Contacts of the helix formed by residues 335 - 359 (chain M) in PDB entry 5D4D
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 THR 335 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ILE* 4.0 15.3 - - + -
25M SER* 3.2 35.1 - - - +
138M SER* 4.6 11.0 - - - -
333M ILE* 4.1 6.5 - - + +
334M ARG* 1.3 78.0 - - - +
336M VAL* 1.3 66.2 + - - +
337M GLY* 3.3 6.2 + - - -
338M GLU* 3.4 13.2 + - - +
339M LEU* 3.1 20.8 + - - +
461M VAL* 4.1 26.0 - - + -
462M ASP 5.5 1.3 - - - +
465M GLY* 5.8 0.7 - - - -
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Residues in contact with VAL 336 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ILE 4.1 3.3 + - - +
22M GLN* 3.5 51.0 - - - +
25M SER* 4.3 2.7 - - - -
26M TYR* 4.1 9.2 - - + +
121M MET* 3.9 4.5 - - + -
127M PHE* 3.8 26.5 - - + -
136M ILE* 3.6 41.3 - - + +
138M SER* 5.1 0.8 + - - +
335M THR* 1.3 69.6 - - - +
337M GLY* 1.3 68.2 + - - +
339M LEU* 3.5 2.5 + - - +
340M MET* 3.0 25.2 + - + +
385M PHE* 5.7 0.4 - - + -
386M PHE* 5.5 0.4 - - + -
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Residues in contact with GLY 337 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M SER* 4.0 10.7 - - - -
26M TYR* 4.4 6.1 - - - -
29M ALA* 3.8 20.9 - - - -
335M THR* 3.2 6.7 + - - -
336M VAL* 1.3 84.2 - - - +
338M GLU* 1.3 55.3 + - - +
340M MET* 3.2 2.8 + - - +
341M THR* 2.9 37.3 + - - +
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Residues in contact with GLU 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M HIS* 4.8 0.2 - - - -
165M LEU* 4.9 9.6 - - + +
332M ARG* 2.7 45.1 + - - -
333M ILE 4.4 1.2 - - - +
334M ARG* 3.7 30.6 + - + +
335M THR* 3.4 22.8 + - - +
337M GLY* 1.3 72.6 - - - +
339M LEU* 1.3 64.0 + - - +
341M THR* 3.2 9.8 + - - +
342M ASP* 3.0 34.9 + - - +
465M GLY* 5.4 0.5 - - - -
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Residues in contact with LEU 339 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M ILE* 3.8 24.0 - - + -
137M VAL 3.8 10.3 - - - +
139M GLN* 4.1 13.2 - - + +
334M ARG* 3.7 42.6 - - + +
335M THR 3.1 13.2 + - - +
336M VAL* 3.8 3.8 - - - +
338M GLU* 1.3 74.5 - - - +
340M MET* 1.3 63.5 + - - +
342M ASP* 3.2 7.7 + - - +
343M GLN* 3.1 19.8 + - - +
385M PHE* 3.5 26.2 - - + -
391M LEU* 3.6 27.8 - - + -
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Residues in contact with MET 340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M TYR* 3.7 32.1 - - + -
29M ALA* 4.4 6.7 - - + -
30M LEU* 4.4 11.9 - - + -
44M ILE* 4.9 8.3 - - + -
118M ILE* 4.9 7.6 - - - -
336M VAL* 3.0 18.8 + - + +
337M GLY 3.6 1.8 - - - +
339M LEU* 1.3 76.9 - - - +
341M THR* 1.3 83.3 + - + +
343M GLN* 3.1 5.6 + - - +
344M PHE* 2.9 32.2 + - + -
382M ILE* 3.7 19.2 - - + +
385M PHE* 3.9 11.8 - - + -
386M PHE* 3.6 29.6 - - + -
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Residues in contact with THR 341 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M ALA* 3.6 24.7 - - + -
43M GLY* 3.8 11.7 - - - -
44M ILE* 3.6 25.1 - - - +
47M ALA* 4.6 1.3 - - - +
337M GLY 2.9 22.4 + - - +
338M GLU* 3.2 13.7 + - - +
340M MET* 1.3 81.9 - - + +
342M ASP* 1.3 60.2 + - - +
344M PHE* 3.3 7.2 - - - +
345M ARG* 2.9 45.2 + - - +
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Residues in contact with ASP 342 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M LEU* 4.7 16.4 - - - +
166M PRO 4.7 6.4 - - - +
168M ARG* 5.1 7.1 + - - +
334M ARG* 3.1 27.9 + - - +
338M GLU* 3.0 24.9 + - - +
339M LEU* 3.5 5.4 - - - +
341M THR* 1.3 74.7 + - - +
343M GLN* 1.3 67.5 + - + +
344M PHE 3.0 1.3 - - - -
345M ARG* 3.1 29.0 + - - +
346M VAL* 3.0 28.2 + - + +
