Contacts of the helix formed by residues 327 - 357 (chain A) in PDB entry 3KSS
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 ARG 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 2.7 51.7 + - - +
38A ALA* 4.3 2.8 + - - -
135A GLY 5.5 0.2 + - - -
136A VAL* 2.7 32.1 + - - +
138A TRP 3.2 17.0 + - - -
139A ILE* 3.6 18.0 + - + +
297A ALA* 4.6 7.5 - - + +
301A ILE* 3.6 13.7 - - + +
325A TYR* 3.2 27.7 + - + -
326A ASP* 1.3 71.4 + - - +
328A SER* 1.3 63.6 + - - +
329A GLN 3.0 2.0 + - - -
330A LEU* 3.1 20.1 + - - +
331A ILE* 3.1 22.7 + - + +
666A ILE* 3.3 38.3 - - - +
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG* 3.8 18.6 - - - +
301A ILE* 3.0 21.2 - - - +
305A LYS* 4.3 3.4 + - - -
326A ASP* 2.7 28.6 + - - -
327A ARG* 1.3 73.8 - - - +
329A GLN* 1.3 48.8 + - - -
331A ILE* 3.2 8.9 + - - +
332A ASP* 2.6 59.4 + - - +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP* 2.8 34.7 + - - +
328A SER* 1.3 78.1 - - - +
330A LEU* 1.3 56.3 + - - +
332A ASP* 3.8 7.5 - - - +
333A ARG* 2.8 49.2 + - - +
629A GLN* 4.8 11.1 + - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 4.2 24.0 - - + -
39A LEU* 5.2 1.6 - - + -
326A ASP 4.3 0.4 + - - -
327A ARG* 3.1 14.2 + - - +
329A GLN* 1.3 78.3 - - - +
331A ILE* 1.3 58.3 + - - +
333A ARG* 4.2 27.9 - - + +
334A ALA* 3.0 33.8 + - + +
390A ILE* 6.4 1.1 - - + -
566A ASN 4.5 9.4 - - - +
567A GLU* 3.7 37.9 - - + -
568A GLY 5.1 2.7 - - - +
666A ILE* 4.3 10.8 - - + -
1004A ALA* 5.1 8.7 - - - -
1005A GLY 5.8 0.2 - - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.9 34.5 - - + +
37A ASP* 3.5 17.0 - - - +
38A ALA* 3.1 41.3 - - + +
298A ARG* 4.2 20.2 - - + +
327A ARG* 3.1 25.8 + - + +
328A SER* 3.4 10.5 - - - +
330A LEU* 1.3 74.6 - - - +
332A ASP* 1.3 62.3 + - - +
334A ALA* 3.9 3.2 - - + +
335A ILE* 2.9 32.5 + - + +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG* 4.0 18.6 + - - +
328A SER* 2.6 44.5 + - - +
329A GLN* 3.8 6.9 + - - +
331A ILE* 1.3 70.8 - - - +
333A ARG* 1.3 67.9 + - + +
335A ILE* 3.0 12.4 + - - +
336A ASP* 2.8 36.3 + - - +
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN* 2.8 38.9 + - - +
330A LEU* 4.0 19.1 - - + +
332A ASP* 1.3 72.8 - - + +
334A ALA* 1.3 61.9 + - - +
336A ASP* 3.5 7.1 + - - +
337A ASN* 3.1 22.2 + - - +
566A ASN* 5.0 4.6 + - - -
567A GLU 4.7 2.4 - - - -
568A GLY* 3.1 37.7 - - - +
1003A GLY* 3.0 29.2 + - - +
1004A ALA* 4.0 7.6 - - + +
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 6.0 1.1 - - + -
330A LEU* 3.0 26.2 + - + +
331A ILE* 3.9 3.8 - - + +
333A ARG* 1.3 76.9 - - - +
335A ILE* 1.3 62.2 + - - +
337A ASN* 3.1 17.5 + - - +
338A LEU* 3.2 10.6 + - - +
390A ILE* 5.3 13.5 - - + -
393A LEU* 5.8 3.5 - - + +
1004A ALA* 3.3 23.5 - - + +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 5.2 9.6 - - + -
331A ILE* 2.9 22.2 + - + +
332A ASP* 3.0 20.9 - - + +
334A ALA* 1.3 74.0 - - - +
336A ASP* 1.3 75.7 + - - +
338A LEU* 3.4 7.5 + - + +
339A SER* 2.9 36.5 + - - +
393A LEU* 3.7 29.6 - - + -
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ASP* 2.8 30.5 + - - +
333A ARG* 3.9 6.0 + - - +
335A ILE* 1.3 87.5 - - - +
337A ASN* 1.3 62.4 + - - +
339A SER* 3.3 9.8 + - - -
340A GLY* 3.2 19.1 + - - -
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Residues in contact with ASN 337 (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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333A ARG 3.1 14.6 + - - +
334A ALA 3.1 12.3 + - - +
336A ASP* 1.3 78.5 - - - +
