Contacts of the helix formed by residues 389 - 412 (chain A) in PDB entry 2E4Y
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 LYS 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.4 5.1 - - - +
68A ARG* 3.5 17.0 - - - +
171A TYR* 3.8 8.1 - - + +
172A ALA* 3.4 34.1 - - + -
174A THR* 5.6 0.2 - - - -
301A ASP* 3.2 23.1 + - - +
324A GLU* 2.7 35.5 + - - +
325A LEU* 4.1 19.7 - - + -
387A GLU* 3.1 15.6 + - - +
388A SER* 1.3 74.2 - - - +
390A ILE* 1.3 67.7 + - - +
391A MET 2.9 3.4 - - - -
392A PHE* 2.6 33.5 + - + +
393A VAL* 3.2 9.9 + - + +
1001A 52A 3.8 12.2 + - - -
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Residues in contact with ILE 390 (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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67A GLN* 3.4 27.4 - - + +
68A ARG* 3.4 45.5 - - + +
71A ALA* 3.8 18.4 - - + -
330A VAL* 4.8 1.8 - - + -
333A PHE* 4.0 17.5 - - + -
386A GLN* 3.5 22.0 - - + +
387A GLU* 3.2 23.1 + - + +
389A LYS* 1.3 75.5 - - - +
391A MET* 1.3 64.2 + - - +
393A VAL* 3.1 15.0 + - + +
394A VAL* 3.2 17.8 + - + +
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Residues in contact with MET 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA 3.7 4.0 - - - +
327A SER* 3.3 34.3 - - - -
328A HIS* 3.3 41.5 - - - +
329A PRO* 5.7 0.4 - - + -
330A VAL* 4.0 20.1 - - + +
386A GLN* 4.7 1.2 + - - -
388A SER 4.2 2.1 + - - +
389A LYS 2.7 4.2 + - - -
390A ILE* 1.3 75.6 - - - +
392A PHE* 1.3 86.0 + - + +
394A VAL* 3.1 4.7 + - - +
395A ASN* 3.0 44.5 + - - +
441A THR* 6.2 3.8 - - + -
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Residues in contact with PHE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.2 20.4 - - - +
190A THR* 2.9 36.5 + - - +
191A VAL* 3.3 15.3 - - + -
192A PRO* 5.3 2.0 - - + -
325A LEU* 3.6 32.5 - - + -
326A ALA 3.7 8.5 - - - -
327A SER* 3.5 20.2 - - - -
388A SER 4.2 0.9 - - - -
389A LYS* 2.6 37.0 + - + +
391A MET* 1.3 89.8 - - + +
393A VAL* 1.3 65.1 + - - +
395A ASN* 3.9 6.1 - - - +
396A ALA* 2.9 26.0 + - - +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.4 7.9 - - + -
68A ARG* 3.7 43.3 - - + +
71A ALA* 3.9 11.2 - - + -
72A MET* 4.0 15.7 - - + +
146A ILE* 5.4 0.4 - - + -
171A TYR* 3.4 35.4 - - + -
389A LYS 3.9 7.2 - - - +
390A ILE* 3.1 12.5 + - - +
392A PHE* 1.3 77.9 - - - +
394A VAL* 1.3 64.2 + - - +
396A ALA* 3.0 13.3 + - - +
397A VAL* 3.1 17.5 + - + +
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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
----------------------------------------------------------
71A ALA* 4.4 22.9 - - + +
74A PHE* 4.5 10.8 - - + -
75A ALA* 4.2 11.2 - - + -
330A VAL* 4.5 13.2 - - + -
333A PHE* 5.6 0.4 - - + -
390A ILE* 3.4 18.6 - - + +
391A MET* 3.1 7.5 + - - +
393A VAL* 1.3 76.2 - - - +
395A ASN* 1.3 63.9 + - - +
397A VAL* 3.5 1.9 + - - +
398A TYR* 3.0 45.7 + - + -
442A ALA* 4.3 4.0 - - + -
444A PHE* 4.0 20.6 - - + -
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Residues in contact with ASN 395 (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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190A THR* 4.3 11.9 - - + -
391A MET* 3.0 33.0 + - - +
392A PHE* 4.0 6.8 - - - +
394A VAL* 1.3 79.7 - - - +
396A ALA* 1.3 57.8 + - - +
398A TYR* 3.8 6.0 - - - +
399A ALA* 2.8 36.4 + - - +
439A GLN* 4.6 1.9 + - - -
441A THR* 3.6 23.7 - - - +
442A ALA* 4.5 6.0 + - - +
454A VAL* 3.2 33.1 - - + +
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Residues in contact with ALA 396 (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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146A ILE* 3.3 20.2 - - + +
169A ILE* 3.9 18.8 - - + +
171A TYR* 4.1 12.6 - - + -
190A THR* 3.6 17.0 - - + +
392A PHE 2.9 20.1 + - - +
393A VAL 3.1 6.5 - - - +
395A ASN* 1.3 78.7 - - - +
397A VAL* 1.3 61.6 + - - +
399A ALA* 3.3 4.6 - - - +
400A MET 3.2 15.4 + - - -
434A TYR* 3.9 3.5 + - - -
