Contacts of the helix formed by residues 390 - 427 (chain A) in PDB entry 2VDE
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 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 3.4 26.9 - - - +
384A PHE* 4.0 3.1 - - - -
389A GLU* 1.3 75.2 + - - +
391A ILE* 1.3 63.4 + - - +
392A VAL* 3.8 20.6 - - + +
393A ASP* 3.0 36.1 + - - +
394A VAL* 3.2 12.6 + - - +
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Residues in contact with ILE 391 (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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158A GLN* 3.7 27.8 - - + +
159A LEU* 4.8 0.9 - - - -
162A THR* 3.2 35.0 - - + +
172A ALA* 6.1 0.4 - - + -
175A ASP* 3.5 35.9 - - - +
179A ALA* 3.8 22.4 - - + -
384A PHE* 3.7 22.4 - - + -
390A THR* 1.3 70.3 - - + +
392A VAL* 1.3 60.3 + - - +
394A VAL* 4.2 4.9 - - + -
395A LEU* 2.8 50.7 + - + +
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Residues in contact with VAL 392 (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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175A ASP* 4.0 20.4 - - + +
178A ASN* 3.6 26.2 - - + +
182A GLN* 5.2 1.1 + - - -
390A THR* 3.2 19.5 - - + -
391A ILE* 1.3 78.8 - - + +
393A ASP* 1.3 65.1 + - - +
395A LEU* 4.1 6.9 - - - +
396A ASP* 3.3 33.8 + - - +
393C ASP* 5.6 6.5 - - - +
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Residues in contact with ASP 393 (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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380A MET* 3.8 29.3 - - + +
389A GLU* 3.6 16.1 - - - +
390A THR* 3.0 23.7 + - - +
392A VAL* 1.3 86.1 - - - +
394A VAL* 1.3 60.5 + - - +
395A LEU 3.3 0.7 - - - -
396A ASP* 3.7 6.5 + - - +
397A ALA* 3.1 27.5 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 3.9 22.7 - - + +
377A LEU* 3.8 12.9 - - + +
380A MET* 3.8 17.5 - - + +
381A GLU* 4.1 20.6 - - + +
384A PHE* 3.5 36.1 - - + -
389A GLU* 4.8 0.4 - - + -
390A THR 3.4 13.0 - - - +
391A ILE* 3.0 9.9 + - + +
393A ASP* 1.3 75.0 - - - +
395A LEU* 1.3 54.9 + - - +
397A ALA* 3.7 4.4 + - - -
398A THR* 2.6 33.8 + - - +
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Residues in contact with LEU 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 3.7 14.1 - - + +
158A GLN* 1.9 56.3 - - + +
178A ASN* 6.4 0.2 - - - -
179A ALA* 3.7 34.5 - - + +
182A GLN* 3.5 37.7 - - + +
391A ILE* 2.8 22.2 + - + +
392A VAL* 4.1 5.4 - - - +
394A VAL* 1.3 74.5 - - - +
396A ASP* 1.3 59.3 + - - +
398A THR* 2.7 15.2 + - - -
399A THR* 2.8 25.9 + - - -
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Residues in contact with ASP 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLN* 4.2 9.2 + - - +
392A VAL* 3.3 26.9 + - - +
393A ASP* 3.8 7.2 - - - +
394A VAL 3.5 0.2 - - - -
395A LEU* 1.3 76.5 - - - +
397A ALA* 1.3 55.6 + - - +
399A THR* 3.5 7.4 + - - -
400A THR* 3.2 39.8 + - + +
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Residues in contact with ALA 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ALA 4.7 1.9 - - - +
376A SER* 4.7 7.9 - - - +
377A LEU* 3.8 30.3 - - + +
380A MET* 4.1 18.6 - - + -
