Contacts of the helix formed by residues 344 - 367 (chain A) in PDB entry 6KJV
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 ASP 344 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A MET* 3.8 14.1 - - + +
341A CYS* 3.2 30.9 + - - +
343A THR* 1.3 91.1 - - - +
345A ILE* 1.3 68.1 + - + +
346A ALA* 3.3 7.4 - - + +
347A PHE* 3.4 3.7 + - - +
348A ARG* 3.2 25.3 + - - +
1091A ASP* 3.9 12.1 - - + +
1092A ALA* 3.6 40.2 + - + +
1093A VAL* 6.3 1.3 - - + -
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Residues in contact with ILE 345 (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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176A ARG* 4.2 28.9 - - - +
254A LEU* 4.7 20.4 - - + -
344A ASP* 1.3 72.3 - - + +
346A ALA* 1.3 70.6 + - + +
348A ARG* 3.3 27.0 - - - +
349A LEU* 2.8 29.4 + - + +
408A GLU* 3.7 11.7 - - - +
1093A VAL* 4.2 19.1 - - + -
1155A GLY 3.8 21.5 - - - +
1156A THR* 5.0 10.3 - - + -
1157A TRP* 6.1 1.6 - - + +
2001A 97Y 5.5 2.6 - - - +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.0 4.7 - - - +
254A LEU* 4.5 24.5 - - + +
255A LEU* 3.8 15.7 - - + +
340A MET* 3.7 27.4 - - + -
344A ASP* 3.3 3.6 - - + +
345A ILE* 1.3 82.4 - - + +
347A PHE* 1.3 58.1 + - - +
349A LEU* 3.9 1.6 - - - +
350A ALA* 2.9 29.1 + - - +
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Residues in contact with PHE 347 (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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331A VAL* 4.0 11.2 - - + -
335A LEU* 3.8 29.6 - - + -
340A MET* 3.8 18.2 - - - -
341A CYS 3.9 8.5 - - - +
342A LYS* 3.3 56.5 - - + -
344A ASP 3.4 8.3 + - - +
345A ILE 3.1 0.4 - - - -
346A ALA* 1.3 77.8 - - - +
348A ARG* 1.3 61.3 + - - +
350A ALA* 3.3 6.6 + - + +
351A LYS* 2.8 53.6 + - + +
2001A 97Y 3.7 36.8 - + - -
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LYS 4.1 13.9 - - - +
343A THR* 3.3 26.1 + - - +
344A ASP* 3.2 14.6 + - - +
345A ILE* 3.3 24.4 - - - +
347A PHE* 1.3 76.7 - - - +
349A LEU* 1.3 59.4 + - - +
351A LYS* 3.0 34.7 + - - +
352A SER* 3.0 10.0 + - - -
407A ASN* 3.2 47.4 - - - +
408A GLU* 2.7 29.5 + - - -
2001A 97Y 3.4 33.8 + - + +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 3.6 34.5 - - + +
180A HIS* 4.0 12.8 - - + +
247A GLU* 4.4 3.6 - - - +
250A TYR* 4.1 14.8 - - + -
251A LEU* 4.0 14.6 - - + -
254A LEU* 3.8 23.8 - - + -
345A ILE 2.8 18.7 + - - +
346A ALA 3.9 2.9 - - - +
348A ARG* 1.3 74.2 - - - +
350A ALA* 1.3 59.5 + - - +
352A SER* 3.2 2.2 + - - +
353A THR* 2.9 38.4 + - - +
402A TYR* 4.0 23.3 - - + -
2001A 97Y 4.5 9.7 + - - +
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Residues in contact with ALA 350 (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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251A LEU* 3.8 25.2 - - + +
255A LEU* 5.6 0.2 - - + -
327A VAL* 4.5 0.4 - - + -
331A VAL* 4.3 25.1 - - + -
346A ALA 2.9 19.3 + - - +
347A PHE* 3.6 6.5 - - + +
349A LEU* 1.3 75.6 - - - +
351A LYS* 1.3 57.6 + - - +
354A LEU* 2.9 47.1 + - + +
2001A 97Y 6.0 0.4 - - - -
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Residues in contact with LYS 351 (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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342A LYS 5.4 0.7 - - - -
347A PHE* 2.8 42.4 + - + +
348A ARG* 3.0 22.4 + - - +
350A ALA* 1.3 76.5 - - - +
352A SER* 1.3 57.4 + - - +
355A THR* 2.9 21.7 + - - -
2001A 97Y 2.5 107.6 + - + +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG 3.0 5.7 + - - -
349A LEU 3.2 3.3 + - - -
350A ALA 3.1 0.2 - - - -
351A LYS* 1.3 78.6 - - - +
353A THR* 1.3 64.5 + - - +
354A LEU 3.4 0.2 - - - -
