Contacts of the helix formed by residues 340 - 364 (chain F) in PDB entry 1QK1
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 SER 340 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F THR* 3.5 27.5 + - - +
105F ASP* 3.5 27.8 + - - +
284F THR* 4.1 1.1 - - - -
339F LYS* 1.3 75.0 - - - +
341F GLU* 1.3 65.8 + - - +
342F VAL* 3.4 4.7 + - - +
343F GLU* 2.9 40.2 + - - +
344F LEU* 3.0 21.0 + - - +
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Residues in contact with GLU 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F THR* 3.3 18.9 + - - +
105F ASP 2.9 41.6 + - - +
106F LEU* 3.3 25.9 - - + +
130F ARG* 4.6 8.5 + - - -
245F PHE* 4.2 8.7 - - + -
248F PHE* 5.9 0.5 - - - -
274F TYR* 4.6 2.1 - - - -
284F THR* 3.4 35.2 - - + +
286F LEU* 3.8 23.9 - - + +
340F SER* 1.3 73.1 - - - +
342F VAL* 1.3 61.5 + - - +
344F LEU* 3.2 6.5 + - - +
345F VAL* 3.0 29.3 + - - +
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Residues in contact with VAL 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ASP* 3.3 33.5 + - - +
107F ASP 3.5 26.5 - - - +
110F LYS* 4.0 23.8 - - + +
111F ILE* 3.8 16.4 - - + +
245F PHE* 4.2 14.8 - - + -
340F SER* 3.2 7.3 + - - +
341F GLU* 1.3 78.6 - - - +
343F GLU* 1.3 66.4 + - + +
345F VAL 3.5 0.2 + - - -
346F GLN* 3.1 24.5 + - + +
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Residues in contact with GLU 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F THR* 5.9 2.1 - - - +
338F GLY 4.8 0.7 - - - +
339F LYS* 3.4 10.9 - - + +
340F SER* 2.9 45.5 + - - +
342F VAL* 1.3 81.0 - - + +
344F LEU* 1.3 56.8 + - - +
346F GLN* 3.5 5.9 + - - +
347F LEU* 3.0 28.6 + - - +
376F HIS* 3.8 32.9 + - + +
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Residues in contact with LEU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F THR* 3.4 26.5 - - + +
286F LEU* 3.9 16.4 - - + -
333F ASN* 4.0 14.9 - - + +
335F ASP* 3.7 39.3 - - + +
336F ARG* 4.2 4.3 - - - +
339F LYS* 3.8 33.0 - - + +
340F SER 3.0 20.0 + - - +
341F GLU 3.7 3.6 - - - +
343F GLU* 1.3 75.2 - - - +
345F VAL* 1.3 65.3 + - - +
347F LEU* 3.3 11.7 + - + +
348F VAL* 3.0 28.0 + - - +
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Residues in contact with VAL 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ILE* 4.2 13.0 - - + -
126F VAL* 4.9 2.9 - - + -
241F MET* 4.2 17.9 - - + -
245F PHE* 3.6 38.1 - - + -
286F LEU* 4.4 6.7 - - + -
288F ALA* 4.2 17.9 - - + -
341F GLU 3.0 20.1 + - - +
342F VAL 4.1 2.5 - - - +
344F LEU* 1.3 73.2 - - - +
346F GLN* 1.3 61.0 + - - +
348F VAL* 3.0 8.8 + - + +
349F ILE* 2.8 46.3 + - + +
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Residues in contact with GLN 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LYS 4.3 1.9 - - - +
111F ILE* 4.0 13.8 - - + +
112F ARG* 3.3 70.1 + - - +
113F SER* 5.2 0.6 - - - -
342F VAL* 3.1 20.6 + - + +
343F GLU* 3.7 6.5 - - - +
345F VAL* 1.3 75.9 - - - +
347F LEU* 1.3 57.6 + - - +
349F ILE* 3.3 9.3 + - - +
350F ASP* 2.9 66.2 + - - +
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Residues in contact with LEU 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F LEU 3.6 20.3 - - - +
311F ARG* 3.9 23.8 - - + +
312F LEU* 4.2 8.2 - - + +
333F ASN* 4.6 6.7 - - + -
335F ASP* 4.4 4.0 - - - +
339F LYS* 3.9 27.6 - - + +
343F GLU 3.0 16.4 + - - +
344F LEU* 3.5 12.8 - - + +
346F GLN* 1.3 78.2 - - - +
348F VAL* 1.3 60.6 + - + +
350F ASP* 3.6 5.9 + - - +
351F GLY* 3.0 24.8 + - - -
374F VAL* 4.5 12.3 - - + -
376F HIS* 4.3 16.6 - - + +