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Residues in contact with GLN 343 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M LEU 3.1 10.7 + - - +
340M MET 3.8 5.8 - - - +
342M ASP* 1.3 76.8 - - + +
344M PHE* 1.3 56.0 + - - +
346M VAL* 3.6 20.2 + - - +
347M GLY 3.0 23.0 + - - -
350M ARG* 5.9 1.0 - - - +
381M ALA* 3.7 32.7 + - - +
382M ILE* 4.1 8.1 - - + -
384M GLU* 5.4 3.0 - - - +
385M PHE* 3.4 44.1 - - + +
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Residues in contact with PHE 344 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M ILE* 3.6 22.0 - - + -
47M ALA* 3.6 16.4 - - + -
48M PHE* 4.2 6.3 - + - -
94M LEU* 3.5 24.5 - - + -
118M ILE* 3.6 30.5 - - + -
340M MET* 2.9 18.6 + - + +
341M THR* 3.3 15.0 - - - +
343M GLN* 1.3 74.1 - - - +
345M ARG* 1.3 65.8 + - - +
347M GLY 3.2 1.4 + - - -
348M LEU* 2.9 52.6 + - + +
378M LEU* 3.5 27.4 - - + +
382M ILE* 3.7 19.7 - - + +
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Residues in contact with ARG 345 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M VAL* 6.0 0.2 - - - +
43M GLY 4.8 3.4 + - - +
46M ALA* 3.3 30.3 - - - +
47M ALA* 3.7 26.0 - - + +
50M GLU* 3.4 28.9 + - + -
51M THR* 4.3 5.5 - - + +
165M LEU* 6.1 3.0 - - - +
168M ARG* 3.1 36.6 + - - +
268M ASP* 5.1 4.8 + - - -
288M ARG* 4.8 8.5 - - - +
341M THR* 2.9 31.6 + - - +
342M ASP* 3.1 30.4 + - - +
344M PHE* 1.3 71.4 - - - +
346M VAL* 1.3 58.2 + - - +
348M LEU* 3.6 2.2 - - - +
349M ALA* 2.9 31.8 + - - +
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Residues in contact with VAL 346 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M LYS* 6.6 0.2 - - + -
168M ARG* 4.5 14.4 - - - +
342M ASP* 3.0 15.1 + - + +
343M GLN* 3.7 25.8 - - - +
345M ARG* 1.3 75.9 - - - +
347M GLY* 1.3 63.8 + - - +
348M LEU 3.1 0.3 + - - -
349M ALA* 3.3 5.8 + - - +
350M ARG* 3.0 51.2 + - - +
381M ALA* 5.5 0.4 - - + -
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Residues in contact with GLY 347 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M GLN 3.0 12.3 + - - -
344M PHE 3.2 2.4 + - - -
346M VAL* 1.3 77.8 - - - +
348M LEU* 1.3 54.7 + - - +
350M ARG* 3.4 9.8 - - - +
351M LEU* 2.9 24.3 + - - +
377M PRO 3.9 6.7 - - - -
378M LEU* 3.8 18.2 + - - -
381M ALA* 3.6 24.9 - - - +
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Residues in contact with LEU 348 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M ALA* 3.4 18.8 - - + +
48M PHE* 3.4 51.1 - - + +
51M THR* 3.7 18.1 + - + +
52M PHE* 4.7 1.1 - - + -
115M LEU* 5.3 0.2 - - + -
344M PHE* 2.9 27.6 + - + +
345M ARG 3.6 4.5 - - - +
347M GLY* 1.3 75.1 - - - +
349M ALA* 1.3 60.0 + - - +
350M ARG 3.1 1.3 - - - -
351M LEU* 3.1 25.1 + - + +
352M ALA 2.9 22.7 + - - -
378M LEU* 3.6 27.5 - - + +
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Residues in contact with ALA 349 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M THR* 3.9 12.7 - - + +
168M ARG* 6.1 2.2 - - - +
345M ARG 2.9 17.8 + - - +
346M VAL* 3.9 4.9 - - - +
348M LEU* 1.3 75.5 - - - +
350M ARG* 1.3 57.8 + - - +
352M ALA* 3.2 10.9 + - - +
353M ARG* 3.0 26.2 + - - +
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Residues in contact with ARG 350 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M GLN* 5.9 1.2 - - - +
346M VAL* 3.0 40.7 + - - +
347M GLY 3.4 11.4 - - - +
349M ALA* 1.3 74.7 - - - +
351M LEU* 1.3 65.5 + - - +
353M ARG* 3.2 14.9 + - + +
354M GLY* 3.0 17.8 + - - -
377M PRO* 3.9 36.4 + - + +
380M ALA 5.7 0.6 - - - -
381M ALA* 4.2 13.5 - - - +
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Residues in contact with LEU 351 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M PHE* 5.9 0.4 - - + -
52M PHE* 4.3 21.3 - - + -
