Contacts of the helix formed by residues 372 - 397 (chain A) in PDB entry 5XRA
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 ASN 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LYS 4.1 2.4 + - - -
371A MET* 1.3 75.1 - - - +
373A LYS* 1.3 64.5 + - - +
374A LEU* 3.7 21.7 - - - +
375A ILE* 3.1 31.1 + - - +
376A LYS* 3.3 23.6 + - - +
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Residues in contact with LYS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 6.2 0.2 - - - -
372A ASN* 1.3 75.9 - - - +
374A LEU* 1.3 62.5 + - - +
376A LYS* 3.5 12.1 + - + +
377A THR* 2.9 38.6 + - - +
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ASN* 3.2 18.8 - - - +
373A LYS* 1.3 80.3 - - - +
375A ILE* 1.3 64.6 + - + +
377A THR* 3.2 11.1 + - + -
378A VAL* 2.9 41.2 + - + +
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.7 23.1 - - + -
365A TYR* 4.4 17.7 - - + -
370A LYS 4.9 3.4 - - - +
371A MET* 3.6 40.6 - - + -
372A ASN* 3.1 25.5 + - - +
374A LEU* 1.3 80.0 - - + +
376A LYS* 1.3 67.3 + - - +
378A VAL* 3.1 9.4 + - + +
379A PHE* 2.8 22.0 + - - +
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS* 2.8 42.2 + - - +
108A PHE* 4.4 8.6 - - - +
110A VAL* 5.1 1.9 - - - +
266A ASP* 3.3 40.4 + - - +
267A ILE* 5.3 7.4 - - + -
371A MET* 4.5 17.4 - - + -
372A ASN 3.3 16.0 + - - +
373A LYS* 3.7 13.2 - - - +
375A ILE* 1.3 76.2 - - - +
377A THR* 1.3 62.8 + - - +
379A PHE* 3.2 10.1 + - - +
380A ALA* 3.2 20.3 + - - +
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Residues in contact with THR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 4.7 15.2 - - + +
115A GLN* 4.1 28.9 + - - +
373A LYS* 2.9 29.9 + - - +
374A LEU* 3.3 14.8 - - + -
376A LYS* 1.3 72.9 - - - +
378A VAL* 1.3 67.4 + - + +
380A ALA* 3.2 11.3 + - - +
381A PHE* 3.3 30.1 - - + -
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.9 11.9 - - + -
374A LEU* 2.9 33.7 + - + +
375A ILE* 3.1 11.2 + - + +
377A THR* 1.3 76.1 - - + +
379A PHE* 1.3 52.3 + - - +
381A PHE* 3.1 9.3 + - + +
382A CYS* 2.6 52.0 + - - +
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Residues in contact with PHE 379 (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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267A ILE* 3.4 27.8 - - + -
268A PHE* 3.5 11.7 - + - -
359A LEU* 3.7 18.8 - - + -
362A ILE* 3.7 32.3 - - + +
363A MET* 3.4 45.1 - - + -
375A ILE 2.8 12.9 + - - +
376A LYS* 3.2 12.3 + - - +
378A VAL* 1.3 76.8 - - - +
380A ALA* 1.3 54.7 + - - +
382A CYS* 4.1 4.7 - - + -
383A SER* 2.5 58.0 + - - -
602A 8D3 3.1 18.2 - + + -
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.6 29.4 - - + -
119A ILE* 4.4 7.9 - - + -
174A PHE* 3.5 27.5 - - + -
178A HIS* 4.1 14.8 - - + +
376A LYS 3.2 6.7 + - - +
377A THR 3.2 8.7 + - - +
379A PHE* 1.3 81.4 - - - +
381A PHE* 1.3 62.5 + - + +
383A SER* 3.5 8.1 + - - -
384A MET* 3.6 7.8 + - - +
602A 8D3 5.2 0.2 - - - -
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Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 5.1 0.9 - - + -
115A GLN* 4.2 28.9 - - + -
118A ALA* 4.3 18.8 - - + -
119A ILE* 4.2 25.1 - - + -
122A LEU* 5.4 8.5 - - + -
377A THR* 3.3 37.8 + - + +
378A VAL* 3.1 9.4 + - + +
380A ALA* 1.3 77.3 - - + +
382A CYS* 1.3 66.6 + - - +
384A MET* 3.2 31.5 + - + +
385A LEU* 3.8 8.6 - - - +
