Contacts of the helix formed by residues 339 - 365 (chain A) in PDB entry 3GIA
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 339 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 3.8 8.1 - - - +
338A PHE* 1.3 76.2 - - - +
340A MET* 1.3 65.8 + - - +
341A GLU* 3.1 14.6 + - - +
342A GLY* 2.9 20.5 + - - +
343A VAL* 2.8 21.5 + - - +
398A ASN* 4.5 16.2 + - - +
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Residues in contact with MET 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.3 30.5 - - - +
29A ILE* 4.0 7.0 - - + -
32A VAL* 3.9 17.5 - - + -
103A LEU* 3.5 31.4 - - - +
106A LYS* 3.5 25.8 - - + +
107A GLY* 3.4 33.7 - - - +
257A GLU* 6.4 2.5 - - + -
339A ASN* 1.3 76.2 - - - +
341A GLU* 1.3 54.5 + - - +
343A VAL* 3.2 1.7 + - - -
344A ALA* 2.8 36.4 + - - +
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Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.6 32.2 - - + +
35A LYS* 4.5 13.5 - - - +
36A ILE* 4.0 17.8 - - - +
196A ILE* 4.2 9.8 - - + +
339A ASN* 3.1 9.9 + - - +
340A MET* 1.3 77.3 - - - +
342A GLY* 1.3 56.7 + - - +
344A ALA* 3.7 2.9 - - - +
345A SER* 2.8 36.4 + - - +
393A TYR* 3.5 26.4 + - - -
394A GLN* 4.9 5.9 - - - +
397A THR* 4.1 11.8 - - - +
398A ASN* 5.8 1.9 - - - +
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Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 4.2 10.5 - - - -
339A ASN* 2.9 17.1 + - - -
341A GLU* 1.3 75.4 - - - +
343A VAL* 1.3 61.8 + - - +
345A SER* 3.1 3.8 + - - -
346A ILE* 3.0 28.9 + - - +
394A GLN* 5.6 0.2 - - - -
401A VAL* 3.8 28.0 - - - -
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.5 33.7 - - + +
102A ALA* 4.1 2.7 - - + -
103A LEU* 3.6 25.8 - - + +
106A LYS* 4.3 11.7 - - + -
334A PHE* 3.8 26.9 - - + +
335A ALA* 4.6 1.8 - - - -
338A PHE* 3.8 13.4 - - + +
339A ASN 2.8 21.3 + - - +
340A MET* 3.9 4.3 - - - +
342A GLY* 1.3 71.9 - - - +
344A ALA* 1.3 58.4 + - - +
346A ILE* 3.4 7.6 + - + +
347A THR* 2.7 34.2 + - - +
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Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.7 25.6 - - + -
32A VAL* 5.3 1.1 - - + -
103A LEU* 3.7 10.9 - - - +
196A ILE* 3.9 20.0 - - + -
199A LEU* 3.3 13.9 - - + +
340A MET 2.8 22.4 + - - +
341A GLU* 3.7 6.5 - - - +
343A VAL* 1.3 73.1 - - - +
345A SER* 1.3 56.9 + - - +
348A SER* 3.0 27.4 + - - -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 3.5 15.0 - - - +
341A GLU* 2.8 23.3 + - - +
342A GLY 3.1 4.7 + - - -
344A ALA* 1.3 74.5 - - - +
346A ILE* 1.3 59.3 + - - +
348A SER* 3.4 1.7 + - - -
349A ALA* 3.0 26.0 + - - +
390A LEU* 3.4 18.1 - - - +
394A GLN* 2.9 39.7 + - - -
401A VAL* 4.0 6.5 - - - -
405A ILE* 4.0 2.2 - - - +
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.9 27.1 - - + -
334A PHE* 4.2 10.5 - - + -
338A PHE* 3.7 46.7 - - + -
342A GLY 3.0 17.7 + - - +
343A VAL* 3.9 5.2 - - - +
345A SER* 1.3 74.4 - - - +
347A THR* 1.3 63.4 + - - +
349A ALA* 3.3 2.3 + - - +
350A VAL* 3.0 27.8 + - + +
401A VAL* 4.2 6.1 - - + -
404A GLY 4.8 6.7 - - - -
405A ILE* 3.8 27.8 - - + -
408A THR* 4.3 14.8 - - - +
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Residues in contact with THR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 4.5 5.2 - - - +
99A ILE* 3.4 25.9 + - + +
100A SER* 3.8 15.7 - - - +
103A LEU* 4.4 6.0 - - + +
199A LEU* 3.8 16.2 - - + -
202A MET* 5.3 1.3 - - + -
343A VAL* 2.7 24.1 + - - +
344A ALA 3.7 4.0 - - - -
346A ILE* 1.3 77.6 - - - +
348A SER* 1.3 57.9 + - - +
350A VAL* 3.3 6.4 + - - +
351A PHE* 3.0 63.1 + - + -
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA 2.8 25.7 + - - -
196A ILE* 3.2 18.0 + - - -
