Contacts of the helix formed by residues 55 - 77 (chain E) in PDB entry 1I3R
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 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLU* 3.9 24.2 - - + +
96D GLN* 4.7 19.1 - - - +
53E SER* 5.8 1.1 - - - +
54E PHE* 1.3 92.6 - - - +
56E ALA* 1.3 65.2 + - - +
57E GLN* 3.4 4.3 - - + +
58E GLY* 3.4 13.9 + - - +
4F VAL* 4.0 26.9 - - + +
5F ILE 5.5 1.0 - - - +
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Residues in contact with ALA 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLU* 4.2 5.4 + - - +
34E VAL* 4.0 12.7 - - + +
39E SER* 3.5 35.2 - - - +
40E GLU* 3.9 4.7 - - - +
41E THR* 3.9 14.8 - - - +
54E PHE 3.4 4.8 + - - -
55E GLU* 1.3 69.2 - - - +
57E GLN* 1.3 61.1 + - - +
59E ALA* 2.8 23.4 + - - +
60E LEU* 3.0 15.2 + - - +
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASN* 5.0 8.7 - - - +
10D GLU 4.8 0.4 + - - +
11D GLY* 3.7 8.8 - - - -
12D LEU* 3.0 48.6 - - - +
87D TRP* 4.2 2.8 + - - -
90D GLN* 2.7 35.1 + - - +
93D PHE* 3.6 31.4 - - + -
96D GLN* 5.6 3.6 - - - +
39E SER* 3.3 9.7 + - - -
55E GLU* 3.4 3.2 - - + +
56E ALA* 1.3 75.9 - - - +
58E GLY* 1.3 52.7 + - - +
60E LEU* 3.0 11.1 + - - +
61E ALA* 2.7 35.4 + - - +
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Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASN* 5.3 6.4 - - - +
54E PHE* 5.2 4.3 - - - -
55E GLU* 3.4 11.8 + - - +
56E ALA 3.2 1.2 - - - -
57E GLN* 1.3 77.6 - - - +
59E ALA* 1.3 56.7 + - - +
61E ALA* 3.2 9.9 - - - +
62E ASN* 3.1 31.5 + - - +
7F ALA* 5.8 3.1 - - - -
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Residues in contact with ALA 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E PHE* 3.6 36.2 - - + -
34E VAL* 3.7 23.8 - - + -
54E PHE* 3.9 10.7 - - + -
55E GLU 3.8 2.4 + - - -
56E ALA 2.8 11.1 + - - +
58E GLY* 1.3 73.9 - - - +
60E LEU* 1.3 67.1 + - - +
61E ALA 3.0 1.1 - - - -
62E ASN* 3.1 4.4 + - - +
63E ILE* 2.9 27.8 + - - +
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 3.7 29.0 - - + +
34E VAL* 4.6 6.3 - - + -
35E ASP 4.4 2.0 - - - +
36E ILE* 3.3 49.1 - - + +
39E SER* 3.5 35.7 - - - +
56E ALA 3.0 13.6 + - - +
57E GLN* 3.5 20.6 - - - +
59E ALA* 1.3 76.5 - - - +
61E ALA* 1.3 62.5 + - - +
63E ILE* 3.4 7.0 + - + +
64E ALA* 2.9 22.5 + - - +
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 6.4 2.0 - - + -
65C VAL* 4.5 11.4 - - + +
9D ASN* 5.3 10.3 - - - +
10D GLU 5.5 2.0 - - - +
12D LEU* 3.7 14.1 - - + +
57E GLN 2.7 13.2 + - - +
58E GLY* 3.2 15.0 - - - +
60E LEU* 1.3 76.9 - - - +
62E ASN* 1.3 63.6 + - - +
64E ALA* 2.9 17.4 + - - +
65E VAL* 3.0 16.6 + - + +
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Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 3.6 3.4 - - - +
11E GLN* 3.4 32.8 + - - +
22E PHE* 4.0 13.9 - - + -
58E GLY 3.1 18.0 + - - +
59E ALA 3.1 7.6 + - - +
61E ALA* 1.3 77.6 - - - +
63E ILE* 1.3 61.9 + - - +
65E VAL* 3.0 13.5 + - - +
66E ASN* 3.0 23.2 + - - +
7F ALA* 4.7 5.4 - - - +
8F PHE 2.9 26.9 + - - +
9F ASN* 4.9 5.4 - - - +
10F GLU* 4.0 16.3 + - - +