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Residues in contact with CYS 382 (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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358A PRO* 4.4 19.1 - - + -
359A LEU* 3.7 22.0 - - + +
362A ILE* 4.2 11.4 - - + -
378A VAL* 2.6 39.8 + - - +
379A PHE* 3.6 7.9 - - - +
381A PHE* 1.3 69.1 - - - +
383A SER* 1.3 61.6 + - - +
384A MET 3.1 1.6 - - - -
385A LEU* 2.8 39.8 + - + +
386A CYS 4.1 0.7 + - - -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 3.9 12.9 - - - -
174A PHE* 4.0 10.3 - - - -
359A LEU* 3.7 9.6 - - - +
379A PHE* 2.5 34.6 + - - -
380A ALA 3.5 8.1 - - - -
381A PHE 3.3 0.2 - - - -
382A CYS* 1.3 72.5 - - - +
384A MET* 1.3 61.3 + - - +
385A LEU 3.2 0.7 + - - -
386A CYS* 3.3 19.9 + - - +
387A LEU 4.3 0.9 + - - -
602A 8D3 2.8 45.3 + - - +
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Residues in contact with MET 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 4.6 0.2 - - - +
119A ILE* 3.7 40.4 - - + +
122A LEU* 3.9 35.4 - - + +
123A SER* 2.9 31.4 - - - +
126A LEU* 4.7 6.9 - - + +
170A PHE* 4.8 3.8 - - - -
174A PHE* 4.2 9.2 - - + -
380A ALA 3.6 12.4 + - - +
381A PHE* 3.2 24.3 + - + +
382A CYS 3.1 0.8 - - - -
383A SER* 1.3 77.2 - - - +
385A LEU* 1.3 63.7 + - + +
386A CYS 3.1 1.1 + - - -
387A LEU* 3.2 29.3 + - + +
388A LEU* 3.6 5.0 + - - +
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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
----------------------------------------------------------
354A ILE* 4.2 31.0 - - + +
355A CYS* 3.7 29.4 - - - +
358A PRO* 6.1 3.1 - - + -
381A PHE 3.8 15.0 - - - +
382A CYS* 2.8 26.8 + - + +
384A MET* 1.3 78.2 - - + +
386A CYS* 1.3 61.0 + - - +
388A LEU* 3.3 27.7 + - + +
389A ASN 3.3 15.1 + - - -
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Residues in contact with CYS 386 (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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170A PHE* 6.0 0.7 - - + -
200A PHE* 4.0 23.5 - - + -
355A CYS* 5.2 6.5 - - - -
356A TRP* 3.8 26.7 - - + -
359A LEU* 3.7 32.5 - - - -
382A CYS 5.2 0.4 - - - -
383A SER 3.3 13.7 + - - +
384A MET 3.1 1.2 - - - -
385A LEU* 1.3 76.6 - - - +
387A LEU* 1.3 65.2 + - + +
389A ASN* 3.1 19.1 + - - +
390A SER* 3.1 13.7 + - - -
602A 8D3 4.3 12.6 - - + -
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Residues in contact with LEU 387 (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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122A LEU 4.7 0.2 - - - +
123A SER* 3.9 25.1 - - - +
126A LEU* 4.3 19.1 - - + -
127A GLY* 4.3 3.1 - - - +
130A THR* 4.1 1.9 + - - +
167A SER* 4.0 24.7 - - - -
170A PHE* 4.0 27.1 - - + -
171A VAL* 3.7 33.0 - - + -
200A PHE* 4.7 7.2 - - + -
383A SER 4.3 0.2 + - - -
384A MET* 3.2 16.8 + - + +
386A CYS* 1.3 77.9 - - - +
388A LEU* 1.3 64.2 + - - +
390A SER* 2.9 17.8 + - - -
391A THR* 2.9 17.7 + - - +
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Residues in contact with LEU 388 (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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126A LEU* 4.2 27.1 - - + +
354A ILE* 5.9 3.1 - - + -
355A CYS* 4.8 7.6 - - - -
384A MET 3.6 4.2 + - - +
385A LEU* 3.3 31.8 + - + +
386A CYS 3.2 0.2 - - - -
387A LEU* 1.3 78.8 - - - +
389A ASN* 1.3 64.1 + - - +
391A THR* 2.9 17.0 + - - -
392A VAL* 3.0 31.4 + - + +
