Contacts of the helix formed by residues 379 - 407 (chain A) in PDB entry 3BRW
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 ALA 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A HIS* 4.2 11.4 - - + -
341A ASP* 3.4 29.8 - - - +
342A VAL* 3.9 21.3 - - + -
343A PRO* 5.4 0.2 - - - -
375A ALA 3.7 1.8 + - - -
376A CYS* 2.8 17.1 + - - +
378A LYS* 1.3 82.0 - - - +
380A GLU* 1.3 67.9 + - - +
381A LYS 3.4 1.4 + - - -
382A PHE* 3.5 2.4 + - + -
383A ALA* 3.1 20.0 + - - +
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP* 2.8 30.1 + - - +
379A ALA* 1.3 73.1 - - - +
381A LYS* 1.3 82.7 + - + +
383A ALA* 4.1 3.2 - - - +
384A LYS* 3.4 23.6 + - - +
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASN* 3.6 35.2 + - - +
315A HIS* 3.7 33.1 + - + +
339A ARG* 6.1 0.6 - - - +
341A ASP* 5.4 0.9 - - - +
379A ALA 3.4 0.8 + - - -
380A GLU* 1.3 96.6 - - + +
382A PHE* 1.3 69.5 + - + +
384A LYS* 3.6 14.2 - - - +
385A LEU* 3.6 7.8 + - - +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 3.6 23.3 - - + -
312A ASN 5.5 0.7 - - - -
313A PHE* 3.5 42.4 - + - -
315A HIS* 3.9 26.0 - + - -
376A CYS* 3.0 45.8 - - + +
377A TYR* 3.9 15.5 - + + +
379A ALA* 3.5 1.7 + - + -
380A GLU 3.4 0.4 - - - -
381A LYS* 1.3 79.9 - - + +
383A ALA* 1.3 60.4 + - - +
384A LYS 3.2 0.4 - - - -
385A LEU* 3.3 13.3 + - + +
386A GLU* 2.8 30.2 + - + +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR 3.8 9.3 + - - +
378A LYS* 3.9 13.0 - - - +
379A ALA 3.1 19.4 + - - +
380A GLU* 4.1 3.8 - - - +
382A PHE* 1.3 74.4 - - - +
384A LYS* 1.3 63.7 - - - +
386A GLU* 3.7 7.2 - - - +
387A GLU* 3.1 31.5 + - + +
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Residues in contact with LYS 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLU* 3.4 18.0 + - - +
381A LYS* 3.6 11.7 - - - +
382A PHE 3.2 0.4 - - - -
383A ALA* 1.3 78.3 - - - +
385A LEU* 1.3 63.6 + - - +
387A GLU* 3.4 36.6 + - - +
388A ARG* 4.0 15.7 + - - +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS 3.6 7.7 + - - +
382A PHE* 3.3 16.4 + - + +
384A LYS* 1.3 76.8 - - - +
386A GLU* 1.3 66.4 + - - +
388A ARG* 3.2 39.6 + - - +
389A THR* 3.1 21.2 + - - +
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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
----------------------------------------------------------
187A HIS* 3.0 31.2 + - - -
188A VAL* 3.9 13.1 - - + +
377A TYR* 5.4 14.8 - - + +
382A PHE* 2.8 19.4 + - + +
383A ALA* 3.7 9.9 - - - +
384A LYS 3.4 0.2 - - - -
385A LEU* 1.3 75.9 - - - +
387A GLU* 1.3 61.5 + - - +
389A THR* 3.8 12.9 - - - +
390A ARG* 2.9 39.0 + - - +
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS 4.7 2.8 - - - +
135A CYS* 5.9 7.1 - - - +
383A ALA* 3.1 20.6 + - - +
384A LYS* 3.4 37.8 + - - +
385A LEU 3.2 0.2 - - - -
386A GLU* 1.3 77.1 - - - +
388A ARG* 1.3 59.1 + - + +
390A ARG* 3.8 5.1 + - - +
391A ALA* 3.5 20.4 + - - +
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LYS* 4.0 14.1 + - - +
385A LEU* 3.2 37.3 + - - +
387A GLU* 1.3 76.9 - - - +
389A THR* 1.3 66.7 + - - +
391A ALA* 3.6 5.0 + - - +
392A ALA* 3.2 24.7 + - + +
