Contacts of the helix formed by residues 56 - 78 (chain E) in PDB entry 1LNU
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 ASP 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E PHE* 1.3 87.4 - - - +
57E PRO* 1.3 65.0 - - - +
58E GLN* 2.7 49.7 + - - +
59E GLY* 3.0 18.7 + - - -
2F GLU* 2.9 17.7 + - - +
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Residues in contact with PRO 57 (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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35E VAL* 4.0 15.4 - - + +
40E LYS* 3.7 22.0 - - + +
41E GLU* 3.7 9.9 - - - +
42E THR* 3.1 32.3 - - - +
55E PHE 2.7 14.8 - - - +
56E ASP* 1.3 80.9 - - - +
58E GLN* 1.3 64.0 + - - +
59E GLY 3.1 0.2 - - - -
60E GLY* 3.3 11.1 + - - -
61E LEU* 3.3 17.1 + - + +
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Residues in contact with GLN 58 (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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56E ASP* 2.7 46.9 + - - +
57E PRO* 1.3 78.9 - - - +
59E GLY* 1.3 83.7 + - - +
61E LEU* 3.6 13.2 - - + +
62E GLN* 2.7 60.9 + - - +
5F LYS* 5.4 0.6 - - - +
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Residues in contact with GLY 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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55E PHE* 4.7 2.0 - - - -
56E ASP 3.0 6.9 + - - -
58E GLN* 1.3 101.1 - - - +
60E GLY* 1.3 54.7 + - - +
62E GLN* 3.1 4.3 - - - +
63E ASN* 3.1 12.6 + - - +
5F LYS* 2.8 46.9 + - - -
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Residues in contact with GLY 60 (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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23E TYR* 3.6 37.0 - - - -
35E VAL* 4.8 4.0 - - - -
37E LEU* 4.9 2.0 - - - -
55E PHE* 4.1 6.7 - - - -
56E ASP 4.1 2.0 + - - -
57E PRO 3.3 8.1 + - - -
58E GLN 3.2 0.4 - - - -
59E GLY* 1.3 73.6 - - - +
61E LEU* 1.3 65.1 + - - +
63E ASN 3.1 1.6 + - - -
64E ILE* 3.1 28.5 + - - +
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Residues in contact with LEU 61 (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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35E VAL* 5.3 2.0 - - + +
36E ASP 4.9 0.2 - - - +
37E LEU* 3.5 43.0 - - + +
40E LYS* 3.4 42.4 - - + -
57E PRO* 3.3 15.8 + - + +
58E GLN* 3.3 15.2 + - + +
60E GLY* 1.3 74.2 - - - +
62E GLN* 1.3 62.3 + - - +
64E ILE* 3.2 17.7 + - + +
65E ALA* 3.3 11.8 + - - +
68E LYS* 5.4 0.3 + - - -
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Residues in contact with GLN 62 (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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58E GLN* 2.7 47.8 + - - +
59E GLY* 3.1 9.7 - - - +
61E LEU* 1.3 76.5 - - - +
63E ASN* 1.3 54.9 + - - +
65E ALA* 3.6 12.2 - - - +
66E VAL* 3.2 21.3 - - + +
5F LYS* 3.4 17.7 + - - +
7F LYS* 4.4 17.8 + - - +
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Residues in contact with ASN 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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10E GLY 3.7 2.0 + - - -
12E SER* 2.4 35.1 + - - +
23E TYR* 3.4 24.2 - - + -
59E GLY 3.1 5.5 + - - +
60E GLY 3.1 0.6 + - - +
62E GLN* 1.3 75.4 - - - +
64E ILE* 1.3 61.2 + - - +
65E ALA 3.2 0.4 - - - -
66E VAL* 3.2 7.9 + - - +
67E VAL* 2.9 33.6 + - - +
5F LYS* 3.2 20.8 + - - +
6F ALA 3.6 4.9 + - - +
7F LYS* 4.7 0.2 - - - +
8F ALA* 3.3 27.2 + - - +
37F PHE* 3.5 20.6 - - - -
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Residues in contact with ILE 64 (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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12E SER* 4.3 13.0 - - - -
13E VAL 4.1 12.3 - - - +
14E TYR* 4.0 20.9 - - + -
22E GLN 3.9 25.6 - - - +
23E TYR* 4.2 8.3 - - + -
