Contacts of the helix formed by residues 380 - 404 (chain K) in PDB entry 6NR8
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 SER 380 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379K ALA* 1.3 79.2 - - - +
381K LYS* 1.3 67.7 + - - +
382K GLU* 3.3 5.9 + - - +
383K ILE* 3.0 24.7 + - - +
384K LEU* 2.6 43.1 + - - +
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Residues in contact with LYS 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K LYS* 2.9 29.9 + - - +
205K PRO* 3.4 19.4 - - - +
206K GLY* 3.2 28.2 - - - +
380K SER* 1.3 82.2 + - - +
382K GLU* 1.3 59.2 + - - +
384K LEU* 3.7 21.2 - - + +
385K SER* 3.8 4.2 + - - -
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Residues in contact with GLU 382 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380K SER* 3.3 4.4 + - - +
381K LYS* 1.3 79.3 - - - +
383K ILE* 1.3 74.7 + - + +
385K SER* 3.2 22.4 + - - -
386K GLU* 3.4 16.1 + - - +
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Residues in contact with ILE 383 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K TRP* 3.5 25.1 - - + -
378K GLY* 4.0 3.0 - - - -
379K ALA* 4.4 8.5 - - + +
380K SER* 3.0 31.7 + - - +
382K GLU* 1.3 91.4 - - + +
384K LEU* 1.3 64.3 - - - +
385K SER 3.2 1.1 - - - -
386K GLU* 3.7 17.7 - - + -
387K VAL* 3.3 24.1 + - - +
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Residues in contact with LEU 384 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K LYS* 3.7 29.8 - - + -
204K ILE 3.3 30.5 - - - +
205K PRO* 4.1 1.3 - - + -
206K GLY 3.9 12.8 - - - +
376K LEU* 3.3 20.0 - - + +
377K ARG* 3.7 9.6 - - - -
378K GLY* 3.3 27.6 - - - +
380K SER 2.6 27.8 + - - +
381K LYS* 3.7 28.0 - - - +
383K ILE* 1.3 74.6 - - - +
385K SER* 1.3 56.1 + - - +
387K VAL* 3.6 1.7 + - - +
388K GLU* 3.2 20.5 + - - +
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Residues in contact with SER 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K LYS* 3.9 11.4 + - - +
381K LYS 3.8 9.4 + - - -
382K GLU* 3.2 14.8 + - - -
384K LEU* 1.3 76.2 - - - +
386K GLU* 1.3 60.3 + - - +
388K GLU* 3.1 18.3 + - - +
389K ARG* 2.8 28.4 + - - +
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Residues in contact with GLU 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163K LYS* 2.9 29.9 + - - -
165K ILE* 3.3 35.2 - - + +
168K TRP* 5.8 3.4 - - + -
382K GLU* 3.4 13.2 + - - +
383K ILE* 3.4 27.5 + - + +
384K LEU 3.3 0.6 - - - -
385K SER* 1.3 76.1 - - - +
387K VAL* 1.3 64.2 + - + +
389K ARG* 3.4 5.3 + - - +
390K ASN* 2.8 36.9 + - - +
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Residues in contact with VAL 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K TRP* 3.6 31.9 - - + +
171K LEU* 5.6 9.6 - - + -
172K ALA 5.9 0.2 - - - +
175K ILE* 6.2 1.1 - - + -
209K ILE* 4.7 1.1 - - + -
212K SER* 5.4 2.0 - - - +
376K LEU* 3.9 17.0 - - + -
377K ARG 3.5 27.6 - - - +
378K GLY* 3.8 2.7 - - - -
383K ILE 3.3 14.9 + - - +
384K LEU 3.8 6.7 - - - +
385K SER 3.3 0.2 - - - -
386K GLU* 1.3 76.3 - - - +
388K GLU* 1.3 57.7 + - - +
390K ASN* 3.1 9.7 + - + +
391K LEU* 3.0 49.9 + - + +
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Residues in contact with GLU 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K VAL* 3.8 33.6 - - + +
202K GLU* 4.5 1.7 - - - -
203K LYS* 4.1 25.9 + - - +
376K LEU* 4.0 22.4 - - + +
384K LEU 3.2 10.9 + - - +
385K SER* 3.1 24.3 + - - +
387K VAL* 1.3 77.5 - - - +
389K ARG* 1.3 58.9 + - - +
391K LEU* 3.6 3.7 + - - +
392K GLN* 3.4 18.7 + - - +
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Residues in contact with ARG 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ASP* 5.9 5.5 + - - +
93K ASP* 4.9 7.3 + - - -
