Contacts of the helix formed by residues 385 - 410 (chain A) in PDB entry 4PKO
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 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ALA* 3.8 2.5 - - - +
384A ALA* 1.3 88.0 - - + +
386A GLU* 1.3 60.4 + - - +
387A VAL* 3.6 17.3 - - + +
388A GLU* 3.3 19.9 + - - +
389A MET* 3.0 29.7 + - - +
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 5.5 10.1 + - - +
385A THR* 1.3 75.5 - - - +
387A VAL* 1.3 64.4 + - + +
389A MET* 3.4 16.5 + - + +
390A LYS* 3.4 33.2 + - + +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 4.7 12.6 - - + -
47A PRO* 3.6 25.6 - - + +
49A ILE* 4.1 34.7 - - + +
385A THR* 3.6 16.8 - - - +
386A GLU* 1.3 79.8 - - + +
388A GLU* 1.3 64.4 + - + +
390A LYS* 3.9 12.6 + - - +
391A GLU* 3.9 13.2 + - - +
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ALA* 4.0 8.0 - - + +
384A ALA* 3.3 30.7 + - - +
385A THR* 3.3 18.8 + - - +
387A VAL* 1.3 80.7 - - + +
389A MET* 1.3 60.1 + - - +
390A LYS 3.4 0.2 - - - -
391A GLU* 3.7 12.3 + - - +
392A LYS* 3.0 36.4 + - + +
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Residues in contact with MET 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 3.7 29.6 - - + +
180A GLY* 3.3 30.1 - - - +
381A VAL* 3.5 27.4 - - - +
382A GLY 4.3 0.4 - - - -
383A ALA* 3.6 33.0 - - + +
385A THR 3.0 15.6 + - - +
386A GLU* 3.5 11.9 - - + +
387A VAL 3.3 0.2 - - - -
388A GLU* 1.3 77.0 - - - +
390A LYS* 1.3 58.6 + - + +
392A LYS* 4.1 0.9 - - - -
393A LYS* 2.6 39.8 + - + +
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Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 3.6 9.3 + - - +
47A PRO 2.7 29.8 + - - -
48A THR* 2.7 41.9 + - + +
49A ILE 4.5 0.9 - - - +
50A THR* 5.0 1.1 + - - -
386A GLU* 3.4 33.7 + - + +
387A VAL* 3.9 15.4 + - - +
388A GLU 3.4 0.2 - - - -
389A MET* 1.3 79.6 - - + +
391A GLU* 1.3 58.0 + - - +
393A LYS* 4.3 17.2 + - - +
394A ALA* 3.1 28.2 + - - +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 4.3 18.4 + - - +
49A ILE* 3.1 26.1 + - + +
50A THR* 4.3 2.7 - - - +
51A LYS* 4.2 21.5 - - + +
153A ASN* 5.6 0.7 + - - -
387A VAL 3.9 5.9 + - - +
388A GLU* 3.7 16.5 + - - +
389A MET 3.2 0.4 - - - -
390A LYS* 1.3 77.0 - - - +
392A LYS* 1.3 69.3 + - - +
394A ALA* 3.5 4.7 + - - +
395A ARG* 2.8 65.4 + - + +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 4.1 11.0 - - - -
158A VAL* 5.2 8.3 - - - -
183A LEU 5.4 1.8 + - - -
185A ASP* 3.9 19.0 + - - -
381A VAL* 3.3 20.2 - - + -
382A GLY 3.4 21.1 + - - +
383A ALA* 4.8 1.7 - - + +
388A GLU* 3.0 27.8 + - + +
389A MET* 3.7 6.7 - - - +
391A GLU* 1.3 78.2 + - - +
393A LYS* 1.3 63.8 + - - +
395A ARG* 3.2 33.0 + - + +
396A VAL* 3.1 29.4 + - + +
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Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.8 14.4 - - + +
179A ASP* 2.9 31.0 - - - +
381A VAL* 4.0 21.2 - - + +
389A MET 2.6 21.9 + - - +
390A LYS* 4.3 16.5 + - - +
392A LYS* 1.3 73.1 - - - +
394A ALA* 1.3 62.1 + - - +
396A VAL* 3.3 3.8 + - - +
397A GLU* 3.0 59.5 + - + +
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 4.3 15.5 - - - +
51A LYS 6.1 0.2 - - - +
52A ASP* 4.4 15.2 - - + +
55A SER* 5.7 0.7 - - - +
390A LYS 3.1 21.8 + - - +
391A GLU 3.8 5.2 - - - +
392A LYS 3.2 0.4 - - - -
