Contacts of the helix formed by residues 385 - 410 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 4.0 11.7 - - + +
77A VAL* 6.1 0.7 - - - -
80A LYS* 4.4 15.7 - - + +
506A TYR* 3.7 26.2 - - + +
509A SER* 3.4 24.2 + - - +
510A VAL* 3.9 14.6 - - + +
383B ALA* 3.7 3.7 - - - +
384B ALA* 1.3 81.9 - - - +
386B GLU* 1.3 59.2 + - - +
387B VAL* 3.7 10.2 - - - +
388B GLU* 3.4 12.6 + - - +
389B MET* 3.1 28.0 + - - +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.7 10.0 + - - +
80A LYS* 5.6 4.2 - - - +
179B ASP* 5.4 7.4 - - - +
385B THR* 1.3 72.3 - - - +
387B VAL* 1.3 61.2 + - + +
389B MET* 3.2 9.9 + - + +
390B LYS* 3.1 52.3 + - + +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 5.8 4.9 - - + -
76A GLU* 3.1 35.6 + - - +
510A VAL* 3.9 13.9 - - + -
513A LEU* 4.2 12.8 - - + +
46B ALA* 5.2 2.9 - - + -
47B PRO 3.5 24.2 - - - +
48B THR* 5.1 1.8 - - - -
49B ILE* 4.2 21.0 + - + +
385B THR* 3.7 11.7 - - - +
386B GLU* 1.3 79.8 - - + +
388B GLU* 1.3 63.0 + - - +
389B MET 3.6 0.2 + - - -
390B LYS* 3.7 17.3 + - - +
391B GLU* 3.6 19.1 + - - +
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Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.3 29.2 + - - -
121A ASP* 5.0 0.3 - - - +
509A SER* 3.2 19.8 + - - +
513A LEU* 3.5 23.8 - - + -
383B ALA* 3.9 7.3 - - + +
384B ALA* 3.5 21.7 + - - +
385B THR* 3.4 16.1 + - - +
386B GLU 3.3 0.4 - - - -
387B VAL* 1.3 80.2 - - - +
389B MET* 1.3 60.1 + - - +
390B LYS 3.4 0.2 - - - -
391B GLU* 3.7 8.6 + - - +
392B LYS* 3.0 34.0 + - + +
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Residues in contact with MET 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 3.8 29.4 - - + +
180B GLY* 3.1 38.1 - - - +
381B VAL* 3.5 17.9 - - - +
382B GLY* 3.6 3.8 - - - -
383B ALA* 3.1 41.5 - - + +
385B THR 3.1 12.9 + - - +
386B GLU* 3.2 15.0 + - + +
388B GLU* 1.3 76.2 - - - +
390B LYS* 1.3 57.6 + - + +
392B LYS* 3.2 2.2 + - - +
393B LYS* 2.7 39.7 + - + +
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Residues in contact with LYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 5.4 0.8 - - - +
46B ALA* 4.5 6.3 + - - +
47B PRO 4.5 4.9 + - - -
48B THR* 3.1 39.3 - - + +
49B ILE 5.0 2.2 - - - +
50B THR* 5.4 0.7 + - - -
179B ASP* 6.2 0.2 - - - +
386B GLU* 3.1 43.3 + - + +
387B VAL* 4.1 17.6 - - - +
388B GLU 3.4 0.4 - - - -
389B MET* 1.3 77.8 - - + +
391B GLU* 1.3 60.9 + - - +
393B LYS* 4.3 16.9 + - - +
394B ALA* 3.4 21.7 + - - +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 5.1 6.1 - - - +
513A LEU* 4.6 19.2 - - + +
37B ASN* 4.7 9.0 + - - +
49B ILE 3.2 25.2 + - - +
50B THR* 4.2 3.4 - - - +
51B LYS* 4.1 26.4 - - + +
387B VAL 3.6 10.5 + - - +
388B GLU* 4.1 10.2 - - - +
389B MET 3.3 0.2 - - - -
390B LYS* 1.3 76.8 - - - +
392B LYS* 1.3 65.6 + - - +
394B ALA* 3.4 6.3 + - + +
395B ARG* 2.4 70.9 + - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASP* 3.6 23.7 + - - -
158B VAL* 4.7 8.3 - - - -
183B LEU 5.6 1.4 + - - -
185B ASP* 3.6 19.1 + - - -
381B VAL* 3.9 16.2 - - + -
382B GLY 3.6 20.7 + - - +
383B ALA* 4.9 1.8 - - + +
388B GLU* 3.0 25.4 + - + +
389B MET* 3.5 7.4 - - - +
391B GLU* 1.3 77.8 + - - +
393B LYS* 1.3 64.8 + - - +
395B ARG* 3.3 28.4 + - - +
