Contacts of the helix formed by residues 55 - 80 (chain C) in PDB entry 5AZS
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 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA 2.7 24.1 + - - +
52C LEU 4.7 0.2 - - - -
53C ASP 3.7 2.6 - - - +
54C ASN* 1.3 70.0 - - - +
56C ARG* 1.3 62.1 + - - +
57C SER* 3.3 11.9 + - - +
58C LEU* 2.9 32.4 + - + +
59C ARG* 3.0 27.4 + - - +
152C LEU* 3.4 29.1 - - + +
231C LEU 4.2 4.4 + - - -
232C LEU* 2.9 33.6 + - - +
234C GLY* 4.9 1.6 - - - -
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.7 23.8 - - - +
352B ALA* 3.7 22.7 - - - +
355B GLU* 3.1 34.5 + - - +
356B GLY* 4.0 13.7 - - - +
359B GLN* 3.5 29.2 + - - +
54C ASN* 2.7 37.8 + - - +
55C ASN* 1.3 75.1 - - - +
57C SER* 1.3 60.7 + - - +
59C ARG* 3.5 39.6 - - - +
60C GLN* 3.0 34.4 + - - +
234C GLY 3.2 10.1 + - - -
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASN* 3.3 12.0 + - - +
56C ARG* 1.3 74.6 - - - +
58C LEU* 1.3 65.1 + - - +
60C GLN* 3.6 11.0 + - - +
61C THR* 3.3 26.5 + - - +
148C ALA* 6.2 0.7 - - - -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA 4.8 0.4 - - - +
52C LEU* 3.4 30.1 - - + +
55C ASN* 2.9 23.2 + - + +
56C ARG 3.4 0.2 - - - -
57C SER* 1.3 73.0 - - - +
59C ARG* 1.3 65.7 + - - +
61C THR* 2.7 24.1 + - - +
62C LEU* 2.9 34.3 + - + +
145C ALA 4.1 6.5 - - - +
148C ALA* 3.9 7.9 - - - +
149C ARG* 3.5 50.5 - - + +
152C LEU* 4.0 18.2 - - + -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASP 5.8 0.2 - - - -
352B ALA* 4.0 21.1 - - + +
355B GLU* 4.6 4.4 + - - -
53C ASP 2.9 27.9 + - - -
54C ASN* 3.7 16.8 + - - +
55C ASN 3.0 16.0 + - - +
56C ARG* 3.5 43.2 - - - +
58C LEU* 1.3 75.6 - - - +
60C GLN* 1.3 56.4 + - - +
62C LEU* 3.4 14.0 + - + +
63C LEU* 3.0 43.8 + - + +
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B SER* 3.8 21.0 + - - +
352B ALA* 3.7 18.3 - - + +
353B ALA* 3.2 35.9 + - - +
356B GLY* 5.4 1.7 - - - -
56C ARG* 3.0 22.4 + - - +
57C SER* 3.7 10.7 + - - +
58C LEU 3.1 0.2 - - - -
59C ARG* 1.3 76.4 - - - +
61C THR* 1.3 58.6 + - + +
63C LEU* 3.2 7.0 + - - +
64C ASP* 2.9 34.2 + - - +
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER 3.3 12.9 + - - +
58C LEU* 2.7 26.2 + - - +
60C GLN* 1.3 73.4 - - + +
62C LEU* 1.3 61.0 + - - +
64C ASP* 3.6 26.3 - - - +
65C ILE* 3.7 6.8 - - - +
141C SER 4.5 1.7 - - - +
144C ALA* 5.6 2.2 - - + +
145C ALA* 3.7 24.3 - - - +
148C ALA* 3.9 23.7 - - + +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU 5.6 2.2 - - - +
58C LEU* 2.9 41.0 + - + +
59C ARG* 3.6 15.9 - - + +
61C THR* 1.3 76.6 - - - +
63C LEU* 1.3 58.3 + - + +
64C ASP 3.2 0.2 - - - -
65C ILE* 3.1 34.4 + - + +
66C GLU* 3.6 8.4 + - - +
145C ALA* 4.1 19.3 - - + +
149C ARG* 6.2 3.1 - - - -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA* 3.9 18.0 - - - +
348B ASP* 3.5 28.0 - - + +
349B SER* 3.4 35.2 - - - +
352B ALA* 4.7 0.4 - - + -
59C ARG* 3.0 37.8 + - + +