355A THR* 3.1 6.9 + - - -
356A LEU* 3.0 25.1 + - - +
401A LEU* 2.9 30.2 + - - +
402A TYR* 3.6 25.1 - - - -
2001A 97Y 3.2 30.1 + - - -
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Residues in contact with THR 353 (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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244A LEU* 5.1 4.3 - - + -
247A GLU* 4.0 15.0 + - + +
248A GLY* 4.5 11.0 - - - +
251A LEU* 4.0 22.5 - - + +
349A LEU* 2.9 23.3 + - - +
352A SER* 1.3 75.5 - - - +
354A LEU* 1.3 57.7 + - - +
356A LEU* 3.1 3.9 + - - +
357A ILE* 3.0 49.2 + - + +
402A TYR* 2.6 27.8 + - - +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 5.2 2.7 - - + -
324A PHE* 3.2 53.4 - - + +
327A VAL* 4.0 24.2 - - + -
328A ILE* 3.8 15.7 - - + -
331A VAL* 5.5 0.4 - - + -
350A ALA* 2.9 28.1 + - + +
351A LYS 5.1 0.9 - - - +
353A THR* 1.3 75.5 - - - +
355A THR* 1.3 56.7 + - - +
357A ILE* 4.9 4.3 - - + -
358A PRO* 3.0 22.6 - - - +
2001A 97Y 3.7 37.5 - - + +
2002A OLC 4.1 12.3 + - - +
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Residues in contact with THR 355 (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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351A LYS 2.9 10.6 + - - -
352A SER 3.1 10.1 + - - -
353A THR 3.1 0.8 - - - -
354A LEU* 1.3 78.4 - - - +
356A LEU* 1.3 66.2 + - - +
358A PRO* 3.3 11.5 - - - +
359A LEU* 3.2 28.9 + - + +
397A MET* 5.5 0.4 - - - -
401A LEU* 3.9 20.9 - - + -
2001A 97Y 2.9 53.3 + - + -
2002A OLC 5.5 1.1 - - - -
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Residues in contact with LEU 356 (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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183A LEU* 5.2 1.6 - - + -
244A LEU* 4.3 17.0 - - + -
352A SER 3.0 16.3 + - - +
353A THR 3.1 4.0 + - - +
355A THR* 1.3 78.2 - - - +
357A ILE* 1.3 63.2 + - - +
359A LEU* 3.1 19.2 + - + -
360A LEU* 2.9 39.7 + - + +
394A GLN 5.5 0.2 - - - +
397A MET* 4.5 5.6 - - + -
398A VAL* 4.2 23.1 - - + -
401A LEU* 4.0 23.1 - - + -
402A TYR* 3.4 45.8 - - + +
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Residues in contact with ILE 357 (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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244A LEU* 4.4 19.3 - - + +
248A GLY* 5.2 2.9 - - - -
251A LEU* 6.2 0.7 - - + -
320A ASN* 3.4 50.3 - - + +
321A PHE* 4.3 9.2 - - + +
323A ILE* 5.2 7.6 - - + -
324A PHE* 4.1 25.4 - - + +
353A THR* 3.0 40.0 + - + +
354A LEU* 4.9 3.1 - - + -
356A LEU* 1.3 76.3 - - - +
358A PRO* 1.3 66.4 - - + +
360A LEU* 3.9 0.5 - - - +
361A CYS* 3.0 31.1 + - + +
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Residues in contact with PRO 358 (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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321A PHE* 3.7 25.4 - - + -
324A PHE* 3.7 15.3 - - + -
354A LEU 3.0 28.7 - - - +
355A THR* 3.3 7.4 - - - +
357A ILE* 1.3 89.4 - - + +
359A LEU* 1.3 56.0 + - - +
360A LEU 3.4 0.2 - - - -
362A THR* 3.2 28.6 - - - +
2002A OLC 3.7 41.1 - - + +
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Residues in contact with LEU 359 (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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355A THR* 3.2 25.6 + - + +
356A LEU* 3.1 26.8 + - + +
358A PRO* 1.3 79.0 - - - +
360A LEU* 1.3 68.1 + - + +
362A THR* 5.0 0.4 - - - +
363A HIS 5.9 0.2 + - - -
390A PHE* 4.6 24.7 - - + -
394A GLN* 5.0 10.7 + - + +
397A MET* 3.8 33.7 - - + -
2001A 97Y 6.4 0.9 - - + -
2002A OLC 4.0 33.6 - - + +
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Residues in contact with LEU 360 (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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183A LEU* 6.2 0.7 - - + -
