Contacts of the helix formed by residues 340 - 365 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D THR* 3.4 26.8 + - - +
105D ASP* 3.5 28.1 + - - +
339D LYS* 1.3 75.5 - - - +
341D GLU* 1.3 66.3 + - - +
342D VAL* 3.4 4.9 + - - +
343D GLU* 2.9 39.9 + - - +
344D LEU* 3.0 21.5 + - - +
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Residues in contact with GLU 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D THR* 3.3 18.4 + - - +
105D ASP 2.9 41.2 + - - +
106D LEU* 3.3 26.0 - - + +
130D ARG* 4.6 8.5 + - - -
245D PHE* 4.1 9.0 - - + -
248D PHE* 5.9 0.2 - - - -
274D TYR* 4.6 2.8 - - - -
284D THR* 3.5 34.1 - - + +
286D LEU* 3.8 23.9 - - + +
340D SER* 1.3 72.9 - - - +
342D VAL* 1.3 60.9 + - - +
344D LEU* 3.3 6.5 + - - +
345D VAL* 3.0 28.9 + - - +
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Residues in contact with VAL 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ASP* 3.2 34.2 + - - +
107D ASP 3.5 26.0 - - - +
110D LYS* 4.0 27.6 - - + +
111D ILE* 3.8 12.7 - - + +
245D PHE* 4.2 15.5 - - + -
340D SER* 3.1 7.3 + - - +
341D GLU* 1.3 77.5 - - - +
343D GLU* 1.3 66.2 + - + +
345D VAL 3.5 0.2 + - - -
346D GLN* 3.0 25.1 + - + +
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Residues in contact with GLU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D THR* 5.9 2.3 - - - +
338D GLY 4.7 0.7 - - - +
339D LYS* 3.4 21.5 - - + +
340D SER* 2.9 43.6 + - - +
342D VAL* 1.3 81.6 - - + +
344D LEU* 1.3 57.1 + - - +
346D GLN* 3.7 6.1 - - - +
347D LEU* 3.0 29.4 + - - +
375D ILE* 5.5 11.6 - - + +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D THR* 3.4 27.1 - - + +
286D LEU* 3.9 21.3 - - + -
333D ASN* 4.1 11.2 - - + +
335D ASP* 3.7 38.4 - - + +
336D ARG* 4.2 4.7 - - - +
339D LYS* 3.8 33.0 - - + +
340D SER 3.0 20.4 + - - +
341D GLU 3.8 3.4 - - - +
343D GLU* 1.3 74.5 - - - +
345D VAL* 1.3 65.0 + - - +
347D LEU* 3.3 12.1 + - + +
348D VAL* 3.0 28.1 + - - +
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Residues in contact with VAL 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 4.0 13.2 - - + -
126D VAL* 4.9 2.2 - - + -
241D MET* 4.2 16.8 - - + -
242D LYS* 6.3 0.2 - - - -
245D PHE* 3.6 38.6 - - + -
286D LEU* 4.4 7.0 - - + -
288D ALA* 4.2 18.8 - - + -
341D GLU 3.0 21.3 + - - +
342D VAL 4.1 2.5 - - - +
344D LEU* 1.3 75.1 - - - +
346D GLN* 1.3 58.1 + - - +
348D VAL* 3.0 8.2 + - + +
349D ILE* 2.8 46.3 + - + +
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Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LYS 4.3 0.5 - - - +
111D ILE* 3.9 11.9 - - + +
112D ARG* 3.1 74.5 + - - +
113D SER* 5.1 0.6 - - - -
342D VAL* 3.0 20.8 + - + +
343D GLU* 3.7 6.7 - - - +
345D VAL* 1.3 76.6 - - - +
347D LEU* 1.3 57.9 + - - +
349D ILE* 3.2 8.1 + - - +
350D ASP* 2.9 60.8 + - - +
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D LEU 3.6 21.6 - - - +
311D ARG* 4.0 13.5 - - + +
312D LEU* 4.2 8.5 - - + -
333D ASN* 4.7 6.3 - - + -
335D ASP* 4.4 8.1 - - - +
339D LYS* 3.9 29.8 - - + +
343D GLU 3.0 18.4 + - - +
344D LEU* 3.5 12.3 - - + +
346D GLN* 1.3 77.7 - - - +
348D VAL* 1.3 60.0 + - + +
350D ASP* 4.1 6.0 - - - +
351D GLY* 3.0 23.9 + - - -
374D VAL* 4.2 20.9 - - + -
375D ILE* 4.2 11.4 - - + -
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Residues in contact with VAL 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 4.9 1.1 - - + -
241D MET* 4.4 20.0 - - + -
288D ALA* 3.5 31.9 - - + +
289D GLY* 4.7 4.5 - - - -
290D VAL* 5.4 0.2 - - + -
312D LEU* 4.3 10.3 - - + +