115M LEU* 5.0 8.1 - - + -
347M GLY 2.9 15.2 + - - +
348M LEU* 3.1 30.1 - - + +
350M ARG* 1.3 75.5 - - - +
352M ALA* 1.3 56.5 + - - +
354M GLY* 2.9 5.1 + - - +
355M VAL* 2.9 36.4 + - + +
373M VAL* 3.8 24.7 - - + -
374M ASN 3.1 29.1 - - - +
375M SER* 3.6 20.9 - - - +
377M PRO* 4.3 8.7 - - + +
378M LEU* 4.6 8.1 - - + -
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Residues in contact with ALA 352 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M THR* 4.2 19.1 - - - +
52M PHE* 6.4 1.1 - - + -
54M ILE* 3.4 15.4 - - + +
348M LEU 2.9 12.9 + - - +
349M ALA* 3.2 13.7 + - - +
351M LEU* 1.3 75.1 - - - +
353M ARG* 1.3 66.1 + - - +
355M VAL* 3.3 1.8 + - - -
356M ARG* 2.9 50.2 + - - +
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Residues in contact with ARG 353 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349M ALA 3.0 13.4 + - - +
350M ARG* 3.5 16.5 - - + +
352M ALA* 1.3 74.0 - - - +
354M GLY* 1.3 58.0 + - - +
356M ARG* 3.6 8.4 + - - +
357M GLU* 2.9 62.8 + - + +
200P LYS 4.1 3.0 + - - -
201P LYS 4.8 0.8 + - - -
203P THR* 2.6 46.6 + - - +
204P GLY* 5.4 2.2 - - - -
9S G 5.5 7.1 + - - -
10S A 5.6 5.4 - - - -
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Residues in contact with GLY 354 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350M ARG 3.0 10.5 + - - -
351M LEU* 2.9 10.1 + - - -
353M ARG* 1.3 78.7 - - - +
355M VAL* 1.3 55.9 + - - -
357M GLU* 3.1 10.6 - - - +
358M ARG* 3.0 47.8 + - - +
377M PRO* 6.3 1.3 - - - -
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Residues in contact with VAL 355 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M PHE* 6.3 0.9 - - + -
54M ILE* 3.4 23.3 - - + -
66M LEU* 3.6 22.0 - - + -
351M LEU* 2.9 28.2 + - + +
352M ALA* 5.0 0.4 - - - -
354M GLY* 1.3 69.0 - - - +
356M ARG* 1.3 61.3 + - - +
358M ARG* 2.9 17.7 + - - +
359M MET* 2.9 21.9 + - + +
372M LEU* 3.6 40.4 - - + +
373M VAL* 3.8 25.1 - - + -
374M ASN 4.9 1.3 - - - +
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Residues in contact with ARG 356 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M THR 4.7 0.6 + - - -
53M PRO 4.7 0.2 + - - -
54M ILE* 3.4 21.2 - - + +
55M GLU* 3.1 35.1 - - - +
265M ARG* 3.9 23.0 - - - +
352M ALA* 2.9 42.7 + - - +
353M ARG* 4.0 6.6 - - - +
355M VAL* 1.3 76.7 - - - +
357M GLU* 1.3 60.6 + - - +
359M MET* 3.6 30.9 + - + +
360M LEU* 3.6 20.4 - - - +
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Residues in contact with GLU 357 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353M ARG* 2.9 56.8 + - + +
354M GLY* 3.1 16.2 - - - +
356M ARG* 1.3 78.4 - - - +
358M ARG* 1.3 58.1 + - + +
359M MET 3.5 0.5 + - - -
360M LEU* 3.6 18.5 + - - +
200P LYS 4.0 1.6 - - - +
201P LYS* 3.6 43.6 - - - +
9S G 5.7 0.9 + - - -
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Residues in contact with ARG 358 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354M GLY* 3.0 29.3 + - - +
355M VAL 2.9 8.9 + - - +
357M GLU* 1.3 74.3 - - + +
359M MET* 1.3 55.9 + - - +
360M LEU 3.0 14.9 + - - +
371M LYS 3.4 24.0 - - - +
372M LEU* 3.1 26.3 + - + +
374M ASN* 3.2 43.3 + - - +
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Residues in contact with MET 359 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M ILE* 4.5 15.3 - - - +
55M GLU 3.3 35.2 - - - +
63M GLY 3.7 29.0 + - - +
65M VAL 5.9 0.2 - - - -
66M LEU* 5.7 3.4 - - - -
355M VAL* 2.9 23.4 + - + +
356M ARG* 3.9 20.0 - - + +
357M GLU 3.4 0.8 - - - -
358M ARG* 1.3 76.4 - - - +
360M LEU* 1.3 74.5 + - + +
372M LEU* 4.0 20.4 - - + -
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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