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 5.9 0.2 + - - -
203A SER* 4.8 6.1 + - - -
207A LEU* 4.7 9.1 - - - +
351A VAL* 3.3 25.6 - - - +
352A LEU* 4.3 8.4 - - - +
355A CYS* 3.9 23.4 - - + -
356A TRP* 4.1 23.6 - - + +
385A LEU 3.3 3.1 + - - +
386A CYS* 3.1 12.9 + - - +
388A LEU* 1.3 77.7 - - - +
390A SER* 1.3 62.8 + - - +
392A VAL* 3.5 5.6 - - - +
393A ASN* 3.1 51.7 + - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 3.5 25.6 - - - +
134A ASN* 3.9 0.7 + - - -
163A ASP* 3.5 37.8 + - - +
167A SER* 5.2 2.9 - - - -
200A PHE* 3.7 19.1 - - - -
386A CYS 3.1 10.1 + - - -
387A LEU* 2.9 14.8 + - - -
389A ASN* 1.3 77.6 + - - +
391A THR* 1.3 56.8 + - - +
393A ASN* 4.8 0.2 - - - +
394A PRO* 3.1 22.3 - - - +
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Residues in contact with THR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.9 20.0 + - + +
129A PHE* 4.8 9.4 - - + -
130A THR* 2.7 23.2 + - - +
133A GLU* 3.2 33.6 - - - +
387A LEU 2.9 9.9 + - - -
388A LEU* 2.9 15.4 + - + -
390A SER* 1.3 77.3 - - - +
392A VAL* 1.3 62.5 + - + +
394A PRO* 3.2 12.6 - - - +
395A ILE* 4.1 7.2 - - + +
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 4.0 24.0 - - + -
388A LEU* 3.0 27.8 + - + +
389A ASN* 3.5 10.8 - - - +
391A THR* 1.3 79.8 - - + +
393A ASN* 1.3 63.9 + - - +
394A PRO 3.4 0.2 - - - -
395A ILE* 2.9 17.6 + - + +
396A ILE* 2.8 49.8 + - + +
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Residues in contact with ASN 393 (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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159A LEU* 3.8 32.2 - - + +
163A ASP* 3.6 21.1 + - - +
203A SER* 4.2 3.8 + - - -
207A LEU* 4.3 9.2 - - - +
351A VAL* 5.2 0.3 - - - +
389A ASN* 3.1 46.0 + - - +
392A VAL* 1.3 77.5 - - - +
394A PRO* 1.3 67.9 - - + +
396A ILE* 4.0 9.9 - - - +
397A TYR* 3.1 43.5 + - - +
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Residues in contact with PRO 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 4.1 21.5 - - + +
134A ASN* 3.7 26.9 - - - +
137A VAL* 4.3 17.7 - - + -
163A ASP* 4.8 0.2 - - - +
390A SER 3.1 22.7 - - - +
391A THR 3.2 12.1 - - - +
393A ASN* 1.3 90.0 - - + +
395A ILE* 1.3 56.5 + - - +
398A ALA* 3.2 14.5 + - + +
399A LEU* 3.0 27.1 + - - +
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 3.8 22.2 - - - +
391A THR* 4.1 11.0 - - + +
392A VAL* 2.9 16.4 + - + +
394A PRO* 1.3 74.7 - - - +
396A ILE* 1.3 69.2 + - + +
399A LEU* 3.4 37.9 - - + +
400A ARG* 4.2 1.4 + - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A THR* 5.4 7.7 - - - +
347A LEU* 4.6 17.7 - - + -
348A ILE* 3.8 26.9 - - + -
351A VAL* 4.4 20.0 - - + -
392A VAL* 2.8 44.7 + - + +
393A ASN* 3.2 11.2 + - - +
395A ILE* 1.3 77.8 - - + +
397A TYR* 1.3 88.2 + - + +
400A ARG* 3.4 19.2 - - - +
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Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.4 33.9 - + + -
156A ILE* 4.4 9.5 - - + +
159A LEU* 3.9 13.5 - - + -
207A LEU* 3.3 31.1 - - + +
210A ALA* 5.9 1.1 - - + -
294A TYR* 5.1 8.3 + - - -
348A ILE* 3.2 47.7 - - + +
393A ASN* 3.1 28.8 + - - +
396A ILE* 1.3 92.0 - - + +
398A ALA* 1.3 68.1 + - - +
399A LEU 3.3 1.1 - - - -
400A ARG* 3.0 14.1 + - - +
401A SER* 3.3 11.6 + - - -
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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