Contacts of the helix formed by residues 40 - 64 (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 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 2.9 15.7 + - - +
39A ARG* 1.3 76.6 - - - +
41A LEU* 1.3 58.0 + - - +
43A GLU* 3.0 32.4 + - - +
44A THR 3.0 9.5 + - - -
180A PRO* 3.6 9.9 - - - +
181A ASP* 2.7 51.7 + - - +
186A ALA* 3.0 27.4 + - - +
187A VAL* 3.8 3.4 - - - +
190A MET* 3.4 23.3 - - + +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.5 44.2 - - + +
33A GLY* 3.7 28.5 - - - +
34A ALA* 4.2 12.8 - - - +
37A ALA* 3.8 10.1 + - + -
38A GLY 3.3 15.5 + - - +
40A ASN* 1.3 74.0 - - - +
42A PRO* 1.4 70.8 - - + +
44A THR* 3.0 22.9 + - + -
45A PHE* 3.1 30.4 + - + -
197A PHE* 4.0 11.0 - - + -
240A ALA* 4.0 4.7 - - + -
244A ILE* 3.8 7.6 - - + -
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Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 3.3 17.0 - - - +
40A ASN 3.4 1.6 - - - -
41A LEU* 1.4 95.4 - - + +
43A GLU* 1.3 70.1 + - - +
45A PHE* 3.5 7.7 + - + +
46A ILE* 3.3 28.4 + - + +
178A VAL 5.5 4.3 - - - +
237A VAL* 3.8 12.2 - - + +
240A ALA* 3.8 23.1 - - + -
241A ILE* 3.9 30.1 - - + +
244A ILE* 3.8 10.3 - - + -
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 3.7 4.7 - - - +
40A ASN* 3.0 30.0 + - + +
42A PRO* 1.3 83.3 - - - +
44A THR* 1.3 60.3 + - - +
46A ILE* 3.4 15.9 + - + +
47A LEU* 3.0 29.3 + - - +
178A VAL 4.5 6.1 - - - +
180A PRO* 3.5 37.0 - - + +
190A MET* 4.0 21.0 - - + +
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 3.4 14.5 - - - +
40A ASN 3.0 4.2 + - - -
41A LEU* 3.2 19.1 - - + +
43A GLU* 1.3 73.4 - - - +
45A PHE* 1.3 60.3 + - - +
47A LEU* 3.3 3.0 + - - +
48A SER* 2.9 33.1 + - - -
190A MET* 2.9 33.2 + - - +
193A ALA* 3.7 12.3 - - + +
194A SER* 3.5 28.0 - - - +
197A PHE* 4.1 15.3 - - + -
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 4.2 9.4 - - - -
26A ILE* 4.8 1.1 - - + -
30A PHE* 4.1 16.8 - + - -
41A LEU* 3.1 44.3 + - + -
42A PRO* 3.7 7.6 - - + +
44A THR* 1.3 75.6 - - - +
46A ILE* 1.3 55.9 + - - +
48A SER* 3.6 3.0 + - - -
49A GLY 2.9 14.9 + - - -
197A PHE* 3.5 36.6 - + + -
200A SER* 3.9 12.3 - - - -
201A TYR* 2.7 25.5 + + - +
233A MET* 5.1 0.9 - - - -
236A TYR* 3.5 60.1 - + + -
237A VAL* 4.4 7.0 - - + -
240A ALA* 4.1 7.0 - - + -
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 3.3 19.6 + - + +
43A GLU* 3.6 17.9 - - + +
44A THR 3.3 0.6 - - - -
45A PHE* 1.3 75.1 - - - +
47A LEU* 1.3 59.6 + - - +
49A GLY* 3.0 3.6 + - - -
50A ILE* 2.9 43.6 + - + +
233A MET* 4.5 17.4 - - + +
237A VAL* 3.7 25.8 - - + -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU 3.0 17.3 + - - +
44A THR* 3.3 4.7 + - - +
46A ILE* 1.3 78.2 - - - +
48A SER* 1.3 61.1 + - - +
50A ILE* 3.0 27.4 + - + +
51A TYR* 3.2 51.1 + - + +
190A MET* 3.7 26.9 - - + -
191A ILE* 4.1 16.6 - - + -
194A SER* 3.8 11.2 - - - +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR 2.9 18.7 + - - -
45A PHE* 3.8 2.9 - - - -
47A LEU* 1.3 76.2 - - - +
49A GLY* 1.3 57.3 + - - +