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Residues in contact with VAL 397 (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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41A LEU* 4.2 19.2 - - + +
72A MET* 4.0 20.0 - - + -
75A ALA* 4.1 18.2 - - + -
76A ILE* 4.4 9.9 - - + -
79A ILE* 4.0 18.4 - - + -
146A ILE* 3.6 30.5 - - + -
393A VAL* 3.1 14.7 + - + +
394A VAL 3.7 5.4 - - - +
396A ALA* 1.3 71.7 - - - +
398A TYR* 1.3 67.5 + - - +
399A ALA 3.1 1.3 - - - -
400A MET* 3.0 6.8 + - - +
401A ALA* 2.9 19.5 + - - +
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Residues in contact with TYR 398 (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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75A ALA* 4.1 9.4 - - + -
78A GLU* 3.3 28.2 - - - +
79A ILE* 3.4 28.3 + - + +
82A ASP* 5.1 4.9 + - - +
85A LEU* 3.7 24.2 - - + -
394A VAL* 3.0 34.3 + - + +
395A ASN* 3.8 4.7 - - - +
397A VAL* 1.3 74.6 - - - +
399A ALA* 1.3 53.6 + - - +
401A ALA* 3.0 6.1 + - - +
402A HIS* 2.6 48.4 + - + -
439A GLN* 3.8 15.5 - - - +
442A ALA* 3.7 29.4 - - + -
443A PRO* 5.2 5.1 - - + +
444A PHE* 3.3 21.6 - + - -
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Residues in contact with ALA 399 (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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190A THR* 5.2 1.1 - - + -
395A ASN 2.8 14.0 + - - +
396A ALA* 3.3 9.6 - - - +
398A TYR* 1.3 77.0 - - - +
400A MET* 1.3 67.2 + - - +
402A HIS* 2.9 1.3 + - - +
403A ALA* 2.7 23.4 + - - +
434A TYR* 3.1 29.7 - - + +
437A LYS* 5.0 2.6 - - + +
439A GLN* 4.1 13.1 - - - +
454A VAL* 4.7 7.6 - - + -
456A PHE* 4.0 13.9 - - + -
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Residues in contact with MET 400 (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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41A LEU* 3.2 33.2 - - + -
144A GLY* 4.1 20.0 - - - +
146A ILE* 4.0 7.2 - - + -
167A PRO* 4.3 10.3 - - + +
169A ILE* 3.1 31.4 - - + -
396A ALA 3.2 4.3 + - - +
397A VAL* 3.0 10.2 + - - +
399A ALA* 1.3 77.7 - - - +
401A ALA* 1.3 57.6 + - - +
403A ALA* 3.1 14.5 - - + +
404A LEU* 2.9 36.7 + - + +
430A LEU* 3.9 29.8 - - + -
434A TYR* 3.7 8.2 + - + -
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Residues in contact with ALA 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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79A ILE* 3.5 33.7 - - + -
85A LEU* 4.0 14.0 - - + +
86A LEU* 4.1 6.1 - - + +
91A LEU* 4.4 13.0 - - + +
397A VAL 2.9 7.4 + - - +
398A TYR* 3.2 7.9 - - - +
399A ALA 2.8 0.6 + - - -
400A MET* 1.3 73.0 - - - +
402A HIS* 1.3 55.5 + - - +
403A ALA 3.0 0.7 - - - -
404A LEU* 3.0 8.8 + - - +
405A HIS* 2.6 36.4 + - - +
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Residues in contact with HIS 402 (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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84A TYR 6.2 0.2 - - - -
85A LEU* 3.8 30.2 - - + +
398A TYR* 2.6 34.8 + - + +
399A ALA 3.6 2.5 - - - +
401A ALA* 1.3 73.2 - - - +
403A ALA* 1.3 63.2 + - - +
405A HIS* 3.1 14.5 + + - +
406A LYS* 2.9 23.4 + - - +
437A LYS* 4.0 18.6 + - + +
439A GLN* 3.4 51.8 - - + +
440A PHE 5.3 0.6 + - - -
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Residues in contact with ALA 403 (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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399A ALA 2.7 6.0 + - - +
400A MET* 3.1 13.0 - - + +
402A HIS* 1.3 75.3 - - - +
404A LEU* 1.3 64.7 + - - +
406A LYS* 3.0 15.6 + - - +
407A MET* 3.1 10.4 + - - +
430A LEU* 3.9 19.0 - - + +
433A GLU* 4.4 10.4 - - - +
434A TYR* 3.3 38.4 - - + -
437A LYS* 4.5 5.7 - - - +
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Residues in contact with LEU 404 (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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39A LEU* 3.4 33.0 - - + -