198A PHE* 3.3 15.8 - - - +
199A LEU* 3.6 10.8 + - - +
344A ALA 3.0 18.3 + - - -
345A SER 3.8 4.3 - - - -
347A THR* 1.3 76.6 - - - +
349A ALA* 1.3 61.6 + - - +
351A PHE* 3.5 5.3 + - - +
352A MET* 3.1 31.5 + - - +
390A LEU* 4.1 4.3 - - - -
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A SER 3.0 18.0 + - - +
346A ILE 3.5 5.4 - - - +
347A THR 3.2 0.2 - - - -
348A SER* 1.3 76.6 - - - +
350A VAL* 1.3 60.7 + - - +
352A MET* 3.3 8.9 + - - +
353A VAL 3.2 16.8 + - - -
387A PHE* 3.7 13.2 - - + -
390A LEU* 3.6 15.2 - - + +
391A LEU* 5.5 0.4 - - + -
405A ILE* 3.8 31.4 - - + -
409A PHE* 3.7 10.4 - - + -
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.8 30.4 - - + +
96A SER* 3.6 32.3 - - - +
99A ILE* 4.1 17.7 - - + -
346A ILE* 3.0 22.2 + - + +
347A THR* 3.7 6.1 - - - +
349A ALA* 1.3 74.9 - - + +
351A PHE* 1.3 65.5 + - - +
353A VAL* 3.2 4.3 + - - +
354A ILE* 3.2 22.1 + - + +
405A ILE* 6.3 0.2 - - + -
408A THR* 4.4 9.6 - - + -
409A PHE* 3.9 22.7 - - + -
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Residues in contact with PHE 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 5.6 3.4 - - + -
96A SER* 3.5 30.3 - - - -
97A TYR* 5.9 4.7 - + - -
100A SER* 4.0 3.4 - - - -
198A PHE* 6.2 1.1 - - + -
199A LEU* 4.3 15.0 - - + +
202A MET* 3.6 43.1 - - + -
205A GLY* 5.8 8.1 - - - -
347A THR* 3.0 46.2 + - + +
348A SER* 3.9 4.9 - - - +
349A ALA 3.4 0.2 - - - -
350A VAL* 1.3 75.7 - - - +
352A MET* 1.3 58.8 + - - +
354A ILE* 3.2 10.8 + - + +
355A TYR* 2.8 69.8 + + + -
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA 3.9 13.9 - - - +
198A PHE* 3.5 35.4 - - + -
348A SER* 3.1 23.9 + - - +
349A ALA* 3.5 8.7 - - - +
350A VAL 3.3 0.2 - - - -
351A PHE* 1.3 76.8 - - - +
353A VAL* 1.3 56.6 + - - +
355A TYR* 3.3 7.4 + - + +
356A LEU* 2.9 35.4 + - - +
383A VAL* 3.7 13.1 - - + +
386A VAL* 3.7 10.5 - - + +
387A PHE* 3.4 43.1 - - + -
390A LEU* 3.5 27.6 - - + -
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.4 1.8 - - + -
92A LEU* 3.7 17.3 - - + -
349A ALA 3.2 5.4 + - - +
350A VAL 3.2 6.7 + - - +
352A MET* 1.3 73.0 - - - +
354A ILE* 1.3 69.8 + - - +
356A LEU* 3.3 11.3 + - + +
357A PHE* 3.2 43.1 + - + -
387A PHE* 3.9 20.2 - - + -
409A PHE* 3.5 35.2 - - + -
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.8 20.4 - - - +
72A PRO* 4.2 21.5 - - + -
73A ILE* 6.2 1.1 - - + -
76A ILE* 4.8 3.6 - - + +
89A LEU* 4.5 12.8 - - + +
92A LEU* 4.1 12.8 - - + +
93A LEU* 3.9 36.8 - - + +
96A SER* 3.9 20.0 - - - +
350A VAL* 3.2 21.6 + - + +
351A PHE* 3.5 12.6 - - + +
353A VAL* 1.3 78.2 - - - +
355A TYR* 1.3 66.7 + - + +
357A PHE* 3.2 3.8 + - - +
358A VAL* 3.1 19.9 + - - +
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Residues in contact with TYR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.8 21.7 - - + +
59A TYR* 3.7 25.6 - + - -
198A PHE* 3.8 41.6 + + - -
199A LEU* 5.7 0.5 - - - -
201A TYR 4.0 1.6 + - - -
202A MET* 4.0 13.3 - - - -
204A PHE* 3.4 35.2 - + + +
351A PHE* 2.8 64.6 + + + +
352A MET* 3.7 8.1 - - - +
353A VAL 3.3 0.2 - - - -
354A ILE* 1.3 74.5 - - + +
356A LEU* 1.3 57.7 + - - +
358A VAL* 3.3 7.6 + - - +
359A ILE* 2.9 34.4 + - - +
383A VAL* 4.6 3.8 - - + -
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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
----------------------------------------------------------
352A MET 2.9 25.9 + - - +
353A VAL* 3.7 12.6 - - + +
354A ILE 3.3 0.2 - - - -
355A TYR* 1.3 75.0 - - - +
357A PHE* 1.3 61.6 + - + +
359A ILE* 3.3 3.0 + - - +
360A LEU* 2.8 29.3 + - - +
380A PHE* 3.4 58.4 - - + +
383A VAL* 3.8 13.7 - - + -
384A LEU* 3.7 36.1 - - + +