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A HIS* 5.0 1.6 - - + +
385A LEU* 3.1 24.5 + - - +
386A GLU* 3.2 19.0 + - - +
388A ARG* 1.3 77.3 - - - +
390A ARG* 1.3 57.2 + - - +
392A ALA* 3.1 6.3 + - - +
393A LEU* 2.9 56.2 + - + +
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Residues in contact with ARG 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 4.1 5.3 - - - +
133A THR 2.6 23.6 + - - +
134A LYS 5.3 1.3 - - - +
135A CYS* 3.7 22.6 + - - +
136A ARG* 2.5 27.7 + - - +
137A THR* 3.6 25.5 - - - +
184A PHE* 3.8 32.0 - - + -
185A ASP* 5.4 1.4 + - - -
187A HIS* 4.0 21.7 - - + -
188A VAL* 5.7 2.0 - - + -
386A GLU* 2.9 31.7 + - - +
387A GLU* 4.0 6.3 - - - +
389A THR* 1.3 77.5 - - - +
391A ALA* 1.3 57.1 + - - +
393A LEU* 3.3 5.9 + - - +
394A LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 4.9 4.3 - - - -
134A LYS* 3.4 44.7 + - + +
387A GLU 3.5 11.9 + - - +
388A ARG* 4.1 4.9 - - - +
389A THR 3.4 0.6 - - - -
390A ARG* 1.3 78.8 - - - +
392A ALA* 1.3 57.4 + - - +
394A LEU* 3.3 7.7 + - - +
395A GLU* 3.0 27.9 + - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 3.2 17.9 + - + +
389A THR* 3.1 5.9 + - - +
391A ALA* 1.3 79.0 - - - +
393A LEU* 1.3 58.1 + - + +
395A GLU* 3.4 9.7 + - - +
396A THR* 3.0 29.5 + - - -
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 4.1 15.7 - - + +
187A HIS* 3.9 35.7 - - + +
389A THR* 2.9 39.6 + - + +
390A ARG 3.8 3.4 - - - +
392A ALA* 1.3 75.0 - - + +
394A LEU* 1.3 60.2 + - - +
396A THR* 3.4 16.8 - - + +
397A LEU* 3.1 25.5 + - - +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 3.4 40.6 - - + +
113A VAL* 3.8 28.7 - - + -
132A ARG* 4.7 5.8 - - + +
133A THR* 3.6 7.4 - - - +
134A LYS* 3.5 24.9 - - + +
184A PHE* 3.9 28.7 - - + -
390A ARG 2.9 17.6 + - - +
391A ALA* 3.5 5.6 - - - +
392A ALA 3.2 0.2 - - - -
393A LEU* 1.3 74.5 - - - +
395A GLU* 1.3 55.7 + - - +
397A LEU* 3.0 7.0 + - + +
398A TYR* 2.7 33.8 + - - +
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 3.5 37.3 - - + +
391A ALA 3.0 13.7 + - - +
392A ALA* 3.4 11.3 + - - +
394A LEU* 1.3 74.3 - - - +
396A THR* 1.3 64.6 + - - +
398A TYR* 3.8 3.1 - - + +
399A GLU* 2.9 52.5 + - + +
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Residues in contact with THR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 6.6 0.2 - - + -
392A ALA 3.0 15.3 + - - -
393A LEU* 3.4 22.7 - - + +
395A GLU* 1.3 77.0 - - - +
397A LEU* 1.3 64.9 + - + +
399A GLU* 3.6 6.4 - - - +
400A GLU* 3.4 31.6 + - + +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 4.2 26.2 - - + -
180A LEU* 3.7 45.3 - - + +
181A ILE* 4.1 8.1 - - + +
184A PHE* 3.9 35.7 - - + -
393A LEU 3.1 9.1 + - - +
394A LEU* 3.0 9.7 + - + +
396A THR* 1.3 79.4 - - + +
398A TYR* 1.3 68.1 + - - +
400A GLU* 2.8 19.1 + - + +
401A LEU* 3.1 32.4 + - + +
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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
----------------------------------------------------------
103A TYR* 3.6 35.2 - + + -
104A SER* 3.4 23.5 - - - -
105A LEU* 3.6 32.5 + - + +
111A HIS* 3.4 42.4 - + + -
112A LEU 4.2 10.8 - - - -
113A VAL* 4.5 11.6 - - + +
170A TYR* 6.0 0.5 - - - -