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Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLN* 4.3 9.4 - - + -
12E PHE 3.9 7.2 - - - +
13E TYR* 4.3 22.6 - - + +
20E GLY* 4.5 8.1 - - - -
21E GLU 3.1 39.7 - - - +
22E PHE* 4.0 10.5 - - + -
36E ILE* 4.2 17.9 - - + -
59E ALA 2.9 21.5 + - - +
60E LEU* 3.5 12.3 - - + +
61E ALA 3.2 0.2 - - - -
62E ASN* 1.3 75.5 - - - +
64E ALA* 1.3 58.0 + - - +
66E ASN* 2.9 8.5 + - - +
67E LYS* 2.9 27.6 + - + +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.1 21.9 - - + +
65C VAL* 4.2 8.1 - - + -
68C ALA* 4.3 8.4 - - + +
12D LEU* 4.0 20.6 - - + -
60E LEU 2.9 12.5 + - - +
61E ALA* 2.9 12.6 + - - +
63E ILE* 1.3 75.4 - - - +
65E VAL* 1.3 64.2 + - - +
67E LYS* 3.1 10.5 + - - +
68E ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 4.4 15.3 - - + +
64C ALA* 4.2 14.8 - - + -
65C VAL* 6.3 0.2 - - + -
61E ALA 3.0 13.2 + - - +
62E ASN* 3.0 13.4 + - - +
64E ALA* 1.3 78.0 - - - +
66E ASN* 1.3 57.5 + - - +
68E ALA* 3.3 2.9 + - - +
69E ASN* 3.0 44.7 + - - +
10F GLU* 3.9 21.3 - - + +
11F GLY 3.7 11.4 - - - +
12F LEU* 3.9 24.7 - - + -
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Residues in contact with ASN 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLN* 2.6 48.8 + - - +
12E PHE* 4.2 6.6 + - - -
13E TYR* 4.1 17.9 - - + +
62E ASN 3.0 9.9 + - - +
63E ILE* 2.9 13.5 + - - +
65E VAL* 1.3 75.1 - - - +
67E LYS* 1.3 58.6 + - - +
69E ASN* 4.3 3.9 - - - +
70E LEU* 2.8 30.1 + - - +
10F GLU* 4.1 18.8 + - - +
35F GLU* 3.5 24.4 + - + +
37F CYS* 4.7 5.9 - - - +
56F TYR* 6.1 0.4 - - - -
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Residues in contact with LYS 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 4.6 12.9 - - - +
68C ALA* 4.2 27.9 - - + +
71C ASP* 2.7 33.0 + - - -
13E TYR* 3.5 54.6 - - + -
15E LEU* 6.1 0.2 - - - +
18E LYS* 6.2 2.0 - - - +
63E ILE* 2.9 12.0 + - + +
64E ALA* 3.1 12.1 + - - +
66E ASN* 1.3 78.6 - - - +
68E ALA* 1.3 62.7 + - - +
70E LEU* 3.3 10.9 + - - +
71E ASP* 3.4 18.1 + - - +
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Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA* 4.2 18.2 - - + +
67C LYS* 4.3 29.5 + - + +
64E ALA 3.0 10.9 + - - +
65E VAL 3.6 7.9 - - - +
67E LYS* 1.3 77.5 - - - +
69E ASN* 1.3 61.8 + - - +
71E ASP* 3.2 14.9 + - - +
72E VAL* 3.4 15.2 + - - +
12F LEU* 4.2 11.0 - - + -
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Residues in contact with ASN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 3.0 28.5 + - - +
66E ASN* 3.8 5.9 - - - +
68E ALA* 1.3 73.9 - - - +
70E LEU* 1.3 66.3 + - - +
72E VAL* 3.1 9.6 + - - +
73E MET* 2.9 27.4 + - - +
10F GLU* 4.6 6.7 - - - +
11F GLY 3.1 22.4 + - - -
12F LEU* 3.7 8.0 - - - +
13F LYS* 2.8 43.3 + - + +
35F GLU* 3.7 21.3 + - + +
56F TYR* 5.7 0.8 - - - -
87F TRP* 5.1 0.4 - - - -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.6 22.7 - - + +
15E LEU* 3.5 40.2 - - + -
66E ASN 2.8 19.0 + - - +
67E LYS* 3.5 7.9 - - - +
68E ALA 3.2 0.2 - - - -
69E ASN* 1.3 77.4 - - - +
71E ASP* 1.3 62.4 + - - +
73E MET* 3.3 3.2 + - - +
74E LYS* 3.0 22.2 + - + +
33F PHE* 3.5 39.3 - - + +
34F LEU 4.0 1.6 - - - -