187A PHE* 3.9 28.3 - - + -
240A ASN* 5.2 7.2 - - + +
241A TYR* 3.2 34.8 + - + +
244A LEU* 4.0 28.7 - - + -
356A LEU* 2.9 34.8 + - + +
359A LEU* 1.3 100.8 - - + +
361A CYS* 1.3 59.3 + - - +
362A THR 3.7 1.1 - - - -
363A HIS* 5.0 4.5 + - - +
364A GLU 5.1 2.3 + - - -
394A GLN* 4.3 29.1 + - + +
398A VAL* 5.4 3.8 - - + -
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Residues in contact with CYS 361 (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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241A TYR* 3.9 13.2 - - - -
244A LEU* 4.8 4.3 - - - -
317A CYS* 2.0 52.3 - - - +
320A ASN* 4.1 17.0 - - - -
321A PHE* 3.6 17.5 - - + -
357A ILE* 3.0 17.9 + - + +
360A LEU* 1.3 75.9 - - - +
362A THR* 1.3 65.9 + - - +
363A HIS 3.3 2.9 - - - -
364A GLU* 3.3 4.6 + - - +
365A VAL* 3.0 24.9 + - - +
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Residues in contact with THR 362 (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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321A PHE* 3.9 16.5 - - - -
358A PRO* 3.2 23.4 + - - +
359A LEU 5.0 1.1 - - - +
361A CYS* 1.3 75.2 - - - +
363A HIS* 1.3 65.6 + - - +
365A VAL* 3.3 2.6 + - - +
366A ILE* 2.9 52.6 + - + +
2002A OLC 3.6 54.4 - - + +
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Residues in contact with HIS 363 (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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360A LEU 5.0 4.6 + - - +
361A CYS 3.3 0.4 - - - -
362A THR* 1.3 82.9 - - - +
364A GLU* 1.3 72.5 + - - +
366A ILE* 4.5 6.1 - - - +
367A PHE* 3.2 58.5 + + + +
384A LEU* 5.3 6.2 - - + +
387A GLU* 3.4 32.9 + - + -
2002A OLC 3.9 35.9 - - + +
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Residues in contact with GLU 364 (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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241A TYR* 4.9 10.2 + - + +
310A ARG* 3.1 48.7 + - - +
313A ILE* 3.7 27.9 - - + +
314A LEU* 3.8 17.1 - - + +
317A CYS* 4.1 13.2 - - - -
360A LEU 5.1 1.0 + - - -
361A CYS* 3.3 11.1 + - - +
363A HIS* 1.3 87.7 + - - +
365A VAL* 1.3 61.7 - - - +
367A PHE 3.9 3.6 - - - +
368A ALA* 3.5 24.3 + - - +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 4.1 14.6 - - + -
317A CYS* 3.9 23.8 - - + -
318A ILE* 4.8 6.5 - - + +
321A PHE* 4.0 20.2 - - + -
361A CYS 3.0 17.0 + - - +
362A THR* 4.0 3.4 - - - +
363A HIS 3.2 0.2 - - - -
364A GLU* 1.3 77.1 - - - +
366A ILE* 1.3 69.4 + - + +
368A ALA* 3.3 16.3 + - + +
267B ARG* 4.6 0.5 + - - -
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Residues in contact with ILE 366 (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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362A THR* 2.9 42.3 + - + +
363A HIS* 3.9 5.4 - - - +
365A VAL* 1.3 79.1 - - + +
367A PHE* 1.3 77.3 + - + +
2002A OLC 6.5 0.2 - - + -
267B ARG* 2.8 58.0 + - + +
268B LEU* 5.3 2.7 - - + -
270B VAL* 5.6 2.7 - - + +
271B ALA* 3.9 23.6 - - + -
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Residues in contact with PHE 367 (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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306A TRP* 5.1 1.9 - - - -
363A HIS* 3.2 52.0 + + + +
364A GLU* 3.9 5.9 - - - +
366A ILE* 1.3 89.6 - - + +
368A ALA* 1.3 64.1 + - - +
369A PHE 3.4 2.3 + - - -
370A VAL* 3.6 23.9 + - + +
384A LEU* 5.3 7.9 - - + -
264B TRP* 3.4 58.1 - + + -
267B ARG* 4.0 17.3 - - + +
268B LEU* 4.7 14.1 - - + -
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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