41A LEU* 4.7 11.0 - - + -
86A LEU* 4.0 11.2 - - + -
91A LEU* 4.4 16.4 - - + -
143A ALA* 4.1 20.0 - - + -
400A MET* 2.9 22.4 + - + +
401A ALA* 3.6 5.8 - - - +
403A ALA* 1.3 73.4 - - - +
405A HIS* 1.3 54.0 + - - +
407A MET* 2.8 8.2 + - + +
408A GLN* 2.7 34.3 + - - +
422A MET* 4.6 3.1 - - - +
425A LEU* 4.4 10.5 - - + -
430A LEU* 3.4 37.9 - - + -
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Residues in contact with HIS 405 (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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84A TYR 3.4 20.2 + - - -
85A LEU* 3.5 23.6 - - + -
86A LEU* 3.1 35.6 + - + +
87A PRO* 4.5 7.6 - - + -
401A ALA 2.6 17.4 + - - +
402A HIS* 3.3 17.3 - + - +
404A LEU* 1.3 72.5 - - - +
406A LYS* 1.3 66.0 + - - +
408A GLN* 3.3 8.2 - - + +
409A ARG* 3.2 48.7 + - - +
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Residues in contact with LYS 406 (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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402A HIS 2.9 12.0 + - - +
403A ALA* 3.0 7.4 + - - +
405A HIS* 1.3 74.2 - - - +
407A MET* 1.3 68.8 + - - +
408A GLN 2.8 1.0 + - - -
409A ARG* 2.9 6.1 + - - +
410A THR* 2.8 35.5 + - - +
433A GLU* 3.2 38.0 + - + +
436A LEU* 4.1 15.6 + - - +
437A LYS* 3.0 37.0 - - - +
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Residues in contact with MET 407 (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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403A ALA 3.1 6.7 + - - +
404A LEU* 2.8 12.9 + - - +
406A LYS* 1.3 74.6 - - - +
408A GLN* 1.3 56.8 + - - +
410A THR* 4.5 2.7 - - - -
411A LEU* 2.8 50.6 + - + +
422A MET* 3.4 16.8 - - + +
425A LEU* 3.6 31.2 - - - -
426A ASP* 4.5 7.0 - - + +
429A LYS* 4.2 8.5 - - + -
430A LEU* 3.3 49.6 - - + +
433A GLU* 3.0 30.9 + - - +
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Residues in contact with GLN 408 (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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86A LEU* 4.2 10.1 - - + -
87A PRO* 5.7 3.1 - - + -
89A VAL* 4.6 3.7 - - + +
404A LEU 2.7 13.4 + - - +
405A HIS* 3.3 24.5 - - + +
406A LYS 2.8 0.8 + - - -
407A MET* 1.3 72.9 - - - +
409A ARG* 1.3 65.7 + - + +
412A CYS* 2.7 50.2 + - - +
415A THR 3.1 27.1 + - - -
416A THR* 4.0 13.9 - - - +
417A LYS 3.1 23.4 - - - +
422A MET* 3.3 25.2 - - + +
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Residues in contact with ARG 409 (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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84A TYR* 4.9 7.3 + - - +
405A HIS* 3.2 35.4 + - + +
406A LYS* 2.9 8.9 + - - +
408A GLN* 1.3 90.4 - - + +
410A THR* 1.3 63.6 + - - +
412A CYS 4.5 1.8 - - - +
413A PRO* 3.7 20.3 - - + +
416A THR* 6.0 4.2 - - - +
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Residues in contact with THR 410 (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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406A LYS* 2.8 39.2 + - - +
407A MET* 4.1 2.5 - - - -
409A ARG* 1.3 76.1 - - - +
411A LEU* 1.3 68.9 + - + +
413A PRO* 4.1 6.4 - - - +
433A GLU* 4.1 10.2 + - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A MET* 2.8 36.2 + - + +
410A THR* 1.3 79.5 - - + +
412A CYS* 1.3 73.4 + - - +
413A PRO* 3.6 6.6 - - - +
421A ALA* 3.7 33.1 - - + +
422A MET* 3.4 24.7 - - + -
425A LEU* 6.5 0.2 - - - -
433A GLU* 6.0 0.7 - - - +
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Residues in contact with CYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLN* 2.7 31.3 + - - +
409A ARG* 3.9 2.5 - - - +
410A THR 3.3 1.0 - - - -
411A LEU* 1.3 88.8 - - - +
413A PRO* 1.3 66.1 - - - +
414A GLN* 3.3 2.8 + - + -
415A THR* 3.2 20.6 + - - +
417A LYS 4.7 1.6 - - - +
419A CYS* 2.0 53.8 - - + -
421A ALA* 3.6 12.3 - - - -
422A MET* 4.9 0.2 - - - -
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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