393A LYS* 1.3 82.5 - - - +
395A ARG* 1.3 58.3 + - + +
397A GLU* 3.5 10.4 + - - +
398A ASP* 3.0 35.1 + - - +
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 5.1 12.6 - - + +
52A ASP 6.2 0.4 - - - +
151A SER 5.5 1.3 - - - +
152A ALA* 3.3 34.4 + - + +
153A ASN* 3.9 26.3 + - + +
155A ASP* 2.9 33.5 + - - -
158A VAL* 5.4 1.1 - - + -
391A GLU* 2.8 47.6 + - + +
392A LYS* 3.2 31.4 - - - +
393A LYS 3.3 0.2 - - - -
394A ALA* 1.3 74.6 - - + +
396A VAL* 1.3 62.2 + - + +
398A ASP* 3.4 11.2 - - - +
399A ALA* 3.0 28.9 + - - +
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.5 30.3 - - + -
162A ILE* 4.6 4.2 - - + +
177A VAL* 3.3 27.4 - - + -
185A ASP* 6.2 0.7 - - - -
379A ILE* 4.5 20.2 - - + -
381A VAL* 3.7 25.8 - - + -
392A LYS* 3.1 18.1 + - + +
393A LYS* 3.6 8.5 - - - +
394A ALA 3.3 0.2 - - - -
395A ARG* 1.3 75.6 - - + +
397A GLU* 1.3 64.5 + - - +
399A ALA* 3.6 2.1 + - - +
400A LEU* 3.2 22.6 + - + +
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 3.2 33.3 - - + +
393A LYS* 3.0 44.2 + - - +
394A ALA* 3.7 7.8 - - - +
395A ARG 3.3 0.2 - - - -
396A VAL* 1.3 77.8 - - - +
398A ASP* 1.3 58.9 + - - +
400A LEU* 3.3 10.9 + - - +
401A HIS* 2.5 41.0 + - + -
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.1 38.1 - - - +
82A ASN* 5.5 0.2 - - - +
86A GLY 3.6 19.7 - - - +
87A ASP* 3.9 19.2 - - - +
151A SER* 3.2 17.9 + - - +
394A ALA 3.0 23.2 + - - +
395A ARG* 3.4 13.2 - - - +
396A VAL 3.3 0.2 - - - -
397A GLU* 1.3 78.2 - - - +
399A ALA* 1.3 61.5 + - - +
400A LEU 3.3 0.7 + - - -
401A HIS* 3.4 6.4 + - - +
402A ALA* 3.3 15.1 + - - +
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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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148A GLY* 3.2 26.9 - - - +
151A SER* 3.6 12.3 + - - -
152A ALA* 3.7 10.5 - - + +
158A VAL* 4.1 3.4 - - + -
162A ILE* 3.9 16.4 - - + -
395A ARG 3.0 17.0 + - - +
396A VAL 4.1 2.0 - - - +
398A ASP* 1.3 75.8 - - - +
400A LEU* 1.3 62.8 + - - +
402A ALA* 3.5 1.8 + - - +
403A THR* 3.3 28.6 + - - +
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Residues in contact with LEU 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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162A ILE* 4.0 25.5 - - + +
166A MET* 6.0 0.9 - - + -
175A ILE* 3.9 41.5 - - + +
177A VAL* 5.4 7.6 - - + -
379A ILE* 5.1 2.0 - - + -
396A VAL* 3.2 14.7 + - + +
397A GLU* 3.4 13.0 - - - +
398A ASP 3.1 0.4 - - - -
399A ALA* 1.3 77.9 - - - +
401A HIS* 1.3 70.9 + - + +
403A THR* 2.8 20.8 + - - +
404A ARG* 3.3 46.3 + - + +
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Residues in contact with HIS 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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82A ASN 5.3 3.1 - - - -
85A ALA 3.0 28.0 - - - +
86A GLY* 4.0 15.9 + - - -
397A GLU* 2.5 38.8 + - + -
398A ASP* 3.8 6.7 - - - +
400A LEU* 1.3 85.2 - - + +
402A ALA* 1.3 57.3 + - - +
404A ARG* 3.4 11.6 + - - +
405A ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 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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85A ALA 6.2 0.2 - - - -
87A ASP* 4.4 9.0 - - + -
147A VAL* 4.6 5.4 - - + +
151A SER* 3.3 37.2 - - - +
398A ASP 3.3 3.2 + - - +
399A ALA 3.8 3.8 - - - +