393A ASP 3.1 18.9 + - - +
394A VAL* 3.8 1.8 - - - +
395A LEU 3.2 0.4 - - - -
396A ASP* 1.3 73.9 - - - +
398A THR* 1.3 62.1 + - - +
400A THR* 3.1 19.0 + - - -
401A LEU* 3.3 13.2 + - - +
178B ASN* 6.1 2.5 - - - +
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Residues in contact with THR 398 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 4.9 2.0 - - - -
154A ALA* 4.4 13.5 - - + -
155A ILE* 4.0 9.3 - - - +
158A GLN* 3.4 29.2 + - - +
377A LEU* 3.5 31.6 - - + -
381A GLU* 5.0 2.2 - - - +
394A VAL 2.6 19.6 + - - -
395A LEU* 2.7 19.1 + - - -
397A ALA* 1.3 73.1 - - - +
399A THR* 1.3 63.5 + - - +
401A LEU* 3.4 1.4 + - - +
402A TYR* 2.9 39.3 + - + -
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Residues in contact with THR 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 3.4 27.4 + - - +
155A ILE* 5.9 1.9 - - - +
182A GLN* 4.2 12.0 + - - +
395A LEU 2.8 20.8 + - - -
396A ASP* 3.6 9.1 - - - -
398A THR* 1.3 78.5 - - - +
400A THR* 1.3 60.4 + - + +
402A TYR* 3.4 2.3 + - - +
403A ASN* 3.0 45.5 + - - +
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Residues in contact with THR 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ALA* 4.2 9.6 + - - +
396A ASP* 3.2 18.8 + - - +
397A ALA* 3.1 17.2 + - - -
399A THR* 1.3 77.9 - - + +
401A LEU* 1.3 63.4 + - - +
402A TYR 3.4 0.2 - - - -
403A ASN* 3.7 9.4 - - + +
404A ALA* 3.2 22.2 + - - +
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Residues in contact with LEU 401 (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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370A VAL* 3.9 10.3 - - + +
373A ALA* 3.7 16.2 - - + +
374A GLN* 3.5 61.0 - - - +
377A LEU* 3.6 16.8 - - + -
397A ALA 3.3 14.3 + - - +
398A THR* 3.8 5.4 - - - +
399A THR 3.3 0.4 - - - -
400A THR* 1.3 80.5 + - - +
402A TYR* 1.3 77.9 + - + +
404A ALA* 3.5 2.9 + - - +
405A LYS* 3.1 42.3 + - + +
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Residues in contact with TYR 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 4.1 33.4 - + + +
150A ALA* 3.3 40.3 + - + +
151A GLN* 3.8 29.2 - - + -
154A ALA* 4.2 13.9 - - + +
377A LEU* 5.6 0.2 - - + -
398A THR* 2.9 34.5 + - + +
399A THR 4.1 3.1 - - - +
400A THR 3.4 0.2 - - - -
401A LEU* 1.3 91.3 - - + +
403A ASN* 1.3 57.5 + - - +
405A LYS* 3.8 14.8 - - + +
406A GLN* 2.8 38.5 + - - +
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Residues in contact with ASN 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 5.3 2.2 - - - +
399A THR* 3.0 42.8 + - - +
400A THR* 3.7 11.0 - - - +
402A TYR* 1.3 76.7 - - - +
404A ALA* 1.3 56.9 + - - +
406A GLN* 3.1 8.7 - - - +
407A GLU* 3.0 42.1 + - + +
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Residues in contact with ALA 404 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 4.5 5.5 - - + +
369A ALA* 3.8 29.4 - - + +
370A VAL* 3.7 17.2 - - + +
373A ALA* 4.6 1.1 - - + -
400A THR 3.2 15.7 + - - +
401A LEU 3.8 4.7 - - - +
402A TYR 3.4 0.2 - - - -
403A ASN* 1.3 78.2 - - - +
405A LYS* 1.3 59.1 + - - +
407A GLU* 3.3 8.3 + - - +
408A LEU* 2.9 30.3 + - - +
