Contacts of the helix formed by residues 10 - 36 (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 THR 10 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 3.8 17.0 - - - +
9F SER* 1.3 70.2 - - - +
11F GLU* 1.3 71.2 + - - +
13F GLU* 3.7 10.9 - - - +
14F ALA* 2.8 32.6 + - - +
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 3.3 12.7 - - - +
10F THR* 1.3 87.7 + - - +
12F VAL* 1.3 55.7 + - - +
14F ALA* 3.7 4.8 - - - +
15F ALA* 3.0 27.0 + - - +
116F LEU* 3.5 25.8 - - + +
120F GLN* 3.8 19.0 + - - +
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.4 28.9 - - + +
9F SER* 3.3 22.7 + - - +
10F THR 3.3 0.2 - - - -
11F GLU* 1.3 73.9 - - - +
13F GLU* 1.3 56.8 + - - +
15F ALA* 2.9 3.0 + - - +
16F VAL* 2.8 34.8 + - + +
113F LEU* 4.4 1.1 - - + -
116F LEU* 3.9 17.9 - - + -
117F GLY* 4.6 3.8 - - - -
120F GLN* 4.1 15.3 - - + -
122F ASP* 4.4 7.6 - - - +
125F LEU* 3.8 36.8 - - + -
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 2.7 37.4 + - - -
8F TYR* 3.8 18.8 - - + -
9F SER 2.9 16.5 + - - +
10F THR* 3.7 14.1 - - - +
12F VAL* 1.3 74.5 - - - +
14F ALA* 1.3 61.8 + - - +
16F VAL 3.5 0.3 + - - -
17F ASN* 3.1 21.3 + - - +
69F GLN* 3.3 25.2 + - - +
74F GLY* 3.6 2.0 - - - -
75F ARG* 2.9 36.9 + - - +
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F THR 2.8 18.1 + - - +
11F GLU* 3.7 5.2 - - - +
13F GLU* 1.3 77.8 - - - +
15F ALA* 1.4 64.0 - - - +
17F ASN* 3.1 11.2 + - - +
18F ARG* 3.0 21.3 + - - +
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Residues in contact with ALA 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLU 3.0 17.7 + - - +
12F VAL 2.9 5.3 + - - +
14F ALA* 1.4 74.4 - - - +
16F VAL* 1.4 60.2 + - - +
18F ARG* 3.1 10.1 + - - +
19F LEU* 2.9 28.8 + - - +
113F LEU* 3.5 28.2 - - + +
116F LEU* 3.9 9.2 - - + -
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Residues in contact with VAL 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.6 14.8 - - - +
12F VAL* 2.8 29.3 + - + +
13F GLU 3.7 4.0 - - - +
15F ALA* 1.4 71.5 - - - +
17F ASN* 1.3 64.3 + - - +
19F LEU* 3.1 8.8 + - - +
20F VAL* 2.9 25.8 + - + +
65F LEU* 4.1 27.8 - - + +
68F MET* 3.9 20.6 - - + -
69F GLN* 3.7 22.4 - - + +
113F LEU* 4.1 16.6 - - + -
125F LEU* 4.2 0.7 - - + -
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Residues in contact with ASN 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 3.1 13.9 + - - +
14F ALA* 3.1 12.6 + - - +
16F VAL* 1.3 78.3 - - - +
18F ARG* 1.3 58.0 + - - +
20F VAL* 3.7 8.2 - - - +
21F ASN* 3.5 15.8 + - - +
66F LEU* 5.2 4.3 - - - +
69F GLN* 3.0 17.4 + - - +
75F ARG 2.8 24.0 + - - -
76F ALA* 3.2 7.3 - - - +
77F LEU* 3.0 48.6 + - + +
79F GLN* 4.3 9.0 + - - +
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Residues in contact with ARG 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ALA 3.0 11.7 + - - +
15F ALA* 3.1 11.4 + - - +
17F ASN* 1.3 74.1 - - - +
19F LEU* 1.3 66.0 + - - +
20F VAL 3.3 0.2 - - - -
21F ASN* 3.0 9.1 + - + +
22F LEU* 3.0 49.2 + - + +
79F GLN* 4.9 13.9 - - - +
109F ALA* 4.2 24.9 + - - +
112F ASP* 5.7 2.8 + - - +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ALA 2.9 13.2 + - - +
16F VAL* 3.1 8.9 + - - +
18F ARG* 1.3 78.6 - - - +
20F VAL* 1.3 62.0 + - - +
22F LEU* 3.2 10.2 + - + +
23F TYR* 2.9 41.9 + - + -
65F LEU* 3.8 25.6 - - + -
106F LEU* 4.8 1.3 - - + +
109F ALA* 3.6 34.5 - - + +
110F LEU* 3.6 28.3 - - + +
113F LEU* 3.6 25.1 - - + -