394A LEU 2.7 20.1 + - - +
395A GLU 3.8 3.8 - - - +
397A LEU* 1.3 72.1 - - - +
399A GLU* 1.3 72.8 + - + +
401A LEU* 3.6 4.7 + - - +
402A HIS* 3.1 32.2 + + + +
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 5.8 0.6 - - - -
395A GLU* 2.9 51.8 + - + +
396A THR* 3.6 7.2 - - - +
398A TYR* 1.3 83.1 - - + +
400A GLU* 1.3 59.9 + - + +
402A HIS* 3.0 10.0 + - - +
403A ILE* 3.0 46.7 + - + +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR* 4.7 3.7 + - + -
180A LEU* 3.9 34.8 - - + +
396A THR* 3.4 23.5 - - + +
397A LEU* 2.8 14.5 + - - +
399A GLU* 1.3 78.0 - - + +
401A LEU* 1.3 61.2 + - + +
403A ILE* 5.1 1.8 - - - -
404A HIS* 3.2 55.2 + - + +
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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
----------------------------------------------------------
103A TYR* 4.1 11.6 - - + -
113A VAL* 3.9 28.0 - - + -
172A VAL* 3.8 24.0 - - + -
174A TYR* 5.0 6.3 - - + -
177A ALA* 3.5 38.6 - - + +
180A LEU* 4.9 3.8 - - + -
181A ILE* 4.4 6.7 - - + -
397A LEU* 3.1 42.9 + - + +
398A TYR* 4.1 3.8 - - - +
400A GLU* 1.3 77.0 - - + +
402A HIS* 1.3 58.1 - - - +
404A HIS* 5.0 0.7 - - - -
405A SER* 2.6 34.9 + - - +
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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
----------------------------------------------------------
103A TYR* 3.2 43.5 + + + -
170A TYR* 6.2 0.7 - + - -
398A TYR* 3.1 23.4 + + + +
399A GLU* 3.0 13.8 + - - +
401A LEU* 1.3 76.4 - - - +
403A ILE* 1.3 88.0 + - + +
406A GLN* 3.1 46.2 + - + +
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU* 3.0 28.6 + - + +
400A GLU* 4.7 2.2 - - - +
402A HIS* 1.3 96.3 - - + +
404A HIS* 1.3 63.1 + - + +
406A GLN* 3.4 6.9 + - + +
407A SER* 3.0 32.2 + - - +
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Residues in contact with HIS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR* 3.3 56.2 + + + -
400A GLU* 3.2 46.7 + - - +
403A ILE* 1.3 80.8 - - + +
405A SER* 1.3 62.3 + - - +
407A SER* 3.7 14.4 + - - -
408A MET* 3.4 22.7 + - - +
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Residues in contact with SER 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.4 7.9 - - - -
171A PRO 4.0 12.3 - - - -
172A VAL* 3.4 9.5 - - - +
173A LEU* 3.0 37.5 + - - +
174A TYR* 3.8 4.7 + - - +
401A LEU* 2.6 26.1 + - - -
402A HIS 4.0 2.0 - - - -
404A HIS* 1.3 77.9 - - - +
406A GLN* 1.3 61.5 + - - +
408A MET* 3.3 6.5 - - - +
409A MET* 3.2 22.9 - - - +
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.5 7.5 + - - +
402A HIS* 3.1 44.4 + - + +
403A ILE* 3.5 8.1 - - + +
404A HIS 3.2 0.2 - - - -
405A SER* 1.3 75.7 + - - +
407A SER* 1.3 51.1 + - - +
408A MET 2.8 8.4 + - - -
409A MET* 3.0 7.8 + - - +
410A GLY 2.7 40.8 + - - +
411A LEU* 3.0 36.4 - - - +
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 3.0 20.1 + - - +
404A HIS* 3.7 15.2 + - - -
405A SER 3.6 0.2 - - - -
406A GLN* 1.3 72.2 - - - +
408A MET* 1.3 59.3 + - - +
409A MET 3.3 1.6 - - - -
410A GLY* 4.0 8.5 - - - +
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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