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Residues in contact with LYS 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 3.6 41.0 + - + +
370A VAL* 3.7 22.4 - - + -
374A GLN* 4.5 16.3 + - - -
401A LEU* 3.1 31.1 + - + +
402A TYR* 3.8 17.4 - - + +
404A ALA* 1.3 72.4 - - - +
406A GLN* 1.3 66.4 + - - +
408A LEU* 3.9 3.1 - - - +
409A ALA* 3.1 24.3 + - - +
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Residues in contact with GLN 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN* 5.5 0.2 - - - +
144A VAL* 3.6 45.3 + - + +
147A TYR* 3.4 32.7 - - - +
148A THR* 5.0 2.0 + - - -
402A TYR* 2.8 15.1 + - - +
403A ASN* 3.1 13.9 - - - +
405A LYS* 1.3 73.7 - - - +
407A GLU* 1.3 63.4 + - + +
409A ALA* 3.3 6.9 + - - +
410A ASN* 2.9 32.4 + - + +
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Residues in contact with GLU 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TYR* 3.6 50.6 + - + -
403A ASN* 3.0 27.1 + - + +
404A ALA* 3.3 3.1 + - - +
406A GLN* 1.3 82.1 - - - +
408A LEU* 1.3 52.9 + - - +
410A ASN* 3.1 12.0 + - - +
411A ALA* 2.7 36.2 + - - +
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Residues in contact with LEU 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ILE* 4.3 18.8 - - + +
366A TYR* 3.7 13.4 - - + +
367A LYS* 3.6 38.6 - - + +
370A VAL* 3.9 21.1 - - + -
404A ALA 2.9 16.5 + - - +
405A LYS* 3.9 5.4 - - - +
407A GLU* 1.3 75.5 - - - +
409A ALA* 1.3 64.3 + - - +
411A ALA* 3.3 3.5 + - - +
412A ARG* 3.3 56.3 + - + +
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Residues in contact with ALA 409 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN* 5.4 0.4 - - - +
143A ASP* 3.4 29.4 - - + +
147A TYR* 4.2 15.3 - - + +
218A LEU* 5.6 0.3 - - - +
405A LYS 3.1 16.5 + - - +
406A GLN* 3.5 4.5 - - - +
408A LEU* 1.3 80.7 - - - +
410A ASN* 1.3 62.0 + - - +
412A ARG* 3.5 17.1 + - - +
413A TYR* 3.3 28.2 + - + -
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Residues in contact with ASN 410 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN* 3.9 33.1 + - - +
406A GLN* 2.9 17.7 + - - +
407A GLU* 3.3 16.7 + - - +
409A ALA* 1.3 76.2 - - - +
411A ALA* 1.3 62.2 + - - +
413A TYR* 3.3 4.8 + - - +
414A ASN* 3.0 38.9 + - - +
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Residues in contact with ALA 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A SER* 3.5 8.3 + - - +
362A SER* 4.6 7.0 - - - +
363A ILE* 3.9 29.5 - - + +
366A TYR* 4.6 10.1 - - + -
407A GLU 2.7 19.1 + - - +
408A LEU* 3.7 7.9 - - - +
409A ALA 3.3 0.4 - - - -
410A ASN* 1.3 73.6 - - - +
412A ARG* 1.3 56.8 + - - +
414A ASN* 3.3 11.0 + - - +
415A TYR* 2.9 25.3 + - - +
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Residues in contact with ARG 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 5.5 3.8 + - - -
218A LEU* 3.8 19.8 - - + +
220A VAL* 3.4 37.4 + - - +
223A PHE* 3.6 42.9 - - + +
363A ILE* 4.0 22.2 - - + -
367A LYS* 5.3 9.1 - - - +
408A LEU* 3.3 40.9 + - - +
409A ALA* 4.0 20.1 + - - +
411A ALA* 1.3 78.6 - - - +
413A TYR* 1.3 63.2 + - - +
415A TYR* 3.2 17.0 + - - +