396B VAL* 3.0 30.7 + - + +
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Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.8 38.8 - - + +
178B GLU 5.1 0.7 - - - +
179B ASP* 4.1 20.9 - - - +
381B VAL* 4.0 16.3 - - + +
389B MET* 2.7 19.7 + - + +
390B LYS* 4.3 18.5 + - - +
392B LYS* 1.3 73.3 - - - +
394B ALA* 1.3 61.5 + - - +
396B VAL* 3.3 3.5 + - - +
397B GLU* 2.8 49.1 + - - +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 4.7 4.3 - - - +
52B ASP* 4.0 25.8 - - + +
55B SER* 5.7 0.7 - - - +
390B LYS 3.4 17.6 + - - +
391B GLU* 3.6 7.4 - - - +
392B LYS 3.2 0.6 - - - -
393B LYS* 1.3 83.8 - - - +
395B ARG* 1.3 58.1 + - + +
397B GLU* 3.8 8.4 - - - +
398B ASP* 2.8 36.6 + - - +
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 5.3 6.1 - - - +
51B LYS* 4.8 15.3 - - + +
52B ASP* 6.1 0.7 - - + +
151B SER 4.8 3.1 - - - +
152B ALA* 2.8 47.8 + - + +
153B ASN* 3.9 23.0 + - - +
155B ASP* 4.3 15.8 + - - +
158B VAL* 5.6 1.6 - - + +
391B GLU* 2.4 52.1 + - + +
392B LYS* 3.3 30.4 + - + +
394B ALA* 1.3 74.6 - - + +
396B VAL* 1.3 60.6 + - + +
398B ASP* 3.6 9.5 - - - +
399B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 4.2 32.5 - - + -
162B ILE* 4.2 5.2 - - + +
177B VAL* 3.3 23.6 - - + -
185B ASP* 6.4 2.0 - - - -
379B ILE* 4.9 13.5 - - + -
381B VAL* 3.8 26.9 - - + -
392B LYS* 3.0 26.4 + - + +
393B LYS 3.6 4.7 - - - +
394B ALA 3.3 0.2 - - - -
395B ARG* 1.3 75.8 - - + +
397B GLU* 1.3 55.8 + - - +
399B ALA* 3.5 1.6 + - - +
400B LEU* 2.7 33.3 + - + +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.0 34.5 - - + +
393B LYS* 2.8 44.1 + - - +
394B ALA* 3.8 7.9 - - - +
396B VAL* 1.3 74.3 - - - +
398B ASP* 1.3 61.1 + - - +
400B LEU* 4.0 6.3 - - - -
401B HIS* 2.8 55.3 + - + +
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Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 3.1 36.4 - - - +
82B ASN* 5.1 0.3 - - - +
86B GLY 2.9 24.0 - - - +
87B ASP* 3.3 20.2 - - - +
151B SER* 3.1 15.9 + - - +
394B ALA 2.8 22.1 + - - +
395B ARG* 3.6 12.1 - - - +
397B GLU* 1.3 77.8 - - - +
399B ALA* 1.3 56.7 + - - +
401B HIS* 3.4 3.3 + - - +
402B ALA* 2.9 25.1 + - - +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLY 3.2 25.6 - - - +
151B SER* 3.4 11.8 + - - -
152B ALA* 3.9 10.5 - - + +
158B VAL* 4.0 2.0 - - + -
162B ILE* 3.6 17.7 - - + -
395B ARG 2.9 18.4 + - - +
396B VAL 3.8 1.6 - - - +
398B ASP* 1.3 76.5 - - - +
400B LEU* 1.3 57.9 + - - +
402B ALA* 3.6 0.3 - - - +
403B THR* 3.0 35.5 + - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 4.0 27.1 - - + -
166B MET* 6.0 1.8 - - + -
175B ILE* 3.6 41.3 - - + +
177B VAL* 5.4 5.4 - - + -
379B ILE* 5.1 0.9 - - + -
396B VAL* 2.7 21.5 + - + +
397B GLU* 3.6 9.2 - - - +
398B ASP 3.2 0.2 - - - -
399B ALA* 1.3 74.9 - - - +
401B HIS* 1.3 73.2 + - + +
403B THR* 2.9 18.6 + - - +
404B ARG* 3.2 43.0 + - + +
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Residues in contact with HIS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASN* 5.3 4.0 - - - -
85B ALA* 3.0 21.7 + - - +
86B GLY* 3.2 29.3 + - - -
397B GLU* 2.8 45.5 + - + +
398B ASP* 3.8 3.8 - - - +
400B LEU* 1.3 85.4 - - + +
402B ALA* 1.3 57.5 + - - +
404B ARG* 3.5 9.5 + - - +
405B ALA* 3.0 29.7 + - - +