129F LEU* 4.9 0.2 - - + -
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F VAL* 2.9 22.7 + - + +
17F ASN* 3.7 12.8 - - - +
19F LEU* 1.3 75.4 - - - +
21F ASN* 1.3 57.0 + - - +
23F TYR* 3.9 3.9 - - - +
24F LEU* 3.0 46.0 + - + +
62F ALA* 4.1 7.6 - - + +
65F LEU* 3.7 29.6 - - + -
66F LEU* 3.6 39.9 - - + +
69F GLN* 6.1 0.2 - - - +
77F LEU 5.8 0.9 - - - +
78F PHE* 4.2 9.4 - - + -
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Residues in contact with ASN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASN 3.5 10.1 + - - +
18F ARG* 3.0 12.8 + - + +
20F VAL* 1.3 79.7 - - - +
22F LEU* 1.3 61.1 + - + +
24F LEU* 3.3 7.1 + - - +
25F ARG* 2.8 35.0 + - - +
77F LEU 6.1 0.2 - - - +
78F PHE* 6.5 0.2 - - - -
79F GLN* 3.5 36.4 + - - +
80F ASP 3.1 25.8 + - - +
81F LEU* 3.7 12.9 - - - +
82F GLN 5.7 0.3 + - - -
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Residues in contact with LEU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ARG* 3.0 50.6 + - + +
19F LEU* 3.5 11.7 - - + +
21F ASN* 1.3 80.8 - - - +
23F TYR* 1.3 57.5 + - - +
25F ARG* 3.3 5.5 + - - +
26F ALA* 2.8 29.6 + - - +
102F LEU* 5.8 0.2 - - - +
105F SER* 4.7 8.1 - - - +
106F LEU* 3.9 21.1 - - + +
109F ALA* 3.7 30.7 - - + -
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Residues in contact with TYR 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 2.9 48.5 + - + +
20F VAL* 4.6 0.2 - - - -
22F LEU* 1.3 72.4 - - - +
24F LEU* 1.3 53.2 + - - +
26F ALA* 3.1 7.4 + - - +
27F SER* 2.8 34.3 + - - -
57F GLU 5.5 0.2 - - - -
58F LYS* 3.6 48.7 - - + +
61F GLY* 4.0 4.7 - - - -
62F ALA* 3.8 26.9 - - + +
65F LEU* 4.0 8.3 - - + -
106F LEU* 4.2 17.7 - - + +
110F LEU* 3.7 18.7 - - + +
133F PHE* 3.4 30.8 - + - -
136F GLU* 5.6 4.2 + - - -
137F GLU* 3.8 10.6 + - - -
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Residues in contact with LEU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 3.0 35.8 + - + +
21F ASN* 3.6 4.7 - - - +
23F TYR* 1.3 75.3 - - - +
25F ARG* 1.3 55.4 + - - +
27F SER* 3.3 7.4 - - - -
28F TYR* 3.0 26.2 + - - +
59F ARG* 4.7 17.0 - - + +
62F ALA* 3.4 24.0 - - + -
63F GLU* 6.1 1.3 - - + -
66F LEU* 5.4 2.7 - - + -
78F PHE* 4.4 18.8 - - + -
81F LEU* 3.9 31.3 - - + +
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Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASN* 2.8 27.2 + - - +
22F LEU* 3.8 6.1 - - - +
24F LEU* 1.3 73.2 - - - +
26F ALA* 1.3 56.6 + - - +
28F TYR* 3.2 6.9 + - - +
29F THR* 2.9 44.5 + - - -
81F LEU* 4.3 6.6 - - + +
82F GLN* 3.2 59.9 + - + +
83F LYS 3.5 15.5 + - - -
84F PRO 4.9 0.2 - - - -
85F SER* 4.7 18.7 + - - +
102F LEU* 5.2 11.1 - - - +
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU 2.8 18.2 + - - +
23F TYR 3.1 7.8 + - - +
25F ARG* 1.3 68.6 - - - +
27F SER* 1.3 66.1 + - - +
29F THR* 3.1 4.4 + - - -
30F TYR* 2.9 30.1 + - + -
58F LYS* 4.1 9.0 - - + -
102F LEU* 4.1 27.4 - - + -
106F LEU* 3.8 27.1 - - + -
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Residues in contact with SER 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR 2.8 12.7 + - - -
24F LEU* 3.3 15.9 - - - -
26F ALA* 1.3 75.6 - - - +
28F TYR* 1.3 56.1 + - - +
30F TYR* 3.2 4.7 + - - +
31F LEU* 2.9 26.6 + - - +
55F ALA* 2.8 32.9 + - - +
58F LYS* 3.8 12.6 - - - +
59F ARG* 3.6 16.3 + - - +
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU 3.0 13.3 + - - +
25F ARG* 3.2 11.2 + - - +
27F SER* 1.3 73.3 - - - +
29F THR* 1.3 62.2 + - - +