338A LEU* 1.3 83.5 + - - +
340A GLY* 3.3 3.3 + - - -
341A LYS* 3.3 21.7 + - - +
1001A GLY 5.2 1.0 - - - +
1002A THR* 4.7 12.1 + - - -
1003A GLY 4.8 1.0 + - - -
1004A ALA* 4.0 25.6 + - + +
1006A SER* 5.2 1.0 + - - -
1009A MET* 4.4 11.6 - - - +
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA 3.2 8.4 + - - +
335A ILE* 4.1 13.9 - - + +
337A ASN* 1.3 98.3 - - - +
339A SER* 1.3 64.6 + - - +
340A GLY 3.2 0.6 + - - -
341A LYS* 4.5 9.6 - - + +
342A LEU* 3.5 38.4 + - + +
393A LEU* 3.8 25.4 - - + +
394A GLY* 5.9 0.2 - - - -
396A ILE* 3.7 30.1 - - + -
397A ALA* 3.9 12.1 - - + -
1009A MET* 4.3 22.9 - - + -
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ILE* 2.9 29.0 + - - +
336A ASP* 3.5 12.6 + - - -
337A ASN 3.3 0.4 - - - -
338A LEU* 1.3 77.1 - - - +
340A GLY* 1.3 60.5 + - - +
342A LEU* 4.1 4.2 + - - +
343A LEU* 3.9 18.6 + - - +
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Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP 3.2 12.5 + - - -
337A ASN 3.3 3.1 + - - -
338A LEU 3.2 0.2 - - - -
339A SER* 1.3 75.8 - - - +
341A LYS* 1.3 58.6 + - - +
342A LEU 3.2 2.0 + - - -
343A LEU* 3.4 14.3 + - - +
344A GLU* 2.9 31.3 + - - +
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Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASN* 3.3 16.8 + - - +
338A LEU* 3.7 15.2 + - + +
339A SER 3.6 0.2 - - - -
340A GLY* 1.3 75.0 - - - +
342A LEU* 1.3 67.3 + - + +
344A GLU* 3.3 17.1 + - - +
345A GLU* 2.8 49.7 + - + +
397A ALA* 3.4 34.2 + - + +
398A ILE* 5.3 0.8 - - - +
400A VAL* 4.9 3.2 - - - +
401A GLY* 5.4 2.4 - - - +
994A GLY* 3.6 24.8 + - - -
995A LEU* 6.1 1.0 - - - +
997A PRO* 4.8 4.5 - - + -
998A ILE* 4.2 21.5 - - + -
1009A MET* 6.3 0.9 - - + -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 3.5 24.7 + - + +
339A SER* 4.3 4.9 - - - +
340A GLY 3.2 0.6 - - - -
341A LYS* 1.3 84.1 - - + +
343A LEU* 1.3 64.9 + - - +
345A GLU* 3.0 14.6 + - - +
346A PHE* 3.1 12.8 + - - +
370A LEU* 5.6 4.5 - - + +
374A LEU* 5.0 17.0 - - + -
396A ILE* 4.3 22.4 - - + -
397A ALA* 4.8 4.5 - - - -
400A VAL* 3.7 36.3 - - + -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER 3.9 12.5 + - - +
340A GLY* 3.4 14.8 + - - +
342A LEU* 1.3 76.5 - - - +
344A GLU* 1.3 72.8 + - + +
346A PHE* 2.7 47.4 + - + -
347A ILE* 3.0 12.6 - - + +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLY 2.9 19.1 + - - +
341A LYS* 3.5 12.2 - - - +
343A LEU* 1.3 82.4 - - + +
345A GLU* 1.3 75.6 + - - +
347A ILE* 3.1 24.5 - - + +
348A VAL* 3.1 26.5 + - + +
997A PRO* 2.9 38.8 - - - +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LYS* 2.8 29.9 + - - +
342A LEU* 3.2 14.8 - - - +
343A LEU 2.9 0.4 + - - -
344A GLU* 1.3 95.8 - - - +
346A PHE* 1.3 62.3 + - - +
348A VAL* 3.8 6.4 - - - +
349A VAL* 3.0 33.4 + - + +
370A LEU* 5.6 3.1 - - + -
400A VAL* 3.9 26.5 - - + -
401A GLY* 5.3 6.3 - - - +
404A VAL* 6.1 0.5 - - - +
990A VAL* 3.7 7.8 - - - +
993A ALA 4.0 2.3 - - - +
994A GLY* 3.0 36.0 + - - +
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Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU 3.1 8.8 + - - +
343A LEU* 2.7 39.8 + - + +
345A GLU* 1.3 77.0 - - - +
347A ILE* 1.3 73.1 + - + +
349A VAL* 3.2 7.8 + - - +
350A ALA* 2.8 45.2 + - + +
363A ALA* 4.8 14.1 - - + -
366A ALA* 5.6 4.8 - - + +
367A ILE* 4.8 27.8 - - + +
370A LEU* 5.6 10.4 - - + +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 3.0 25.4 - - + +
344A GLU* 3.1 21.8 - - + +
346A PHE* 1.3 91.1 - - + +
348A VAL* 1.3 71.7 + - + +