60C GLN* 3.2 4.9 + - - +
62C LEU* 1.3 73.7 - - + +
64C ASP* 1.3 61.1 + - - +
65C ILE 3.2 0.7 - - - -
66C GLU* 3.4 26.5 + - - +
67C ALA* 3.1 27.0 + - - +
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B SER* 4.3 9.4 + - - -
60C GLN* 2.9 22.1 + - - +
61C THR* 3.6 25.1 + - - +
62C LEU 3.2 0.2 - - - -
63C LEU* 1.3 74.7 - - - +
65C ILE* 1.3 57.4 + - - +
67C ALA* 3.7 8.7 + - - +
68C ALA* 3.2 21.5 + - - +
141C SER* 3.2 14.7 + - - +
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR 3.7 3.6 - - - +
62C LEU* 3.1 23.1 + - + +
64C ASP* 1.3 75.3 - - - +
66C GLU* 1.3 63.0 + - + +
68C ALA* 3.0 3.6 + - - +
69C ARG* 2.8 29.7 + - + +
138C TYR* 4.5 15.1 - - + +
141C SER* 3.4 29.8 - - - +
142C GLU* 3.9 30.3 - - + +
145C ALA* 3.8 25.8 - - + -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B SER* 5.1 1.7 - - - +
342B LEU* 5.1 0.2 - - - -
345B ALA* 4.1 17.0 - - + +
348B ASP* 5.6 0.7 - - - +
62C LEU 3.6 9.1 + - - +
63C LEU* 3.4 28.0 + - - +
65C ILE* 1.3 78.7 - - + +
67C ALA* 1.3 60.9 + - - +
69C ARG* 3.9 8.5 - - - +
70C ALA* 3.3 20.1 + - - +
73C ARG* 4.3 5.4 + - - +
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.5 29.2 - - + +
345B ALA* 4.2 8.6 - - + +
346B ARG* 4.9 11.4 - - + +
63C LEU 3.1 16.6 + - - +
64C ASP* 3.8 10.5 - - - +
66C GLU* 1.3 75.9 - - - +
68C ALA* 1.3 63.9 + - - +
70C ALA* 3.3 5.0 + - - +
71C GLN* 3.2 24.5 + - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ASP 3.2 17.1 + - - +
65C ILE 3.0 4.9 + - - +
67C ALA* 1.3 73.0 - - - +
69C ARG* 1.3 64.8 + - - +
71C GLN* 3.5 10.1 + - - +
72C TYR* 3.1 18.2 + - - +
134C ALA* 4.3 2.6 - - - +
137C GLN* 4.5 5.3 - - + +
138C TYR* 3.4 36.1 - - + +
141C SER* 4.0 9.0 - - - -
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 2.8 20.5 + - + +
66C GLU* 3.9 9.6 - - - +
68C ALA* 1.3 73.4 - - - +
70C ALA* 1.3 56.4 + - - +
72C TYR* 3.0 30.1 + - - +
73C ARG* 2.9 50.4 + - - +
76C ARG* 5.0 8.3 - - - +
138C TYR* 3.5 47.4 + - + +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA* 3.3 23.8 - - - +
342B LEU* 3.7 21.8 - - + +
66C GLU 3.3 11.6 + - - +
67C ALA 3.3 10.9 + - - +
69C ARG* 1.3 79.3 - - - +
71C GLN* 1.3 51.3 + - - +
73C ARG* 3.0 21.5 + - - +
74C ILE* 2.8 38.7 + - - +
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Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 4.2 19.2 - - + +
346B ARG* 3.3 28.3 - - - +
67C ALA* 3.2 14.0 + - - +
68C ALA* 3.9 10.8 - - - +
69C ARG 3.3 0.4 - - - -
70C ALA* 1.3 73.4 - - - +
72C TYR* 1.3 64.4 + - - +
74C ILE* 3.6 12.3 + - + +
75C GLN* 3.3 24.4 + - - +
134C ALA* 3.9 8.5 - - + +
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Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA 3.1 12.6 + - - +
69C ARG* 3.0 39.9 + - - +
71C GLN* 1.3 76.6 - - - +
73C ARG* 1.3 62.0 + - + +
75C GLN* 3.5 2.1 + - - +
76C ARG* 3.0 65.7 + - + +
79C ARG* 5.9 0.3 + - - -
131C THR* 3.7 37.0 - - + -