163K LYS* 3.4 28.0 - - + +
385K SER 2.8 15.4 + - - +
386K GLU* 3.7 10.3 - - - +
388K GLU* 1.3 77.2 - - - +
390K ASN* 1.3 61.5 + - - +
392K GLN* 3.2 45.5 + - - +
393K ASP* 3.5 17.1 + - - +
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Residues in contact with ASN 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K ILE* 3.4 36.6 - - + +
163K LYS* 3.5 19.4 + - - -
165K ILE* 4.7 8.1 - - - +
168K TRP* 4.2 19.4 + - - +
169K SER* 5.2 0.2 - - - -
172K ALA* 3.8 18.4 - - + -
386K GLU* 2.8 33.3 + - - +
387K VAL* 3.1 12.0 + - - +
389K ARG* 1.3 77.0 - - - +
391K LEU* 1.3 58.6 + - - +
393K ASP* 3.6 3.5 + - - +
394K ALA* 3.1 23.9 + - - +
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Residues in contact with LEU 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K LEU 4.9 2.2 - - - +
172K ALA* 3.7 30.5 - - + +
175K ILE* 4.6 8.1 - - + -
176K ALA* 3.7 32.8 - - + +
201K VAL* 4.0 19.7 - - + -
374K ILE* 3.8 25.1 - - + -
376K LEU* 4.8 8.5 - - + -
387K VAL* 3.0 41.0 + - + +
388K GLU* 4.1 4.0 - - - +
389K ARG 3.3 0.4 - - - -
390K ASN* 1.3 74.2 - - - +
392K GLN* 1.3 60.1 + - - +
393K ASP 3.4 0.2 - - - -
394K ALA* 3.5 2.1 - - + +
395K MET* 3.1 34.1 + - + +
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Residues in contact with GLN 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K VAL 3.7 17.8 - - - +
92K GLY* 4.1 10.5 - - - -
93K ASP* 4.2 8.3 + - - +
196K LYS* 5.2 12.5 + - - +
201K VAL* 5.1 10.3 - - + +
388K GLU 3.4 11.2 + - - +
389K ARG* 3.2 39.8 + - - +
390K ASN 3.2 0.4 - - - -
391K LEU* 1.3 78.4 - - - +
393K ASP* 1.3 81.7 + - - +
394K ALA 3.4 0.2 + - - -
395K MET* 3.5 12.3 + - - +
396K GLN* 3.6 9.9 + - - +
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Residues in contact with ASP 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K ASP* 3.0 30.7 - - - +
159K SER* 3.8 29.2 - - - +
160K ILE* 4.3 12.3 - - + +
162K THR* 4.8 4.2 + - - -
163K LYS* 5.0 10.2 - - - +
389K ARG* 3.5 20.0 + - - +
390K ASN* 3.6 7.2 + - - +
391K LEU 3.4 0.2 - - - -
392K GLN* 1.3 91.1 + - - +
394K ALA* 1.3 63.3 + - - +
395K MET 3.4 0.2 - - - -
396K GLN* 3.7 9.2 + - - +
397K VAL* 3.5 20.1 + - - +
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Residues in contact with ALA 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K ILE* 3.7 27.3 - - + +
160K ILE* 4.6 3.1 - - + +
172K ALA* 4.0 9.9 - - + +
176K ALA* 3.7 14.1 - - + -
390K ASN 3.1 19.1 + - - +
391K LEU* 3.5 11.4 - - - +
392K GLN 3.2 0.4 - - - -
393K ASP* 1.3 78.5 - - - +
395K MET* 1.3 62.0 + - - +
397K VAL* 3.2 6.4 + - - +
398K CYS* 3.1 26.3 + - - -
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Residues in contact with MET 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K ALA* 4.7 9.0 - - + -
179K ALA* 5.9 0.9 - - + -
180K VAL* 4.4 15.0 - - + -
194K ASP* 4.4 8.4 - - - +
196K LYS* 5.6 10.1 - - - +
199K ALA* 4.3 30.5 - - + +
200K ARG 3.8 10.1 - - - +
201K VAL* 3.7 28.9 - - + -
372K CYS* 6.1 0.2 - - - -
374K ILE* 3.8 28.0 - - + -
391K LEU* 3.1 19.3 + - + +
392K GLN* 3.5 5.8 + - - +
393K ASP 3.4 0.4 - - - -
394K ALA* 1.3 74.1 - - - +
396K GLN* 1.3 63.2 + - - +
398K CYS* 3.8 7.3 - - - +
399K ARG* 3.1 28.8 + - - +
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Residues in contact with GLN 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K VAL* 3.5 45.2 - - + +
93K ASP* 4.5 20.2 + - + +
159K SER* 4.2 9.9 + - - -
392K GLN 3.6 9.1 + - - +
393K ASP 3.9 8.9 + - - +
394K ALA 3.2 0.8 - - - -
395K MET* 1.3 77.9 - - - +
397K VAL* 1.3 64.8 + - - +
399K ARG* 3.2 20.5 - - - +
400K ASN* 3.3 12.1 + - - +
498K PRO* 3.8 29.0 - - - +
500K ALA* 4.8 2.1 - - - +
501K VAL* 3.5 24.1 - - - +
