Contacts of the helix formed by residues 45 - 72 (chain F) in PDB entry 1IES
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 GLU 45 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE 5.0 0.4 - - - -
38F ASP* 6.3 0.2 - - - +
43F ALA 3.8 4.4 + - - +
44F LEU* 1.3 73.0 - - - +
46F GLY* 1.3 58.5 + - - +
48F CYS* 3.4 10.4 + - + +
49F HIS* 2.9 33.7 + - - +
167F GLU* 3.5 9.0 + - - +
168F ARG* 4.4 7.0 + - - +
172F LYS* 3.4 29.3 + - + -
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Residues in contact with GLY 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F GLU* 1.3 71.7 - - - +
47F VAL* 1.3 60.6 + - - +
49F HIS* 3.3 7.9 - - - +
50F PHE* 2.9 27.9 + - - +
167F GLU* 2.8 23.7 + - - -
171F LEU* 3.8 26.5 - - - +
172F LYS* 5.0 4.6 - - - +
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 3.6 27.6 - - + -
44F LEU* 3.0 23.4 + - + +
46F GLY* 1.3 72.6 - - - +
48F CYS* 1.3 66.9 + - - +
50F PHE* 3.2 5.8 + - + +
51F PHE* 3.1 44.5 + - + -
92F THR* 3.9 27.6 - - + +
96F MET* 5.6 1.3 - - + -
166F PHE* 5.3 0.2 - - + -
167F GLU* 4.1 10.3 - - + -
171F LEU* 3.7 24.0 - - + -
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Residues in contact with CYS 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F GLY* 3.4 29.9 - - - +
35F PHE* 5.2 1.1 - - - -
37F PHE* 3.7 14.2 - - + +
38F ASP* 4.2 15.3 - - + -
44F LEU 3.0 12.5 + - - +
45F GLU* 3.5 12.3 - - - +
47F VAL* 1.3 76.1 - - - +
49F HIS* 1.3 65.3 + - - +
51F PHE* 3.2 0.9 + - - -
52F ARG* 2.9 46.8 + - - +
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Residues in contact with HIS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F GLU* 2.9 20.6 + - - +
46F GLY* 3.3 14.1 - - - +
48F CYS* 1.3 80.6 - - - +
50F PHE* 1.3 63.2 + - - +
52F ARG* 3.3 4.9 + - + +
53F GLU* 2.9 59.0 + - + +
171F LEU 6.2 0.2 - - - +
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Residues in contact with PHE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F GLY 2.9 10.7 + - - +
47F VAL* 3.4 11.4 - - - +
49F HIS* 1.3 82.2 - - - +
51F PHE* 1.3 93.4 + + - +
53F GLU* 3.1 17.7 + - + +
54F LEU* 3.2 32.6 + - + +
96F MET* 3.5 29.4 - - + -
140F LEU* 4.9 1.1 - - + -
143F LYS* 4.0 22.9 - - + -
144F MET* 4.2 15.9 - - + -
147F HIS* 3.8 28.7 - + - -
171F LEU* 4.5 15.9 - - + -
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Residues in contact with PHE 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.5 34.1 - + + +
33F LEU* 3.9 15.9 - - + -
34F GLY* 3.7 20.4 - - - +
37F PHE* 4.0 7.6 - + - -
47F VAL* 3.1 40.2 + - + +
50F PHE* 1.3 104.5 - + - +
52F ARG* 1.3 64.4 + - - +
54F LEU* 3.2 5.1 + - + +
55F ALA 2.9 19.8 + - - -
92F THR 5.8 0.2 - - - -
95F ALA* 3.8 35.7 - - + -
96F MET* 4.3 8.7 - - + -
99F ALA* 3.8 21.8 - - + -
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Residues in contact with ARG 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR 4.9 1.1 - - - -
31F LEU* 4.8 12.2 - - - +
34F GLY* 4.0 9.0 - - - -
35F PHE* 3.5 50.5 - - - -
48F CYS* 2.9 39.5 + - - +
49F HIS* 3.9 6.1 - - + +
51F PHE* 1.3 74.9 - - - +
53F GLU* 1.3 63.3 + - + +
55F ALA* 3.3 16.2 + - - +
56F GLU* 3.3 29.2 + - - +
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F HIS* 2.9 44.9 + - + +
50F PHE* 3.4 11.2 + - + +
52F ARG* 1.3 75.7 - - + +
54F LEU* 1.3 64.2 + - + +
56F GLU* 3.1 8.7 + - - +
57F GLU* 2.9 27.4 + - - +
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.7 31.6 - - + -
50F PHE* 3.2 29.1 + - + +
51F PHE* 3.2 13.1 + - + +