51A TYR* 3.3 15.3 + - - +
52A ALA* 3.0 26.0 + - - +
194A SER* 2.8 28.3 + - - -
197A PHE* 3.3 29.0 + - - +
198A PHE* 4.4 4.3 - - - -
201A TYR* 3.6 14.0 - - - -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE 2.9 11.8 + - - -
46A ILE 3.0 6.4 + - - -
48A SER* 1.3 74.0 - - - +
50A ILE* 1.3 59.2 + - - +
52A ALA* 3.4 3.1 + - - +
53A LEU* 3.0 34.8 + - - +
201A TYR* 3.4 24.0 - - - -
233A MET* 3.8 14.9 - - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 2.9 30.6 + - + +
47A LEU* 3.0 19.9 + - + +
49A GLY* 1.3 76.3 - - - +
51A TYR* 1.3 69.2 + - + +
53A LEU* 3.2 16.0 + - + +
54A LEU* 3.0 37.0 + - + +
233A MET* 5.5 4.0 - - - -
378A PHE* 6.3 1.1 - - + -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.3 35.2 - - + +
48A SER* 3.4 17.5 - - - +
50A ILE* 1.3 78.5 - - + +
52A ALA* 1.3 60.8 + - - +
54A LEU* 3.3 9.6 + - - +
55A VAL* 3.1 27.4 + - - +
191A ILE* 4.7 6.2 + - - +
194A SER* 3.0 44.8 + - - -
198A PHE* 3.4 35.4 - + + -
382A VAL* 3.7 23.6 - - + -
383A VAL* 4.8 2.2 - - + +
386A VAL* 3.6 29.1 - - + +
389A LEU* 5.8 0.7 - - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 3.0 8.6 + - - +
49A GLY 3.5 8.5 - - - +
50A ILE 3.2 0.2 - - - -
51A TYR* 1.3 76.9 - - - +
53A LEU* 1.3 52.5 + - - +
55A VAL* 3.4 0.7 + - - -
56A ALA* 2.8 34.3 + - - +
198A PHE* 3.9 9.8 - - + -
201A TYR* 3.4 43.7 - - + -
204A PHE* 3.3 12.0 - - + -
229A ILE* 4.3 10.1 - - + -
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Residues in contact with LEU 53 (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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49A GLY 3.0 22.2 + - - +
50A ILE* 3.2 15.9 + - + +
52A ALA* 1.3 73.9 - - - +
54A LEU* 1.3 61.5 + - - +
56A ALA* 3.3 5.6 + - + +
57A TYR* 3.0 26.9 + - - +
226A PHE* 3.7 36.1 - - + -
229A ILE* 3.9 24.5 - - + -
230A LEU* 4.5 9.2 - - + -
233A MET* 3.8 18.2 - - + -
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Residues in contact with LEU 54 (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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50A ILE* 3.0 30.1 + - + +
51A TYR* 3.5 10.1 - - - +
53A LEU* 1.3 77.5 - - + +
55A VAL* 1.3 61.8 + - + +
57A TYR* 3.3 20.1 - - + +
58A SER* 3.9 4.0 + - - -
375A ILE* 4.9 9.6 - - + -
378A PHE* 3.9 24.9 - - + -
379A SER* 3.4 35.2 + - - +
382A VAL* 3.8 42.0 - - + -
383A VAL* 5.5 1.6 - - + -
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR 3.1 14.1 + - - +
52A ALA* 3.6 7.6 - - - +
54A LEU* 1.3 73.7 - - - +
56A ALA* 1.3 63.8 + - - +
58A SER* 3.0 15.9 + - - -
59A TYR* 3.1 38.0 + - + -
198A PHE* 3.7 20.9 - - + -
204A PHE* 3.6 13.5 - - + -
355A TYR* 3.8 26.7 - - + +
358A VAL* 5.8 0.2 - - + -
359A ILE* 4.1 12.8 - - + -
383A VAL* 3.8 16.8 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 2.8 21.2 + - - +
53A LEU* 3.3 14.3 + - + +
55A VAL* 1.3 70.6 - - - +
57A TYR* 1.3 53.1 + - - +
59A TYR* 4.3 2.0 - - - -
60A THR* 2.6 46.0 + - + +
204A PHE* 3.7 12.8 - - + -
225A ILE* 3.9 8.7 - - + -