134C ALA* 3.7 20.3 - - + +
135C LEU* 3.7 34.9 - - + +
138C TYR* 4.3 8.5 - + + -
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY 4.1 5.5 - - - +
334B GLY 5.2 1.3 - - - +
337B ARG* 4.9 2.4 - - - +
338B ALA* 3.6 24.2 - - + +
341B SER* 3.1 36.6 + - - -
66C GLU* 4.3 4.9 + - - +
69C ARG* 2.9 37.4 + - + +
70C ALA* 3.0 27.6 + - - +
72C TYR* 1.3 81.8 - - + +
74C ILE* 1.3 57.5 + - - +
76C ARG* 3.7 30.9 + - - +
77C ALA* 3.1 26.0 + - - +
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 4.3 20.0 - - + +
338B ALA* 3.9 12.8 - - + -
339B ASN* 3.4 33.7 - - - +
342B LEU* 4.3 18.4 - - + -
70C ALA 2.8 22.5 + - - +
71C GLN* 3.8 13.2 - - + +
72C TYR 3.3 0.4 - - - -
73C ARG* 1.3 71.8 - - - +
75C GLN* 1.3 68.1 + - + +
77C ALA* 3.3 15.0 + - - +
78C ASP* 3.1 23.7 - - - +
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Residues in contact with GLN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLN 3.3 15.1 + - - +
72C TYR 4.0 2.9 - - - +
74C ILE* 1.3 79.3 - - + +
76C ARG* 1.3 67.9 + - - +
77C ALA 3.4 0.2 + - - -
78C ASP* 3.5 30.5 + - - +
79C ARG* 3.7 2.8 + - - +
127C VAL* 4.8 5.4 - - - +
130C LEU* 3.9 43.6 - - - +
131C THR* 3.4 26.7 + - - +
134C ALA* 4.4 7.0 - - + -
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Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY 4.9 4.7 + - - +
69C ARG* 5.0 7.1 - - - +
72C TYR* 3.0 52.2 + - + +
73C ARG* 3.7 30.4 + - - +
75C GLN* 1.3 75.8 - - - +
77C ALA* 1.3 57.4 + - - +
79C ARG* 2.8 43.9 + - + +
80C VAL* 3.7 5.6 + - - +
131C THR* 3.9 23.6 + - + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY* 3.3 38.0 + - - +
335B ARG* 3.5 34.5 + - + +
73C ARG 3.1 10.8 + - - +
74C ILE 3.4 10.8 - - - +
75C GLN 3.2 0.6 - - - -
76C ARG* 1.3 74.1 - - - +
78C ASP* 1.3 62.9 + - - +
79C ARG 3.1 1.2 + - - -
80C VAL* 3.1 24.9 + - - +
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 2.8 31.3 + - - +
74C ILE* 3.1 16.8 - - - +
75C GLN* 3.5 24.2 + - - +
76C ARG 3.3 0.2 - - - -
77C ALA* 1.3 73.4 - - - +
79C ARG* 1.3 61.6 + - - +
80C VAL 3.6 4.1 + - - +
118C GLU* 5.7 0.7 - - - +
119C TYR* 4.9 5.4 - - - -
120C GLU* 5.1 7.6 + - - +
127C VAL* 5.0 15.9 - - + +
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 5.9 0.4 + - - -
75C GLN 3.7 3.2 + - - +
76C ARG* 2.8 38.4 + - + +
78C ASP* 1.3 73.7 - - - +
80C VAL* 1.3 60.2 + - + +
119C TYR* 3.3 20.4 + - - -
120C GLU 4.7 2.6 - - - +
122C ASP* 4.4 9.1 + - - +
127C VAL* 3.8 29.9 - - + +
128C LYS* 3.7 40.2 - - - +
131C THR* 4.0 23.1 + - - +
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP 4.3 5.2 - - - +
333B GLY* 3.8 22.0 + - - -
76C ARG 4.5 3.8 - - - +
77C ALA* 3.1 22.4 - - - +
78C ASP 4.0 3.5 - - - +
79C ARG* 1.3 85.3 - - + +
81C PRO* 1.4 77.0 - - + +
82C GLY 3.7 1.7 + - - -
119C TYR* 3.5 6.4 - - - -
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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