350A ALA* 3.2 7.0 + - - +
351A VAL* 2.8 42.2 + - + +
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 3.1 36.9 + - + +
345A GLU* 3.8 9.9 - - - +
346A PHE 3.3 0.2 - - - -
347A ILE* 1.3 87.6 - - + +
349A VAL* 1.3 60.7 + - + +
351A VAL* 3.5 5.6 + - - +
352A VAL* 3.0 35.9 + - + +
990A VAL* 4.9 4.5 - - + -
993A ALA* 3.5 39.7 - - + +
997A PRO* 6.0 0.2 - - + -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU* 3.0 28.6 + - + +
346A PHE* 3.5 5.4 - - - +
348A VAL* 1.3 75.4 - - + +
350A ALA* 1.3 61.8 + - - +
352A VAL* 3.2 1.9 + - - +
353A CYS* 2.8 33.3 + - + +
362A SER* 6.1 1.6 - - - +
366A ALA* 3.7 29.8 - - + -
370A LEU* 6.3 3.4 - - + -
404A VAL* 4.8 15.3 - - + -
408A ILE* 6.0 4.5 - - + -
990A VAL* 3.5 31.9 - - + +
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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
----------------------------------------------------------
346A PHE* 2.8 27.4 + - + +
347A ILE* 3.2 9.2 + - - +
349A VAL* 1.3 77.3 - - + +
351A VAL* 1.3 57.6 + - + +
353A CYS* 3.3 8.5 + - - +
354A ALA* 2.9 30.1 + - - +
362A SER* 5.3 2.9 - - - -
363A ALA* 4.8 21.5 - - + +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ILE* 2.8 34.2 + - + +
348A VAL* 3.7 6.3 - - - +
350A ALA* 1.3 73.3 - - + +
352A VAL* 1.3 69.0 - - + +
354A ALA* 3.2 9.4 + - - +
355A LEU* 3.2 35.0 + - + +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A VAL* 3.0 28.1 + - + +
349A VAL 3.2 3.8 + - - +
351A VAL* 1.3 78.0 - - + +
353A CYS* 1.3 67.0 + - - +
355A LEU* 3.2 9.8 + - + +
356A PHE* 3.1 28.2 + - + +
986A MET* 3.7 27.6 - - + +
989A ALA* 3.9 28.5 - - + -
990A VAL* 4.0 16.2 - - + +
993A ALA* 5.3 2.2 - - + -
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Residues in contact with CYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A VAL* 2.8 20.8 + - + +
350A ALA* 3.4 10.5 - - - +
352A VAL* 1.3 73.8 - - - +
354A ALA* 1.3 60.1 + - - +
356A PHE 2.8 3.6 + - - -
357A LEU* 2.7 47.1 + - + +
360A VAL* 4.4 15.3 - - - -
362A SER* 2.6 36.1 - - - +
408A ILE* 6.3 1.1 - - + -
986A MET* 4.0 15.9 - - - -
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 2.9 14.5 + - - +
351A VAL* 3.2 13.4 + - - +
353A CYS* 1.3 79.0 - - - +
355A LEU* 1.3 61.1 + - + +
358A TRP* 2.9 33.1 - - - -
359A HIS* 3.2 21.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 3.2 25.6 + - + +
352A VAL* 3.7 11.2 - - + +
353A CYS 3.1 0.8 - - - -
354A ALA* 1.3 81.2 - - + +
356A PHE* 1.3 70.3 + - + +
358A TRP* 4.2 13.7 - - + -
517A LEU* 3.5 28.9 - - - +
518A ASN* 4.2 0.3 + - - +
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 3.1 18.1 + - + +
353A CYS 2.8 3.4 + - - +
355A LEU* 1.3 90.0 - - + +
357A LEU* 1.3 61.9 + - + +
358A TRP 3.4 2.2 - - - -
518A ASN* 2.7 42.4 + - - +
520A PHE* 6.3 3.1 - + - -
521A LEU* 4.1 15.9 - - + -
981A VAL 4.3 0.4 - - - -
982A ARG* 3.0 28.5 - - + -
985A ALA* 3.5 28.3 - - + -
986A MET* 3.2 55.6 - - + -
989A ALA* 5.5 2.7 - - + -
----------------------------------------------------------
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A CYS* 2.7 27.9 + - + +
356A PHE* 1.3 82.3 - - + +
358A TRP* 1.3 71.6 + - - +
359A HIS 3.2 7.3 - - - +
360A VAL* 4.2 14.6 - - + +
362A SER* 5.1 0.2 - - - -
411A ILE* 3.3 35.2 - - + -
412A GLU* 5.8 5.4 - - - +
415A HIS* 3.3 36.1 + - + +
518A ASN* 4.9 3.1 - - - +
982A ARG* 5.8 1.6 - - + +
986A MET* 3.8 27.8 - - + -
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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