31F LEU* 3.3 23.4 + - + +
32F SER* 3.1 20.1 + - - -
81F LEU* 4.4 22.0 - - + -
82F GLN 3.7 17.5 - - - +
83F LYS* 3.7 23.7 - - - +
84F PRO* 3.7 16.8 - - + +
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Residues in contact with THR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ARG* 2.9 29.1 + - - -
26F ALA* 3.1 7.7 + - - -
28F TYR* 1.3 76.5 - - - +
30F TYR* 1.3 57.7 + - - +
32F SER* 3.1 5.2 + - - -
33F LEU* 2.8 35.0 + - + +
84F PRO* 3.6 18.7 - - + +
85F SER* 5.0 3.0 + - - +
89F TRP* 3.8 27.5 - - + -
102F LEU* 4.0 22.0 - - + +
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Residues in contact with TYR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ALA* 2.9 24.3 + - + -
27F SER 3.6 4.5 - - - +
29F THR* 1.3 70.6 - - - +
31F LEU* 1.3 59.8 + - - +
33F LEU* 3.7 12.5 - - + +
34F GLY* 2.8 29.1 + - - -
51F PHE* 3.5 49.2 - + - +
54F LEU* 3.7 29.8 - - + -
55F ALA* 3.6 9.9 - - - +
58F LYS* 4.0 11.9 - - + -
99F ALA* 3.6 19.5 + - + -
102F LEU* 3.8 18.2 - - + +
103F GLU* 2.6 39.0 + - - +
144F MET* 3.6 7.8 - - - +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F SER 2.9 13.2 + - - +
28F TYR* 3.4 29.2 - - + +
30F TYR* 1.3 72.9 - - - +
32F SER* 1.3 62.4 + - - +
34F GLY* 3.9 0.8 - - - -
35F PHE* 3.1 56.7 + - + -
52F ARG* 4.8 13.0 - - - +
55F ALA* 3.9 13.1 - - + +
56F GLU* 5.8 2.7 - - - +
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Residues in contact with SER 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TYR* 3.1 11.9 + - - -
29F THR 3.3 8.1 - - - -
31F LEU* 1.3 78.4 - - - +
33F LEU* 1.3 64.0 + - - +
35F PHE* 3.6 2.8 + - - +
36F TYR* 3.2 22.3 + - - +
84F PRO* 3.9 16.8 - - - +
86F GLN 4.0 5.7 + - - -
87F ASP* 4.9 4.0 + - - -
89F TRP* 3.0 21.8 + - - -
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F THR* 2.8 30.0 + - + +
30F TYR* 3.7 33.7 - - + +
32F SER* 1.3 70.9 + - - +
34F GLY* 1.3 63.9 + - - +
36F TYR* 3.1 17.7 + - - +
37F PHE* 3.2 16.8 - - + -
51F PHE* 3.9 20.6 - - + -
89F TRP* 3.5 43.3 - - + +
95F ALA* 3.7 30.7 - - + +
98F ALA* 5.3 1.1 - - + -
99F ALA* 4.8 9.0 - - + +
102F LEU* 5.6 0.2 - - + -
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Residues in contact with GLY 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR 2.8 19.9 + - - -
31F LEU 3.9 0.9 - - - -
33F LEU* 1.3 73.6 - - - +
35F PHE* 1.3 61.8 + - - +
36F TYR 3.1 1.0 + - - -
37F PHE 3.2 9.9 + - - -
38F ASP 3.5 1.2 + - - -
48F CYS* 3.4 36.2 - - - +
51F PHE* 3.7 15.3 - - - +
52F ARG* 4.0 7.9 - - - -
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Residues in contact with PHE 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.1 51.6 + - + +
32F SER* 4.4 3.4 - - - +
34F GLY* 1.3 71.6 - - - +
36F TYR* 1.3 65.7 + - - +
37F PHE 3.4 0.2 - - - -
38F ASP* 3.4 34.2 + - + +
39F ARG* 3.6 9.2 + - - +
48F CYS* 5.7 0.9 - - - -
52F ARG* 3.5 42.4 - - - -
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Residues in contact with TYR 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F SER 3.2 12.8 + - - +
33F LEU 3.1 10.6 + - - +
35F PHE* 1.3 75.7 - - - +
37F PHE* 1.3 83.7 + + - +
39F ARG* 3.0 64.1 + - - +
42F VAL* 3.8 21.5 - - + +
87F ASP 4.4 4.7 - - - +
88F GLU* 3.8 19.8 + - + +
89F TRP* 3.5 34.3 - + + -
90F GLY* 2.9 42.1 + - - -
----------------------------------------------------------
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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