8 0.2 - - - +
304A GLU* 4.2 12.5 + - - +
305A ASN 3.6 6.1 - - - +
306A LYS* 3.7 33.2 - - + +
349A ASP* 5.5 2.2 - - - +
350A GLU* 1.3 80.2 - - - +
352A LEU* 1.4 61.7 + - - +
353A GLN* 4.4 8.3 - - - +
384A ARG* 4.0 0.7 - - - +
385A ASN* 3.5 2.5 + - - -
386A ASP* 3.0 33.8 + - + +
2001A PO4 2.5 34.9 + - - +
3B KDO 3.5 31.0 + - - -
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN 3.6 15.3 - - - +
113A GLY* 3.9 7.6 - - - -
114A ASN 3.9 18.4 - - - +
117A ASN* 3.4 14.8 - - + +
303A ALA 3.7 0.2 - - - +
304A GLU* 3.1 6.6 - - - +
305A ASN* 2.9 52.4 + - - +
351A LYS* 1.4 69.1 - - - +
353A GLN* 1.3 84.7 + - - +
354A ASN* 3.6 10.5 - - + +
383A MET* 3.6 22.7 - - + -
384A ARG 2.7 15.0 - - - +
385A ASN* 3.3 22.2 - - + +
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A PHE* 3.8 6.8 - - + -
303A ALA 3.0 8.3 - - - +
304A GLU* 2.5 37.3 + - - +
351A LYS* 4.4 4.3 - - - +
352A LEU* 1.3 84.2 + - - +
354A ASN* 1.3 62.2 + - - +
382A ARG* 4.0 15.5 + - - +
383A MET* 3.4 2.4 - - - -
384A ARG* 2.9 38.2 + - + +
1011A FTT 3.6 23.1 - - - +
1013A FTT 3.9 12.8 + - - -
2001A PO4 4.1 5.2 + - - -
2B GCN 4.1 8.5 - - - +
3B KDO 3.7 19.6 + - - -
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Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS 3.4 6.9 + - - +
111A LEU* 3.8 2.6 - - - -
112A GLN* 2.9 39.2 + - - +
301A ARG* 3.8 1.7 + - - +
302A PHE* 3.4 4.9 - - - -
303A ALA* 2.7 47.3 + - + +
305A ASN* 5.7 0.7 - - - +
352A LEU* 3.6 14.4 - - + -
353A GLN* 1.3 76.0 - - - +
355A PHE* 1.3 69.4 + - - +
356A SER* 3.8 8.7 + - - -
381A MET* 3.6 17.6 - - - +
382A ARG 3.2 11.8 + - - -
383A MET* 4.4 1.3 - - + +
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 3.6 30.3 - - + -
301A ARG 3.4 9.4 - - - -
302A PHE* 3.9 18.6 - + + -
353A GLN 4.4 0.2 - - - -
354A ASN* 1.3 74.9 - - - +
356A SER* 1.3 65.2 + - - +
357A VAL* 3.1 37.5 - - + -
380A PHE* 4.0 17.3 - + - -
381A MET* 3.1 25.6 - - - +
382A ARG* 3.0 16.1 + - + +
1009A FTT 3.8 19.7 - - + -
1011A FTT 5.0 3.6 - - + -
1012A DAO 3.4 55.9 - - + +
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Residues in contact with SER 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.1 28.7 - - - +
110A LYS* 4.1 13.3 + - - +
300A LEU* 3.2 8.5 - - - +
301A ARG* 2.7 42.7 + - - +
354A ASN* 3.8 12.5 + - - -
355A PHE* 1.3 81.8 + - - +
357A VAL* 1.3 63.9 + - - +
379A ASP* 5.8 0.4 - - - -
380A PHE 3.4 9.9 - - - -
381A MET* 3.8 6.6 - - - +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.3 1.6 - - - -
298A GLN* 3.8 27.6 - - + +
299A ASN 3.3 4.7 - - - -
300A LEU* 3.3 29.4 - - + -
355A PHE* 3.1 36.1 - - + -
356A SER* 1.3 71.1 - - - +
358A ASP* 1.3 62.2 + - - +
359A THR* 4.2 4.0 - - - +
378A VAL 4.2 0.5 - - - +
379A ASP* 3.5 2.6 - - - +
380A PHE* 2.9 38.5 + - + +
1009A FTT 4.0 15.3 - - + -
1100A DDQ 4.8 9.2 - - + -
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 2.6 29.7 + - - +
108A GLY 4.9 2.1 - - - +
109A LEU* 3.9 16.4 - - + +
297A ARG 4.1 0.7 - - - +
298A GLN* 3.2 5.7 - - - +
299A ASN* 2.9 38.3 + - + +
357A VAL* 1.3 73.5 - - - +
359A THR* 1.3 68.0 + - - +
360A GLN* 2.8 18.8 + - - +
378A VAL 3.3 11.1 - - - +