331D ILE 5.2 1.8 - - - +
333D ASN* 3.6 27.4 - - + +
344D LEU 3.0 18.1 + - - +
345D VAL* 3.0 8.7 + - - +
347D LEU* 1.3 75.2 - - - +
349D ILE* 1.3 62.9 + - + +
352D VAL* 2.8 45.3 + - + +
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Residues in contact with ILE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 3.7 24.2 - - + -
112D ARG 4.0 3.8 - - - +
113D SER* 4.0 2.5 - - - +
114D GLY* 3.7 35.2 - - - +
116D PHE* 3.7 23.4 - - + -
241D MET* 4.0 13.7 - - + -
242D LYS 5.2 0.7 - - - +
345D VAL* 2.8 28.7 + - + +
346D GLN* 3.2 21.3 + - - +
348D VAL* 1.3 77.1 - - + +
350D ASP* 1.3 63.4 + - - +
353D ASN* 3.1 40.5 + - - +
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Residues in contact with ASP 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ARG* 4.6 6.9 + - - -
113D SER* 5.7 1.4 - - - -
310D LEU* 5.6 0.7 - - - -
346D GLN* 2.9 45.1 + - - +
347D LEU* 4.1 5.9 - - - +
349D ILE* 1.3 79.4 - - - +
351D GLY* 1.3 62.8 + - - +
353D ASN* 3.4 7.7 + - - +
354D TYR* 3.1 22.9 + - - +
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Residues in contact with GLY 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D LEU* 3.7 19.4 - - - +
312D LEU* 3.9 20.9 - - - -
347D LEU 3.0 18.2 + - - -
348D VAL 3.8 0.7 - - - -
350D ASP* 1.3 77.4 - - - +
352D VAL* 1.3 61.8 + - - +
354D TYR* 3.2 4.3 + - - +
355D LEU* 3.0 26.5 + - - +
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Residues in contact with VAL 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 3.6 32.1 - - + -
121D VAL* 4.3 4.7 - - + -
290D VAL* 3.9 21.3 - - + -
292D ILE* 4.1 15.5 - - + -
312D LEU* 4.9 1.3 - - + -
331D ILE* 4.6 16.4 - - + -
348D VAL* 2.8 36.3 + - + +
351D GLY* 1.3 70.5 - - - +
353D ASN* 1.3 61.2 + - - +
355D LEU* 3.1 8.5 + - + +
356D ILE* 2.9 38.3 + - + +
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Residues in contact with ASN 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D SER* 3.6 22.2 + - - -
115D TYR 5.1 2.5 + - - +
116D PHE* 3.5 21.7 - - - -
117D ASP 5.5 0.3 + - - -
349D ILE* 3.1 29.9 + - - +
350D ASP* 3.8 7.1 + - - +
352D VAL* 1.3 76.4 - - - +
354D TYR* 1.3 62.2 + - - +
356D ILE* 3.4 12.3 + - - +
357D ASP* 3.1 22.3 + - - +
360D ARG* 5.6 1.0 + - - -
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Residues in contact with TYR 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ILE* 4.3 2.9 - - + -
310D LEU* 4.1 22.7 - - + -
350D ASP 3.1 13.7 + - - +
351D GLY* 3.5 8.7 - - - +
352D VAL 3.1 0.2 - - - -
353D ASN* 1.3 75.6 - - - +
355D LEU* 1.3 59.6 - - - +
357D ASP* 3.4 14.5 + - + +
358D CYS* 3.1 45.5 + - - -
369D ARG* 2.7 29.3 + - - +
371D PRO* 3.6 35.7 - - + +
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ILE* 4.9 4.9 - - + -
294D LEU* 4.1 23.1 - - + +
297D LEU* 3.7 24.2 - - + +
303D PHE* 5.2 0.2 - - + -
306D ILE* 4.1 12.3 - - + -
307D LEU* 3.9 29.2 - - + -
310D LEU* 3.6 28.0 - - + -
312D LEU* 4.4 5.2 - - + -
331D ILE* 4.1 24.9 - - + -
351D GLY 3.0 9.1 + - - +
352D VAL* 3.1 13.9 + - + +
354D TYR* 1.3 72.8 - - - +
356D ILE* 1.3 66.7 + - - +
358D CYS* 3.2 6.2 + - - +
359D GLU* 3.1 19.1 + - - +
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Residues in contact with ILE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 4.4 3.1 - - + -
117D ASP* 4.1 27.8 - - + +
120D TYR* 4.0 22.6 - - + -
121D VAL* 4.2 12.1 - - + -
292D ILE* 3.8 15.9 - - + -
294D LEU* 4.9 2.5 - - - -
352D VAL* 2.9 31.9 + - + +
353D ASN* 3.5 15.5 - - - +
355D LEU* 1.3 76.3 - - - +
357D ASP* 1.3 62.0 + - - +
359D GLU* 3.1 9.5 + - - +