416A LEU* 3.3 13.8 + - - +
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Residues in contact with TYR 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.7 33.4 - + + +
139A LEU* 3.6 53.0 + - + +
140A ASN* 3.7 22.0 - - - +
143A ASP* 3.2 32.5 + - - -
217A ALA* 4.5 3.5 - - - +
218A LEU* 3.8 35.7 + - + +
409A ALA* 3.3 16.5 + - + -
410A ASN* 3.3 8.0 + - - +
411A ALA 3.3 0.6 - - - -
412A ARG* 1.3 73.7 - - - +
414A ASN* 1.3 65.0 + - - +
416A LEU* 3.5 15.0 + - + +
417A ILE* 3.5 19.0 + - - +
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Residues in contact with ASN 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A SER* 4.0 7.2 - - - +
410A ASN* 3.0 36.2 + - - +
411A ALA* 3.4 11.5 - - - +
413A TYR* 1.3 73.7 - - - +
415A TYR* 1.3 68.5 + - - +
417A ILE* 3.1 12.0 + - - +
418A ASN* 3.0 31.0 + - - +
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Residues in contact with TYR 415 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.9 10.3 - + - -
224A LYS 4.7 4.2 + - - -
225A THR* 3.7 17.4 - - + -
226A ASP* 3.1 29.8 + - - -
356A ILE* 3.7 18.7 - - + +
359A SER* 3.4 16.1 + - - +
360A ILE* 3.6 34.1 - - + -
363A ILE* 3.8 13.7 - - + -
411A ALA 2.9 12.9 + - - +
412A ARG 3.2 9.9 - - - +
414A ASN* 1.3 74.7 - - - +
416A LEU* 1.3 81.0 + - + +
418A ASN* 3.1 8.6 + - - +
419A GLN* 2.9 56.3 + - - +
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Residues in contact with LEU 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.7 36.8 - - + -
218A LEU* 4.4 20.4 - - + -
223A PHE* 4.0 13.2 - - + -
412A ARG 3.6 12.8 - - - +
413A TYR* 3.8 10.5 - - + +
414A ASN 3.3 0.8 - - - -
415A TYR* 1.3 94.5 - - + +
417A ILE* 1.3 61.9 - - - +
419A GLN* 3.1 11.9 + - - +
420A LEU* 3.1 26.2 + - - +
437A LEU* 3.8 32.6 - - + +
440A ALA* 5.3 5.6 - - + -
441A LEU* 5.0 2.2 - - + -
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Residues in contact with ILE 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.2 3.8 - - + -
132A ALA* 3.9 16.6 - - + +
133A THR* 3.9 28.3 - - + +
136A PHE* 3.7 31.4 - - + -
413A TYR 3.5 15.3 - - - +
414A ASN* 3.1 12.9 + - - +
416A LEU* 1.3 71.7 - - - +
418A ASN* 1.3 51.5 + - - +
419A GLN 3.0 4.3 - - - -
420A LEU* 2.9 10.1 + - + +
421A ASN* 2.8 56.9 + - - +
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Residues in contact with ASN 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A SER* 4.3 5.7 - - - +
355A ASN* 3.6 27.5 + - + +
356A ILE* 3.7 23.7 - - + +
359A SER* 3.5 26.9 + - - -
414A ASN* 3.0 24.3 + - - +
415A TYR 3.4 5.4 - - - +
417A ILE* 1.3 74.9 - - - +
419A GLN* 1.3 60.0 + - - +
421A ASN* 3.7 19.7 + - - +
422A ILE* 3.3 22.5 + - - +
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Residues in contact with GLN 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP* 5.1 9.5 + - - +
356A ILE* 3.7 14.8 - - + -
415A TYR* 2.9 45.9 + - - +
416A LEU* 3.2 12.1 - - - +
417A ILE 3.0 0.2 - - - -
418A ASN* 1.3 78.1 - - - +
420A LEU* 1.3 61.9 + - + +
422A ILE* 3.1 24.4 - - + +
423A LYS* 3.7 9.4 + - - +
437A LEU* 3.3 27.5 - - - +