53F GLU* 1.3 76.8 - - + +
55F ALA* 1.3 61.9 + - - +
57F GLU* 3.1 19.8 + - + +
58F LYS* 2.9 28.9 + - - +
140F LEU* 3.8 34.8 - - + -
143F LYS* 5.8 1.1 - - - +
144F MET* 3.5 27.6 - - + -
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Residues in contact with ALA 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F SER* 2.8 42.0 + - - +
30F TYR* 3.6 16.0 - - + +
31F LEU* 3.9 18.4 - - + +
51F PHE 2.9 9.9 + - - +
52F ARG* 3.3 12.1 + - - +
54F LEU* 1.3 73.2 - - - +
56F GLU* 1.3 70.6 + - - +
58F LYS 3.3 0.5 + - - -
59F ARG* 3.0 11.4 + - - +
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 5.8 2.8 - - - +
52F ARG* 3.3 26.0 + - - +
53F GLU* 3.1 10.3 + - - +
55F ALA* 1.3 84.7 - - - +
57F GLU* 1.3 64.5 + - - +
59F ARG* 3.1 40.7 + - - +
60F GLU* 3.0 33.4 + - - +
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 5.5 0.3 - - - -
53F GLU* 2.9 17.8 + - - +
54F LEU* 3.1 27.8 + - + +
56F GLU* 1.3 78.1 - - - +
58F LYS* 1.3 61.6 + - + +
60F GLU* 3.3 14.7 + - - +
61F GLY* 2.9 23.4 + - - -
136F GLU* 3.9 31.2 - - - +
140F LEU* 4.9 7.7 - - - +
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Residues in contact with LYS 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 3.6 45.4 - - + +
26F ALA* 4.1 4.7 - - + -
27F SER* 3.8 10.1 - - - +
30F TYR* 4.0 17.5 - - + -
54F LEU* 2.9 25.7 + - - +
55F ALA 3.8 1.3 - - - +
57F GLU* 1.3 73.0 + - - +
59F ARG* 1.3 64.5 + - - +
61F GLY* 3.1 1.4 + - - -
62F ALA* 3.0 22.3 + - - +
103F GLU* 2.9 40.4 + - - -
106F LEU* 3.9 11.3 - - + +
136F GLU* 4.6 10.3 + - - +
137F GLU* 3.3 16.8 + - - -
140F LEU* 4.0 11.9 - - - +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU* 4.7 9.8 - - + +
27F SER* 3.6 13.8 + - - +
55F ALA 3.0 16.0 + - - +
56F GLU* 3.1 41.4 + - - +
58F LYS* 1.3 75.0 - - - +
60F GLU* 1.3 94.4 + - - +
62F ALA* 3.5 7.6 + - - +
63F GLU* 3.1 55.0 + - + +
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Residues in contact with GLU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLU* 3.0 18.8 + - - +
57F GLU* 3.5 17.6 - - - +
59F ARG* 1.3 103.4 + - - +
61F GLY* 1.3 64.8 + - - +
63F GLU* 3.2 9.1 + - - +
64F ARG* 3.0 36.9 + - - +
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Residues in contact with GLY 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 4.0 9.6 - - - -
57F GLU 2.9 14.6 + - - -
58F LYS 3.1 4.6 + - - -
60F GLU* 1.3 72.4 - - - +
62F ALA* 1.3 61.4 + - - +
64F ARG* 3.1 10.4 + - - +
65F LEU* 3.0 20.8 + - - +
133F PHE* 3.6 28.9 - - - -
136F GLU* 6.1 1.1 - - - -
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Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 4.1 15.1 - - + +
23F TYR* 3.8 17.6 - - + +
24F LEU* 3.4 33.2 - - + -
58F LYS 3.0 10.5 + - - +
59F ARG 3.6 4.5 - - - +
61F GLY* 1.3 73.9 - - - +
63F GLU* 1.3 57.6 + - + +
65F LEU* 3.3 10.4 + - - +
66F LEU* 3.0 32.8 + - + +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU* 6.1 1.1 - - + -
59F ARG* 3.1 49.3 + - + +
60F GLU* 3.2 10.6 + - - +
62F ALA* 1.3 74.8 - - + +
64F ARG* 1.3 57.2 + - - +
66F LEU* 3.3 17.6 + - + +
67F LYS* 2.9 29.1 + - - +
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Residues in contact with ARG 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F GLU* 3.0 27.7 + - - +
61F GLY* 3.5 10.4 - - - +
63F GLU* 1.3 75.6 - - - +
65F LEU* 1.3 62.6 + - - +
67F LYS* 3.4 12.8 + - + +
68F MET* 3.1 22.0 + - - +
128F PHE* 3.7 10.3 - - + -
132F HIS* 3.7 49.6 + - + +
133F PHE* 4.2 11.4 - - + -
136F GLU* 5.6 4.2 + - - -