360D ARG* 3.0 50.3 + - - +
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Residues in contact with ASP 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ASN 3.1 13.9 + - - +
354D TYR* 3.4 19.5 - - + +
356D ILE* 1.3 78.2 - - - +
358D CYS* 1.3 64.3 + - - +
360D ARG* 3.2 22.0 + - - +
361D ARG* 2.8 60.0 + - - +
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Residues in contact with CYS 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D LEU* 3.9 19.3 - - + -
306D ILE* 4.4 14.6 - - - -
354D TYR* 3.1 45.4 + - - -
355D LEU* 3.2 10.1 + - - +
357D ASP* 1.3 76.5 - - - +
359D GLU* 1.3 63.5 + - - +
361D ARG* 3.2 6.0 + - - +
362D LEU* 3.1 28.0 + - - +
368D ILE* 3.8 29.7 - - + +
369D ARG 5.0 0.7 - - - -
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Residues in contact with GLU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D TYR* 3.6 29.6 - - + -
293D LYS 4.5 0.7 - - - +
294D LEU* 3.8 20.9 - - + -
295D PRO* 3.1 13.4 - - - +
296D LEU* 2.7 33.6 + - - +
297D LEU* 2.6 38.7 + - - +
355D LEU 3.1 8.7 + - - +
356D ILE* 3.1 10.8 + - - +
358D CYS* 1.3 78.5 - - - +
360D ARG* 1.3 63.1 + - - +
361D ARG 3.1 0.3 + - - -
362D LEU* 3.2 6.8 + - - +
363D GLU* 3.0 28.5 + - - +
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Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP* 2.9 29.7 + - - +
119D ARG* 4.6 10.4 - - - +
120D TYR* 3.3 25.3 - - + +
353D ASN 5.6 0.8 + - - -
356D ILE* 3.0 33.8 + - - +
357D ASP* 3.2 25.4 + - - +
359D GLU* 1.3 76.8 - - - +
361D ARG* 1.3 55.2 + - + +
363D GLU* 3.2 14.2 - - - +
364D ARG* 2.7 51.1 + - - +
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Residues in contact with ARG 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D ASP* 2.8 48.2 + - - +
358D CYS* 3.5 6.7 - - - +
359D GLU 3.1 0.4 - - - -
360D ARG* 1.3 73.0 - - + +
362D LEU* 1.3 66.7 + - - +
363D GLU 2.9 1.8 - - - -
364D ARG 3.0 3.8 + - - -
365D GLY 2.9 5.4 + - - -
366D GLN* 2.8 67.7 + - + +
367D ASP 3.5 21.6 + - - +
368D ILE* 3.9 13.2 - - + +
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Residues in contact with LEU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LEU* 3.8 23.7 - - + +
297D LEU* 3.5 45.3 - - + +
300D ASP* 4.5 11.9 - - + +
302D ARG* 4.5 4.3 - - - +
358D CYS 3.1 15.6 + - - +
359D GLU* 3.7 7.2 - - - +
361D ARG* 1.3 79.4 - - - +
363D GLU* 1.3 62.3 + - - +
365D GLY* 3.4 9.5 + - - -
366D GLN 4.1 15.3 - - - +
367D ASP* 5.4 0.4 - - - -
368D ILE* 4.2 23.6 - - + -
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Residues in contact with GLU 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D TYR* 2.7 39.0 + - - -
295D PRO* 6.1 0.3 - - - +
296D LEU* 3.7 18.2 - - + -
359D GLU* 3.0 22.8 + - - +
360D ARG* 3.2 15.3 - - - +
361D ARG 2.9 0.4 - - - -
362D LEU* 1.3 79.6 - - - +
364D ARG* 1.3 73.0 + - - +
365D GLY 3.3 2.8 + - - -
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Residues in contact with ARG 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ARG* 5.6 5.7 - - - +
360D ARG* 2.7 47.0 + - - +
361D ARG 3.0 3.0 + - - +
363D GLU* 1.3 89.8 + - - +
365D GLY* 1.3 60.8 + - - +
366D GLN* 3.3 26.6 + - + +
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Residues in contact with GLY 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D ARG 2.9 3.6 + - - -
362D LEU* 3.4 9.0 + - - -
363D GLU 3.2 5.9 + - - -
364D ARG* 1.3 79.1 - - - +
366D GLN* 1.3 64.8 + - - +
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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