226A PHE* 5.6 4.9 - - + -
229A ILE* 3.8 20.9 - - + -
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Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 3.0 11.7 + - - +
54A LEU* 3.3 15.5 - - - +
56A ALA* 1.3 75.2 - - - +
58A SER* 1.3 60.8 + - - +
60A THR* 3.2 15.5 + - - -
61A LYS* 3.2 41.4 - - - +
362A HIS* 3.8 22.0 - + - -
371A GLY* 3.1 9.7 - - - -
372A ARG* 2.7 34.7 + - - +
375A ILE* 3.7 41.5 - - + +
376A VAL* 4.0 12.3 - - + -
379A SER* 5.1 0.7 - - - -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 3.9 2.6 + - - -
55A VAL 3.0 9.6 + - - -
57A TYR* 1.3 78.8 - - - +
59A TYR* 1.3 64.9 + - - +
61A LYS* 3.3 1.7 + - - +
62A LEU* 3.0 31.5 + - - +
358A VAL* 4.3 7.4 - - - -
359A ILE* 3.7 30.9 - - - +
362A HIS* 2.8 37.5 + - - +
376A VAL* 4.6 3.1 - - - +
379A SER* 5.5 0.9 - - - -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.1 40.9 + - + +
56A ALA* 4.0 5.2 - - - +
58A SER* 1.3 75.8 - - - +
60A THR* 1.3 58.0 + - - +
62A LEU* 4.1 3.7 - - - +
63A GLY* 2.8 28.1 + - - -
72A PRO* 3.9 9.1 - - + +
75A PHE* 4.1 17.6 - + - -
93A LEU* 5.9 0.2 - - - +
204A PHE* 3.5 38.7 - + + +
205A GLY* 6.0 0.2 - - - -
208A THR* 3.7 33.4 - - + -
221A VAL* 5.3 1.2 - - - +
225A ILE* 4.0 11.4 - - + +
354A ILE* 3.8 10.0 - - - +
355A TYR* 3.7 21.3 - + - -
358A VAL* 3.8 34.1 - - + +
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Residues in contact with THR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 2.6 30.7 + - + +
57A TYR* 3.2 12.6 + - - -
59A TYR* 1.3 75.2 - - - +
61A LYS* 1.3 68.1 + - - +
64A ALA* 3.3 24.3 + - - +
222A PRO* 3.6 46.4 - - + +
225A ILE* 4.2 15.3 - - + -
226A PHE* 5.0 6.5 - - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.2 36.0 + - + +
58A SER 3.3 2.5 + - - +
60A THR* 1.3 84.7 + - - +
62A LEU* 1.3 64.0 + - - +
64A ALA* 3.6 8.7 + - - +
65A LYS* 3.8 9.2 - - - +
362A HIS* 3.7 26.9 - - + +
369A VAL* 3.7 34.8 - - + +
370A GLY* 4.0 6.3 - - - -
371A GLY* 3.9 19.3 - - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER 3.0 20.0 + - - +
61A LYS* 1.3 79.1 - - - +
63A GLY* 1.3 51.6 + - - +
65A LYS* 3.1 4.9 + - - +
66A ILE* 2.8 49.4 + - + +
75A PHE* 3.7 33.7 - - + -
358A VAL* 3.6 39.7 - - + +
361A SER 4.6 0.2 - - - -
362A HIS* 3.9 22.4 - - + +
365A LEU* 4.0 26.9 - - + -
369A VAL* 4.1 15.0 - - + -
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR 2.8 21.3 + - - -
60A THR 4.2 0.9 - - - -
62A LEU* 1.3 69.6 - - - +
64A ALA* 1.3 60.7 + - - +
65A LYS 3.2 2.4 + - - -
66A ILE 3.6 17.8 + - - +
67A VAL* 4.5 2.4 - - - +
75A PHE* 3.9 9.8 - - - -
217A PRO 4.1 4.9 - - - +
218A LYS* 3.8 15.2 - - - +
221A VAL* 4.7 13.9 - - - +
222A PRO* 4.3 6.9 - - - +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR 3.3 19.2 + - - +
61A LYS* 3.9 6.5 - - - +
62A LEU 3.2 0.8 - - - -
63A GLY* 1.3 78.0 - - - +
65A LYS* 1.3 68.1 + - + +
218A LYS* 3.3 42.6 - - - +
222A PRO* 4.1 4.2 - - + +
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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