379A ASP* 3.7 14.7 - - - +
446A TYR* 2.6 22.1 + - - -
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 4.7 11.7 - - + -
297A ARG 3.7 2.9 - - - +
298A GLN* 3.3 39.0 + - + +
357A VAL* 4.4 2.8 - - - +
358A ASP* 1.3 79.4 + - - +
360A GLN* 1.3 64.9 + - - +
377A GLY* 3.2 2.8 - - - -
378A VAL* 2.8 44.3 + - - +
1100A DDQ 4.0 20.9 - - + +
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.1 25.4 - - - +
295A THR 4.2 0.2 - - - +
296A VAL* 3.2 9.1 - - - +
297A ARG* 2.7 83.1 + - + +
299A ASN* 5.1 8.1 - - - +
358A ASP* 2.8 30.6 + - - +
359A THR* 1.3 79.2 - - - +
361A LEU* 1.3 60.1 - - - +
375A LEU* 3.7 18.0 - - + +
376A THR 3.6 6.3 - - - +
377A GLY* 4.1 0.2 - - - -
446A TYR* 3.1 14.8 + - - +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 5.5 5.2 - - + -
294A PHE* 4.0 28.0 - - + -
295A THR 3.6 12.6 - - - +
296A VAL* 4.5 8.5 - - + +
360A GLN* 1.3 74.1 - - - +
362A GLN* 1.3 62.4 + - - +
363A SER* 3.2 25.1 - - - +
374A LEU* 3.5 3.2 - - + +
375A LEU* 3.8 3.1 - - - +
376A THR* 2.9 48.1 + - + +
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Residues in contact with GLN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 3.8 19.6 - - + +
40A ASP 4.6 1.6 + - - -
293A THR 3.2 3.6 - - - +
294A PHE* 3.5 3.1 - - - -
295A THR* 2.9 56.4 + - - +
297A ARG* 2.4 41.3 + - - +
360A GLN 4.2 0.4 - - - -
361A LEU* 1.3 72.4 - - - +
363A SER* 1.3 64.1 + - - +
364A LYS* 4.2 22.4 + - + +
373A THR* 3.9 24.5 - - + -
374A LEU 3.6 5.4 - - - +
375A LEU* 4.6 4.7 - - + -
1106A GOL 4.9 1.5 + - - -
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A THR* 2.9 6.5 - - - -
294A PHE* 2.8 30.4 - - - -
361A LEU* 3.2 16.5 - - - +
362A GLN* 1.3 72.9 - - - +
364A LYS* 1.3 62.5 + - - +
365A PHE* 4.1 21.3 + - - -
372A HIS 3.6 1.9 - - - +
373A THR* 4.6 0.2 - - - -
374A LEU* 2.8 45.2 + - - +
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Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP 4.4 13.9 - - - +
293A THR* 2.3 42.2 + - - +
362A GLN* 4.1 24.0 - - - +
363A SER* 1.3 72.5 - - - +
365A PHE* 1.3 60.0 + - - +
372A HIS 3.1 8.3 - - - +
373A THR* 3.3 24.2 + - + +
1106A GOL 3.6 33.5 + - - -
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Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A THR* 4.0 6.5 - - - +
294A PHE* 6.1 0.4 - + - -
363A SER* 4.1 17.9 - - - -
364A LYS* 1.3 79.4 - - - +
366A ALA* 1.3 68.9 + - - +
367A THR* 5.2 1.3 - - - -
371A ASP* 3.6 4.4 - - - -
372A HIS* 2.7 75.1 + + + +
374A LEU* 4.1 29.6 - - + -
449A ASP* 5.0 0.9 - - - -
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 1.3 85.8 - - - +
367A THR* 1.3 64.5 + - - +
368A GLY 3.8 15.7 - - - +
370A ILE 3.2 6.3 - - - +
371A ASP* 3.2 20.9 - - - +
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Residues in contact with THR 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 5.2 1.4 - - - -
366A ALA* 1.3 74.8 + - - +
368A GLY* 1.3 59.8 + - - +
369A ASP 2.9 1.4 + - - -
370A ILE* 2.7 50.1 + - + +
372A HIS* 3.2 24.3 - - + +
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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).
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