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 6.5 0.2 - - - -
87B ASP* 4.2 11.9 - - + -
147B VAL* 4.6 5.8 - - - +
151B SER* 3.4 26.0 - - - +
398B ASP 2.9 18.7 + - - +
399B ALA 3.6 2.9 - - - +
401B HIS* 1.3 76.0 - - - +
403B THR* 1.3 55.8 + - - +
405B ALA* 3.3 2.9 + - - -
406B ALA* 2.7 36.9 + - - +
496B PRO* 3.7 20.2 - - + +
499B VAL* 5.1 0.7 - - - -
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Residues in contact with THR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 3.7 14.1 - - + +
147B VAL* 3.8 7.6 - - + -
148B GLY* 3.4 31.4 - - - +
162B ILE* 3.5 25.2 - - + +
166B MET* 4.0 17.8 - - - -
399B ALA 3.0 18.4 + - - +
400B LEU* 2.9 18.0 + - - +
402B ALA* 1.3 70.9 - - - +
404B ARG* 1.3 65.6 + - - +
406B ALA* 3.7 0.9 - - - +
407B VAL* 2.9 31.6 + - - +
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Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 5.0 9.2 - - - -
171B LYS 5.6 3.6 + - - -
173B GLY 4.0 14.1 + - - -
174B VAL* 4.1 6.1 - - - +
175B ILE* 3.5 38.8 + - - +
400B LEU* 3.2 31.7 + - + +
401B HIS* 3.6 13.7 - - - +
403B THR* 1.3 84.3 + - - +
405B ALA* 1.3 62.5 + - - +
407B VAL* 3.5 7.0 + - - +
408B GLU* 3.4 26.0 + - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 5.3 5.6 - - + +
401B HIS 3.0 19.7 + - - +
402B ALA 3.7 3.8 - - - +
404B ARG* 1.3 73.6 - - - +
406B ALA* 1.3 65.9 + - - +
408B GLU* 3.2 26.3 - - - +
409B GLU* 3.2 12.1 + - - +
410B GLY 4.6 0.2 - - - +
496B PRO* 4.1 6.7 - - + -
498B LYS* 3.5 33.5 - - + +
499B VAL* 4.5 7.9 - - + -
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 3.8 9.5 - - - +
147B VAL* 3.7 22.9 - - + -
402B ALA 2.7 23.0 + - - +
403B THR 3.7 4.0 - - - +
405B ALA* 1.3 72.0 - - - +
407B VAL* 1.3 58.9 + - - +
410B GLY* 2.9 31.9 + - - -
411B VAL* 3.8 13.7 - - + -
496B PRO* 3.4 23.3 - - + +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 4.3 23.9 + - - +
144B ILE* 4.3 21.3 - - + -
166B MET* 3.5 29.8 - - + -
171B LYS* 5.2 13.2 - - + -
403B THR 2.9 20.8 + - - +
404B ARG* 3.7 6.5 - - - +
405B ALA 3.2 0.2 - - - -
406B ALA* 1.3 78.9 - - - +
408B GLU* 1.3 65.2 + - + +
410B GLY* 4.1 2.9 + - - -
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Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ARG* 3.4 15.3 + - - +
405B ALA* 3.2 15.4 - - - +
407B VAL* 1.3 85.5 - - + +
409B GLU* 1.3 75.9 + - + +
410B GLY 3.8 0.2 + - - -
498B LYS* 3.1 35.4 + - - +
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LYS* 4.0 13.8 + - + +
135B SER* 2.9 17.3 + - - -
405B ALA 3.2 10.9 + - - +
408B GLU* 1.3 85.7 - - + +
410B GLY* 1.3 61.0 + - - +
497B THR* 3.4 14.6 - - + +
498B LYS* 3.7 28.1 + - + +
501B ARG* 2.7 50.4 + - - +
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Residues in contact with GLY 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 3.7 3.1 - - - -
136B VAL 3.6 12.6 - - - -
137B PRO* 4.5 2.2 - - - -
138B CYS 4.3 9.0 - - - -
406B ALA* 2.9 17.1 + - - +
407B VAL 4.1 1.9 + - - -
408B GLU 3.5 2.8 + - - -
409B GLU* 1.3 76.1 - - - +
411B VAL* 1.3 59.7 + - - +
496B PRO* 3.6 0.9 - - - +
497B THR* 2.7 34.5 + - - -
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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