387A PHE* 4.9 11.2 - - + -
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Residues in contact with PHE 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.0 14.6 - - + -
80A ILE* 5.2 3.8 - - + -
85A ILE* 3.6 28.9 - - + -
89A LEU* 3.5 34.5 - - + -
353A VAL* 3.2 35.1 + - + +
354A ILE 3.2 8.1 + - - +
356A LEU* 1.3 79.7 - - + +
358A VAL* 1.3 54.9 + - - +
360A LEU* 3.7 25.7 - - + +
361A SER* 2.7 36.6 + - - -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 4.3 7.9 - - - -
59A TYR* 3.8 38.4 - - + +
62A LEU* 3.6 20.5 - - + +
72A PRO* 3.6 34.3 - - + +
75A PHE* 4.2 6.3 - - + -
76A ILE* 4.4 6.3 - - + -
354A ILE* 3.1 18.2 + - + +
355A TYR 3.3 8.0 + - - +
357A PHE* 1.3 75.0 - - - +
359A ILE* 1.3 61.0 + - + +
361A SER* 3.1 7.6 + - - -
362A HIS* 2.8 28.2 + - - +
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Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.1 26.9 - - + +
58A SER* 3.7 23.8 - - - +
355A TYR 2.9 28.3 + - - +
356A LEU* 3.3 7.8 + - - +
358A VAL* 1.3 76.8 - - + +
360A LEU* 1.3 55.8 + - - +
362A HIS* 3.2 4.9 + - - +
363A TYR 2.9 23.9 + - - -
376A VAL* 3.4 37.1 - - + +
379A SER* 4.3 17.3 - - - +
380A PHE* 3.7 18.4 - - + +
383A VAL* 4.1 15.7 - - + -
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 5.1 7.9 - - + -
356A LEU 2.8 20.3 + - - +
357A PHE* 3.7 31.2 - - + +
359A ILE* 1.3 74.2 - - - +
361A SER* 1.3 57.7 + - - +
363A TYR* 3.1 15.5 + - + +
364A ILE* 2.9 49.2 + - + +
380A PHE* 4.4 17.4 - - + -
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Residues in contact with SER 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.6 0.7 - - - -
75A PHE* 3.8 26.2 - - - -
76A ILE* 3.4 22.9 - - - +
79A ALA* 3.7 14.2 - - - +
80A ILE* 5.5 1.7 - - - +
357A PHE 2.7 22.9 + - - -
358A VAL* 3.1 8.7 + - - -
360A LEU* 1.3 71.9 - - - +
362A HIS* 1.3 61.6 + - - +
364A ILE* 3.3 2.5 + - - -
365A LEU* 2.9 37.6 + - - +
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Residues in contact with HIS 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.8 20.6 - + - -
58A SER* 2.8 33.7 + - - +
61A LYS* 3.7 18.5 - - + +
62A LEU* 3.9 15.3 - - + +
358A VAL 2.8 11.1 + - - +
359A ILE 3.3 9.6 - - - +
361A SER* 1.3 75.4 - - - +
363A TYR* 1.3 55.4 - - - +
365A LEU 3.3 0.9 + - - -
366A ILE* 2.9 29.4 + - + +
369A VAL* 3.4 19.7 - - + -
370A GLY 2.8 23.0 + - - -
371A GLY* 4.6 0.4 - - - -
376A VAL* 3.3 26.6 - - + +
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Residues in contact with TYR 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE 2.9 12.9 + - - +
360A LEU* 3.1 19.0 + - + +
362A HIS* 1.3 76.1 - - - +
364A ILE* 1.3 71.2 + - + +
366A ILE* 3.2 26.1 + - + +
373A LYS* 4.1 37.8 + - + +
376A VAL* 3.8 23.1 - - + +
377A ILE* 3.8 34.9 - - + +
----------------------------------------------------------
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Residues in contact with ILE 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA* 3.7 29.2 - - + +
80A ILE* 3.9 28.3 - - + -
360A LEU* 2.9 43.3 + - + +
361A SER* 3.8 4.3 - - - +
363A TYR* 1.3 79.9 - - + +
365A LEU* 1.3 63.1 + - + +
366A ILE* 3.5 2.8 + - - +
367A ASP* 5.1 2.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.0 16.8 - - + -
66A ILE* 4.4 4.0 - - + -
75A PHE 3.9 16.8 - - - +
78A LYS* 3.6 41.7 - - + +
79A ALA* 4.0 10.1 - - + -
361A SER 2.9 17.6 + - - +
362A HIS 3.4 3.8 - - - +
363A TYR 3.2 0.2 - - - -
364A ILE* 1.3 80.1 - - + +
366A ILE* 1.3 59.1 + - - +
367A ASP 3.4 2.9 - - - -
368A GLU* 3.1 29.6 + - + +
369A VAL* 2.9 34.8 + - + +
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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