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F VAL* 4.1 12.2 - - + +
19F LEU* 3.8 39.3 - - + -
20F VAL* 3.7 23.3 - - + +
23F TYR* 4.0 16.4 - - + -
61F GLY 3.0 17.4 + - - +
62F ALA* 3.6 6.5 - - - +
64F ARG* 1.3 74.6 - - - +
66F LEU* 1.3 57.2 + - - +
68F MET* 3.0 16.9 + - + +
69F GLN* 2.9 29.9 + - - +
128F PHE* 3.7 22.6 - - + -
129F LEU* 4.7 4.9 - - + -
133F PHE* 3.7 12.3 - - + -
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASN* 5.2 2.9 - - - +
20F VAL* 3.6 33.2 - - + -
24F LEU* 5.4 2.7 - - + -
62F ALA* 3.0 16.4 + - + +
63F GLU* 3.3 21.7 + - + +
65F LEU* 1.3 74.8 - - - +
67F LYS* 1.3 61.2 + - - +
69F GLN* 3.3 8.0 - - + +
70F ASN* 3.2 25.1 + - - +
76F ALA* 4.1 18.9 - - + +
78F PHE* 3.8 34.3 - - + -
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS* 4.6 14.5 - - - +
63F GLU 2.9 15.8 + - - +
64F ARG* 3.8 12.7 - - + +
65F LEU 3.4 0.2 - - - -
66F LEU* 1.3 75.3 - - - +
68F MET* 1.3 57.8 + - - +
70F ASN* 3.3 10.2 + - + +
71F GLN* 2.9 47.7 + - + +
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Residues in contact with MET 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 4.2 9.9 - - - -
16F VAL* 3.9 20.0 - - + -
64F ARG 3.1 13.3 + - - +
65F LEU* 3.0 16.7 + - + +
67F LYS* 1.3 73.0 - - - +
69F GLN* 1.3 59.6 + - - +
71F GLN* 2.8 29.7 + - - +
72F ARG* 2.9 38.7 + - + +
124F HIS* 4.5 11.9 - - + -
125F LEU* 3.6 32.3 - - + -
128F PHE* 3.6 45.3 - - + -
129F LEU* 5.5 0.2 - - + -
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Residues in contact with GLN 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 2.6 42.7 + - - -
13F GLU* 3.3 15.6 + - - +
16F VAL* 3.7 13.6 - - + +
17F ASN* 3.0 36.8 + - - +
65F LEU 2.9 11.9 + - - +
66F LEU* 3.3 15.3 - - + +
68F MET* 1.3 77.8 - - - +
70F ASN* 1.3 62.2 + - - +
72F ARG* 3.4 1.4 + - - +
73F GLY 3.3 3.1 + - - -
74F GLY* 2.9 39.4 + - - +
75F ARG 3.7 6.9 + - - -
76F ALA* 3.9 17.7 - - + +
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Residues in contact with ASN 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 3.2 26.8 - - - +
4F ILE* 3.9 4.5 - - - +
66F LEU 3.2 11.6 + - - +
67F LYS* 3.6 12.4 - - + +
68F MET 3.2 0.4 - - - -
69F GLN* 1.3 82.0 - - - +
71F GLN* 1.3 59.4 + - + +
72F ARG 3.6 0.2 + - - -
73F GLY* 3.7 7.3 + - - -
74F GLY 4.0 12.2 - - - +
75F ARG* 4.3 13.8 + - - +
76F ALA* 5.3 7.9 + - - +
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Residues in contact with GLN 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ASP* 4.6 4.4 + - - -
138D VAL* 4.0 26.5 - - + +
139D LYS* 3.4 47.3 + - - +
142D LYS* 3.5 24.6 - - + +
4F ILE* 3.4 14.6 - - - +
67F LYS* 2.9 36.2 + - + +
68F MET* 2.8 19.1 + - - +
70F ASN* 1.3 73.3 - - - +
72F ARG* 1.3 62.4 + - + +
124F HIS* 5.0 4.6 - - - -
128F PHE* 6.2 1.6 - - - -
----------------------------------------------------------
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 5.8 1.0 + - - -
138D VAL* 4.0 18.5 - - - +
4F ILE* 4.4 2.3 - - - +
5F ARG* 3.3 26.7 - - - +
6F GLN* 2.8 27.4 + - - +
7F ASN* 3.2 16.6 + - - +
8F TYR* 3.6 42.4 - - + +
68F MET* 2.9 32.5 + - - +
69F GLN 3.9 0.2 - - - +
70F ASN 3.3 0.2 - - - -
71F GLN* 1.3 76.8 - - + +
73F GLY* 1.3 58.7 + - - +
74F GLY 3.5 0.4 - - - -
122F ASP* 2.8 38.4 + - - -
124F HIS* 3.5 34.6 + - + +
125F LEU* 5.2 1.6 - - - +
----------------------------------------------------------
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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