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Residues in contact with VAL 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K MET 4.8 0.4 - - - +
155K ILE* 3.8 29.8 - - + +
156K ILE* 3.8 34.1 - - + +
159K SER* 3.3 30.3 - - - +
177K LEU* 5.6 1.1 - - + -
393K ASP 3.5 13.5 - - - +
394K ALA 3.2 6.4 + - - +
396K GLN* 1.3 80.8 - - - +
398K CYS* 1.3 54.4 + - - +
400K ASN* 2.9 7.8 + - + +
401K VAL* 2.7 36.6 + - + +
498K PRO* 5.8 2.2 - - + -
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Residues in contact with CYS 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K ILE* 3.7 6.7 - - - -
176K ALA* 3.2 33.2 - - - +
177K LEU* 3.7 24.0 - - - -
180K VAL* 3.7 31.0 - - + +
181K LYS* 4.1 5.6 + - - +
394K ALA 3.1 20.0 + - - +
395K MET* 3.5 2.2 + - - +
396K GLN 3.4 0.2 - - - -
397K VAL* 1.3 76.8 - - - +
399K ARG* 1.3 61.2 + - - +
401K VAL* 3.5 10.9 - - + +
402K LEU* 3.2 22.0 + - - +
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Residues in contact with ARG 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K GLU* 2.4 43.3 + - - +
91K VAL* 4.0 18.0 - - + +
180K VAL* 4.0 7.2 - - - +
193K ILE* 3.3 50.9 - - + +
194K ASP* 3.2 46.1 + - - +
196K LYS* 4.3 15.2 - - - +
395K MET 3.1 18.3 + - - +
396K GLN* 3.2 19.1 - - - +
398K CYS* 1.3 77.3 - - - +
400K ASN* 1.3 52.3 + - + +
402K LEU* 3.3 5.4 + - - +
403K LEU 2.6 29.1 + - - -
500K ALA* 6.4 0.7 - - + -
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Residues in contact with ASN 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193K ILE* 4.8 1.1 - - - -
396K GLN* 3.4 17.5 + - - +
397K VAL* 2.9 7.9 + - + +
399K ARG* 1.3 82.2 - - + +
401K VAL* 1.3 55.8 + - - +
403K LEU* 3.9 4.5 - - - +
404K ASP* 2.4 51.8 + - - +
407K LEU* 5.6 3.2 - - - +
498K PRO* 3.3 18.8 - - - +
499K LEU* 3.0 28.8 + - - +
500K ALA* 3.2 31.8 + - + +
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Residues in contact with VAL 401 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K VAL* 4.0 20.6 - - + -
146K ILE* 3.3 30.7 - - + +
152K MET* 3.8 30.5 - - + -
155K ILE* 4.3 12.8 - - + -
177K LEU* 5.3 1.6 - - + -
181K LYS* 3.4 21.8 - - - +
397K VAL* 2.7 24.8 + - + +
398K CYS* 3.5 10.1 - - - +
400K ASN* 1.3 71.6 - - - +
402K LEU* 1.3 66.0 + - - +
404K ASP 3.7 8.7 - - - +
405K PRO* 3.8 9.6 - - + +
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Residues in contact with LEU 402 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K ILE* 5.4 3.3 - - + +
180K VAL* 3.8 26.0 - - + +
181K LYS* 3.9 31.9 - - + +
183K VAL 4.1 10.3 - - - +
191K LYS* 3.7 39.1 - - + +
192K GLU* 3.2 42.5 - - - +
193K ILE* 4.4 4.3 - - - +
194K ASP 4.6 1.8 - - - +
398K CYS 3.2 19.5 + - - +
399K ARG 3.4 3.8 - - - +
400K ASN 3.2 0.4 - - - -
401K VAL* 1.3 79.6 - - - +
403K LEU* 1.3 62.4 + - - +
405K PRO* 4.8 3.3 - - - +
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Residues in contact with LEU 403 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192K GLU* 3.2 55.1 - - + +
193K ILE* 3.6 28.3 - - + +
399K ARG 2.6 20.2 + - - +
400K ASN* 2.9 5.6 + - - +
402K LEU* 1.3 74.2 - - - +
404K ASP* 1.3 81.8 + - - +
405K PRO* 3.8 5.9 - - - +
406K GLN* 5.2 0.3 + - - -
500K ALA* 3.7 29.8 - - + -
503K LEU* 5.3 7.4 - - + -
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Residues in contact with ASP 404 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K LYS* 4.8 2.7 + - - -
400K ASN* 2.4 32.2 + - - +
401K VAL* 3.7 8.7 - - - +
403K LEU* 1.3 103.4 - - - +
405K PRO* 1.3 68.0 - - - +
406K GLN* 3.1 33.5 + - - +
407K LEU* 4.9 3.8 - - - +
499K LEU* 3.7 23.9 - - + +
500K ALA 4.3 1.0 + - - -
503K LEU* 4.3 13.3 - - - +
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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