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Residues in contact with VAL 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F PHE* 4.9 1.3 - - + -
241F MET* 4.4 20.2 - - + -
288F ALA* 3.6 32.1 - - + +
289F GLY* 4.7 4.3 - - - -
290F VAL* 5.4 0.2 - - + -
312F LEU* 4.3 11.2 - - + -
331F ILE 5.1 1.8 - - - +
333F ASN* 3.6 27.4 - - + +
344F LEU 3.0 17.7 + - - +
345F VAL* 3.0 8.9 + - - +
347F LEU* 1.3 74.4 - - + +
349F ILE* 1.3 61.7 + - + +
352F VAL* 2.8 45.5 + - + +
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Residues in contact with ILE 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ILE* 3.6 31.4 - - + -
112F ARG 4.1 1.8 - - - +
113F SER* 3.9 14.4 - - - +
114F GLY* 3.7 19.7 - - - +
116F PHE* 3.7 22.8 - - + -
241F MET* 4.0 13.5 - - + -
242F LYS 5.2 0.4 - - - +
345F VAL* 2.8 28.0 + - + +
346F GLN* 3.5 20.6 - - - +
348F VAL* 1.3 77.3 - - + +
350F ASP* 1.3 64.3 + - - +
353F ASN* 3.1 40.0 + - - +
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Residues in contact with ASP 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F ARG* 4.0 11.0 + - - -
113F SER* 5.8 0.9 - - - -
310F LEU* 5.6 0.7 - - - -
346F GLN* 2.9 48.9 + - - +
347F LEU* 4.0 6.1 - - - +
349F ILE* 1.3 74.8 - - - +
351F GLY* 1.3 64.0 + - - +
353F ASN* 3.4 7.6 + - - +
354F TYR* 3.1 22.5 + - - +
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Residues in contact with GLY 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F LEU* 3.7 19.7 - - - +
312F LEU* 4.0 19.3 - - - -
347F LEU 3.0 17.8 + - - -
348F VAL 3.8 0.4 - - - -
350F ASP* 1.3 78.2 - - - +
352F VAL* 1.3 61.9 + - - +
354F TYR* 3.2 5.2 + - - +
355F LEU* 3.1 26.2 + - - +
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Residues in contact with VAL 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F PHE* 3.6 32.8 - - + -
121F VAL* 4.3 4.3 - - + -
290F VAL* 3.9 21.1 - - + -
292F ILE* 4.1 20.0 - - + -
312F LEU* 4.9 1.8 - - + -
331F ILE* 4.6 10.8 - - + +
348F VAL* 2.8 35.2 + - + +
351F GLY* 1.3 69.5 - - - +
353F ASN* 1.3 66.2 + - - +
355F LEU* 3.0 17.8 + - + +
356F ILE* 2.9 26.2 + - + +
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Residues in contact with ASN 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F SER* 3.6 23.0 + - - -
115F TYR 5.1 2.3 - - - +
116F PHE* 3.5 21.5 - - - -
117F ASP 5.5 0.2 + - - -
349F ILE* 3.1 29.0 + - - +
350F ASP* 3.8 7.9 + - - +
352F VAL* 1.3 76.7 - - - +
354F TYR* 1.3 63.0 + - - +
356F ILE* 3.3 11.1 + - - +
357F ASP* 2.9 26.9 + - - +
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Residues in contact with TYR 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ILE* 4.3 7.4 - - + -
310F LEU* 4.1 22.4 - - + -
350F ASP 3.1 13.2 + - - +
351F GLY* 3.5 9.4 - - - +
352F VAL 3.2 0.2 - - - -
353F ASN* 1.3 77.5 - - - +
355F LEU* 1.3 61.1 + - + +
357F ASP* 3.7 10.2 + - + +
358F CYS* 3.1 51.0 + - - -
369F ARG* 2.3 42.6 + - + +
370F ILE 3.6 0.7 - - - -
371F PRO* 3.2 41.8 - - + +
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Residues in contact with LEU 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F ILE* 4.8 5.2 - - + -
294F LEU* 4.4 17.3 - - + -
297F LEU* 3.8 21.5 - - + +
303F PHE* 4.9 1.3 - - + -
306F ILE* 4.0 16.8 - - + -
307F LEU* 4.4 15.0 - - + -
310F LEU* 3.7 19.3 - - + -
312F LEU* 4.0 16.4 - - + -
331F ILE* 4.3 19.7 - - + -
351F GLY 3.1 20.3 + - - +
352F VAL* 3.0 17.8 + - + +
354F TYR* 1.3 78.0 - - + +
356F ILE* 1.3 66.2 + - - +
358F CYS* 3.0 6.1 + - - +
359F GLU* 3.0 21.5 + - - +
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Residues in contact with ILE 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F PHE* 4.2 6.3 - - + -