400A LEU 3.2 0.8 - - - -
401A HIS* 1.3 75.9 - - - +
403A THR* 1.3 55.4 + - - +
405A ALA* 3.2 2.1 + - - -
406A ALA* 2.6 38.1 + - - +
496A PRO* 3.5 24.9 - - + +
499A VAL* 5.0 1.3 - - - -
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Residues in contact with THR 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 3.7 16.8 - - + +
147A VAL* 3.6 22.0 - - + -
148A GLY* 3.7 14.4 - - - -
162A ILE* 3.8 19.2 - - + +
166A MET* 3.8 17.3 - - - -
399A ALA 3.3 13.7 + - - +
400A LEU* 2.8 22.3 + - - +
402A ALA* 1.3 72.7 - - - +
404A ARG* 1.3 59.0 + - - +
406A ALA* 3.5 6.9 - - - +
407A VAL* 2.7 42.0 + - - +
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Residues in contact with ARG 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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166A MET* 4.9 11.5 - - - +
171A LYS 5.8 3.7 + - - -
173A GLY 4.6 4.0 + - - -
174A VAL* 4.3 7.7 - - - +
175A ILE* 3.6 41.8 + - - +
400A LEU* 3.3 38.0 + - + +
401A HIS* 3.4 15.5 + - - +
403A THR* 1.3 84.7 + - - +
405A ALA* 1.3 59.4 + - - +
407A VAL* 3.5 7.7 + - - +
408A GLU* 3.2 31.7 + - - +
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Residues in contact with ALA 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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85A ALA* 5.3 5.8 - - - +
401A HIS 2.9 17.4 + - - +
402A ALA 3.6 3.6 - - - +
404A ARG* 1.3 74.5 - - - +
406A ALA* 1.3 66.6 + - - +
408A GLU* 3.3 11.1 - - - +
409A GLU* 3.1 28.1 + - - +
410A GLY 4.0 1.2 + - - +
496A PRO* 4.0 9.2 - - + -
498A LYS* 4.0 27.7 - - + +
499A VAL* 4.3 9.4 - - + -
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A CYS* 3.4 13.6 - - - +
147A VAL* 4.1 14.6 - - + -
402A ALA 2.6 20.9 + - - +
403A THR* 3.2 9.4 + - - +
405A ALA* 1.3 74.2 - - - +
407A VAL* 1.3 58.2 + - - +
410A GLY* 2.9 33.4 + - - -
411A VAL* 3.6 20.4 - - + -
496A PRO* 3.5 13.6 - - + +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 5.9 0.3 - - - +
138A CYS* 3.9 23.2 + - - +
144A ILE* 4.5 17.5 - - + -
166A MET* 3.5 28.7 - - + -
171A LYS* 4.1 25.1 - - + -
403A THR 2.7 26.7 + - - +
404A ARG* 3.6 6.5 - - - +
405A ALA 3.2 0.2 - - - -
406A ALA* 1.3 76.6 - - - +
408A GLU* 1.3 66.8 + - + +
410A GLY 4.2 1.7 + - - -
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ARG* 3.2 21.4 - - - +
405A ALA* 3.3 10.0 - - - +
407A VAL* 1.3 87.1 - - + +
409A GLU* 1.3 72.5 + - + +
498A LYS* 3.0 35.2 + - + +
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Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 2.9 27.9 + - + +
135A SER* 2.8 17.7 + - - -
405A ALA 3.1 12.7 + - - +
408A GLU* 1.3 80.8 - - + +
410A GLY* 1.3 60.4 + - - +
497A THR* 3.6 7.8 - - + +
498A LYS* 3.8 30.1 + - + +
501A ARG* 2.8 42.8 + - - +
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Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 3.7 2.7 - - - -
136A VAL 3.2 14.8 - - - -
137A PRO* 4.4 2.7 - - - -
138A CYS 4.2 6.5 - - - -
405A ALA 4.2 0.3 - - - +
406A ALA* 2.9 20.0 + - - +
407A VAL 4.2 0.8 + - - -
408A GLU 3.5 2.2 + - - -
409A GLU* 1.3 75.9 - - - +
411A VAL* 1.3 58.3 - - - +
496A PRO* 3.4 3.3 - - - +
497A THR* 2.5 33.5 + - - -
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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