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Residues in contact with LEU 420 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE 5.0 2.9 - - - +
129A LEU* 4.0 16.8 - - + -
132A ALA* 3.6 31.6 - - + -
416A LEU 3.1 14.9 + - - +
417A ILE* 2.9 9.9 + - + +
419A GLN* 1.3 78.1 - - + +
421A ASN* 1.3 59.2 + - - +
422A ILE 3.1 1.8 - - - -
423A LYS* 3.0 8.6 + - - +
424A SER* 2.9 27.7 + - - -
429A LEU* 3.9 14.6 - - + +
433A ASP* 4.0 37.9 - - + +
434A LEU* 3.9 16.6 - - + -
437A LEU* 4.2 16.8 - - + -
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Residues in contact with ASN 421 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.3 26.4 - - - +
348A THR* 5.6 0.5 - - - +
352A SER* 3.9 14.3 + - - +
355A ASN* 5.9 1.8 - - - +
417A ILE* 2.8 39.1 + - - +
418A ASN* 3.7 22.0 + - - +
420A LEU* 1.3 72.3 - - - +
422A ILE* 1.3 55.6 + - - +
424A SER* 3.3 9.0 + - - -
425A ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 4.7 7.2 - - + -
234A LEU* 3.7 42.4 - - + -
349A VAL* 4.7 3.6 - - + +
352A SER* 3.7 38.6 - - - +
353A PHE* 3.8 5.4 - - - +
356A ILE* 4.3 11.0 - - + -
418A ASN 3.3 9.6 + - - +
419A GLN* 3.1 26.5 - - + +
420A LEU 3.1 0.8 - - - -
421A ASN* 1.3 75.9 - - - +
423A LYS* 1.3 75.3 + - + +
425A ALA* 3.3 11.3 + - + +
426A LEU* 3.4 17.9 + - + +
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Residues in contact with LYS 423 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLN 4.1 10.8 - - - +
420A LEU* 3.0 11.7 + - - +
422A ILE* 1.3 83.8 - - + +
424A SER* 1.3 58.6 + - - +
426A LEU* 3.4 15.5 + - + +
427A GLY 2.9 22.3 + - - -
428A THR* 2.7 48.0 + - - +
429A LEU* 3.9 14.6 - - + -
433A ASP* 3.1 41.3 - - - +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN* 3.8 24.2 + - - +
129A LEU* 4.2 17.5 - - - +
242A ASN* 4.1 5.5 + - - -
420A LEU 2.9 12.0 + - - -
421A ASN* 3.4 13.7 - - - -
423A LYS* 1.3 76.6 - - - +
425A ALA* 1.3 59.2 + - - +
427A GLY* 3.4 10.4 + - - -
429A LEU* 4.1 17.0 - - - +
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASN* 2.9 26.2 + - - +
345A VAL* 3.8 9.4 - - - +
348A THR* 3.9 25.6 - - + -
349A VAL* 3.8 23.1 - - + -
352A SER* 4.0 8.1 - - - +
421A ASN 3.0 15.1 + - - +
422A ILE* 3.7 7.6 - - + +
423A LYS 3.2 0.4 - - - -
424A SER* 1.3 76.8 - - - +
426A LEU* 1.3 56.9 + - + +
427A GLY 3.2 1.3 - - - -
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.5 51.4 - - + +
237A GLU* 3.8 20.0 - - + +
238A ALA* 3.7 24.5 - - + +
241A ARG* 3.4 20.8 - - - +
242A ASN* 3.6 4.2 + - - -
349A VAL* 5.6 2.2 - - + -
422A ILE* 3.4 13.2 + - + +
423A LYS* 4.0 16.2 - - + +
425A ALA* 1.3 78.2 - - - +
427A GLY* 1.3 62.2 + - - +
428A THR* 3.2 38.6 - - + +
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Residues in contact with GLY 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN* 3.2 22.0 - - - +
241A ARG* 3.7 22.2 + - - +
242A ASN* 4.4 5.2 - - - -
243A LEU* 4.6 12.1 - - - +
423A LYS 2.9 8.7 + - - -
424A SER 3.4 9.6 + - - -
425A ALA 3.2 3.4 - - - -
426A LEU* 1.3 79.0 - - - +
428A THR* 1.3 58.9 + - - +
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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