35F GLU* 3.8 21.3 - - + +
58F TYR* 4.1 11.4 - - + -
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Residues in contact with ASP 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LYS* 5.9 5.4 - - - +
67C LYS* 2.8 30.8 + - - +
15E LEU* 4.3 18.0 - - - +
67E LYS* 3.4 11.5 + - - +
68E ALA 3.2 10.1 + - - +
69E ASN 3.2 0.8 - - - -
70E LEU* 1.3 79.5 - - - +
72E VAL* 1.3 62.7 + - + +
74E LYS* 3.1 13.4 + - - +
75E GLU* 3.1 25.6 + - - +
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Residues in contact with VAL 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ALA 3.4 13.0 + - - +
69E ASN* 3.1 10.6 + - - +
71E ASP* 1.3 78.5 - - + +
73E MET* 1.3 57.9 + - - +
75E GLU* 3.0 9.5 + - + +
76E ARG* 2.8 46.6 + - + +
13F LYS* 4.0 23.1 - - + +
14F GLY 3.3 27.6 - - - +
15F GLY* 5.1 2.5 - - - -
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Residues in contact with MET 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ASN 2.9 14.4 + - - +
70E LEU 3.7 6.7 - - - +
72E VAL* 1.3 76.0 - - - +
74E LYS* 1.3 62.9 + - - +
76E ARG* 3.4 30.9 + - - +
77E SER* 3.1 27.6 + - - -
13F LYS* 3.4 24.7 - - - +
35F GLU* 3.3 23.8 - - - +
58F TYR* 3.6 27.0 + - + -
63F ASN* 3.8 21.5 - - - +
79F LEU* 3.7 33.0 - - + +
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Residues in contact with LYS 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 4.2 22.2 - - + +
70E LEU* 3.0 19.6 + - + +
71E ASP* 3.1 15.6 + - - +
73E MET* 1.3 78.0 - - - +
75E GLU* 1.3 60.8 + - + +
77E SER 3.5 0.2 + - - -
78E ASN* 3.1 2.9 + - - -
79E ASN* 2.9 65.8 + - - +
33F PHE* 3.8 43.4 - - + -
58F TYR* 3.9 17.3 - - - +
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Residues in contact with GLU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LYS* 5.3 13.5 - - - +
71E ASP* 3.1 14.2 + - + +
72E VAL* 3.0 12.2 + - + +
74E LYS* 1.3 77.1 - - + +
76E ARG* 1.3 63.0 + - - +
78E ASN* 3.1 15.2 + - - +
79E ASN* 4.9 6.0 - - - +
18F SER* 4.7 8.7 + - - +
19F LEU 5.3 0.3 - - - +
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Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E VAL* 2.8 31.4 + - + +
73E MET* 3.5 22.4 - - - +
75E GLU* 1.3 71.7 - - - +
77E SER* 1.3 56.5 + - - +
78E ASN 3.5 0.2 - - - -
13F LYS* 4.0 3.6 - - - +
14F GLY 3.3 21.2 + - - -
16F GLY 3.7 13.7 + - - +
17F GLY 3.2 23.1 - - - +
18F SER* 4.3 9.0 - - - +
19F LEU* 2.9 30.3 + - - +
79F LEU* 2.7 47.7 + - + +
82F PRO* 3.9 16.3 - - - +
83F ASP* 2.6 45.8 + - - -
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Residues in contact with SER 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E MET 3.1 17.5 + - - -
74E LYS 3.6 3.3 + - - -
76E ARG* 1.3 76.9 - - - +
78E ASN* 1.3 58.4 + - - +
79E ASN 3.8 3.5 + - - -
80E THR* 2.6 37.5 + - - -
19F LEU* 3.9 6.5 - - - -
21F GLY* 3.3 9.9 - - - -
58F TYR* 3.3 31.1 + - - -
79F LEU* 4.3 14.4 - - - -
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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) + - + + + + + -
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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