117F ASP* 3.8 37.0 - - + +
120F TYR* 3.8 25.1 - - + -
121F VAL* 4.1 19.1 - - + -
292F ILE* 3.9 16.4 - - + -
294F LEU* 4.8 2.7 - - - +
352F VAL* 2.9 21.9 + - + +
353F ASN* 3.7 13.2 - - - +
355F LEU* 1.3 75.6 - - - +
357F ASP* 1.3 59.4 + - - +
359F GLU* 3.2 7.6 + - - +
360F ARG* 2.9 39.2 + - - +
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Residues in contact with ASP 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F ASN 2.9 17.3 + - - +
354F TYR* 3.9 12.5 - - + +
356F ILE* 1.3 76.5 - - - +
358F CYS* 1.3 66.5 + - - +
360F ARG* 3.6 8.9 + - - +
361F ARG* 3.1 41.9 + - - +
364F ARG* 5.9 0.9 + - - -
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Residues in contact with CYS 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F LEU* 3.9 20.4 - - + -
306F ILE* 5.2 4.0 - - - -
354F TYR* 3.1 50.3 + - - -
355F LEU* 3.0 9.9 + - - +
357F ASP* 1.3 78.1 - - - +
359F GLU* 1.3 58.6 + - - +
361F ARG* 3.2 5.1 + - - +
362F LEU* 2.9 30.0 + - - +
368F ILE* 3.7 38.0 - - + +
369F ARG 4.7 0.9 - - - -
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Residues in contact with GLU 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F TYR* 3.5 28.7 - - + -
293F LYS 4.6 0.2 - - - +
294F LEU* 3.5 23.5 - - + +
295F PRO* 3.4 10.3 - - + +
296F LEU* 2.7 36.8 + - - +
297F LEU* 2.8 37.7 + - - +
355F LEU 3.0 11.9 + - - +
356F ILE 3.6 8.1 - - - +
358F CYS* 1.3 77.6 - - - +
360F ARG* 1.3 60.1 + - - +
362F LEU* 3.2 5.5 + - - +
363F GLU* 2.9 33.5 + - - +
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Residues in contact with ARG 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ASP* 3.9 14.5 + - - -
119F ARG* 4.0 28.7 - - - +
120F TYR* 3.2 30.9 + - + +
356F ILE* 2.9 26.6 + - - +
357F ASP* 4.0 8.3 - - - +
359F GLU* 1.3 76.6 - - - +
361F ARG* 1.3 61.1 + - + +
363F GLU* 3.5 18.9 + - - +
364F ARG* 3.4 56.0 + - - +
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Residues in contact with ARG 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F ASP* 3.1 39.2 + - - +
358F CYS* 3.5 5.4 - - - +
360F ARG* 1.3 75.0 - - + +
362F LEU* 1.3 61.8 + - - +
364F ARG* 3.5 8.7 + - - +
365F GLY 3.5 2.8 + - - -
366F GLN* 2.9 71.8 + - + +
367F ASP* 2.5 39.9 + - - +
368F ILE* 4.2 14.1 - - + +
369F ARG* 4.7 19.5 - - - +
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Residues in contact with LEU 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F LEU* 3.6 24.9 - - + +
297F LEU* 3.6 44.2 - - + +
300F ASP* 4.9 9.0 - - + +
302F ARG* 5.2 3.4 - - - +
358F CYS 2.9 12.2 + - - +
359F GLU* 3.2 6.7 + - - +
361F ARG* 1.3 77.0 - - - +
363F GLU* 1.3 64.6 + - - +
364F ARG 3.2 0.6 + - - -
365F GLY* 3.4 9.7 + - - -
366F GLN 4.1 13.7 - - - +
367F ASP* 5.1 0.9 - - - +
368F ILE* 3.7 36.6 - - + +
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Residues in contact with GLU 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F TYR* 2.6 38.5 + - - -
295F PRO* 6.0 1.2 - - - +
296F LEU* 3.7 17.3 - - + -
359F GLU* 2.9 25.6 + - + +
360F ARG* 3.7 17.5 + - - +
362F LEU* 1.3 78.3 - - - +
364F ARG* 1.3 61.3 + - + +
365F GLY 3.6 0.7 + - - -
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Residues in contact with ARG 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F ASP* 5.9 1.0 + - - -
360F ARG* 3.4 51.0 + - - +
361F ARG* 3.8 22.0 - - - +
362F LEU 3.2 0.6 - - - -
363F GLU* 1.3 78.5 - - + +
365F GLY* 1.3 59.0 + - - +
366F GLN* 2.8 40.9 + - + +
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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