37E LEU* 4.0 29.6 - - + -
60E GLY 3.1 14.9 + - - +
61E LEU* 3.2 8.9 + - + +
63E ASN* 1.3 75.5 - - - +
65E ALA* 1.3 55.5 + - - +
67E VAL* 3.5 3.4 - - + +
68E LYS* 2.5 53.2 + - - +
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Residues in contact with ALA 65 (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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61E LEU 3.3 8.9 + - - +
62E GLN* 3.6 12.8 - - - +
64E ILE* 1.3 79.1 - - - +
66E VAL* 1.3 53.3 + - + +
68E LYS* 3.2 21.0 + - - +
69E HIS* 2.7 35.2 + - - +
10F LYS* 6.4 0.4 - - - -
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Residues in contact with VAL 66 (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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62E GLN* 3.2 20.0 - - + +
63E ASN* 3.4 13.0 - - - +
64E ILE 3.2 0.2 - - - -
65E ALA* 1.3 76.8 - - + +
67E VAL* 1.3 54.8 + - - +
69E HIS* 2.9 6.2 + - - +
70E ASN* 2.7 44.3 + - - +
8F ALA* 3.2 43.7 - - + +
9F ASN 3.7 14.4 - - - +
10F LYS* 4.1 22.7 - - + +
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Residues in contact with VAL 67 (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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12E SER* 3.2 40.8 - - - +
14E TYR* 3.7 16.8 - - + +
63E ASN* 2.9 27.3 + - - +
64E ILE* 3.6 5.8 - - + +
66E VAL* 1.3 76.6 - - + +
68E LYS* 1.3 62.9 + - - +
70E ASN* 3.8 2.9 - - - +
71E LEU* 3.0 23.9 + - - +
8F ALA* 4.9 2.2 - - + -
35F TYR* 3.1 39.8 - - + +
37F PHE* 4.4 9.6 - - + -
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Residues in contact with LYS 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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14E TYR* 3.1 50.2 - - + +
19E ASP* 4.4 6.9 + - - +
61E LEU 5.4 0.4 + - - -
64E ILE* 2.5 36.4 + - - +
65E ALA* 3.2 28.5 - - - +
67E VAL* 1.3 75.1 - - - +
69E HIS* 1.3 64.8 + - - +
71E LEU* 3.4 11.8 + - - +
72E GLY* 3.6 3.5 + - - -
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Residues in contact with HIS 69 (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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65E ALA 2.7 17.2 + - - +
66E VAL* 2.9 10.7 + - - +
68E LYS* 1.3 74.6 - - - +
70E ASN* 1.3 65.2 + - - +
71E LEU 2.8 12.1 + - - -
72E GLY* 3.0 10.9 + - - -
73E VAL* 3.4 21.8 + - + +
10F LYS* 4.2 27.9 - - + +
11F ALA 3.8 21.2 + - - -
13F ASP* 5.5 2.7 + - - -
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Residues in contact with ASN 70 (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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66E VAL* 2.7 28.2 + - - +
67E VAL 3.8 2.7 - - - +
69E HIS* 1.3 72.4 - - - +
71E LEU* 1.3 61.2 + - - +
73E VAL* 3.5 2.3 - - - +
74E LEU* 3.1 30.9 + - - +
8F ALA* 5.4 1.0 - - - +
9F ASN 2.9 23.4 + - - -
10F LYS* 3.5 8.0 - - - -
11F ALA* 3.1 36.5 + - + +
35F TYR* 3.7 33.9 + - + -
56F TYR* 4.5 3.4 - - - -
63F TYR* 4.0 2.6 + - - +
87F TRP* 4.4 4.0 - - - -
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Residues in contact with LEU 71 (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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14E TYR* 3.8 22.0 - - + +
15E GLN 4.0 0.7 - - - -
16E SER* 3.2 41.7 - - - +
67E VAL 3.0 18.1 + - - +
68E LYS* 3.5 5.8 - - - +
69E HIS 2.8 4.6 + - - -
70E ASN* 1.3 69.6 - - - +
72E GLY* 1.3 62.9 + - - +
73E VAL 2.9 0.5 + - - -
74E LEU* 3.1 2.3 + - - -
75E THR* 2.4 40.6 + - - +
33F PHE* 4.0 10.8 - - + +
34F VAL 4.1 4.3 - - - -
35F TYR* 3.8 29.6 - - + +
58F TYR* 4.1 18.4 - - + -
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Residues in contact with GLY 72 (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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16E SER* 6.2 0.2 - - - -
68E LYS 3.6 4.5 + - - -
69E HIS 3.0 7.7 + - - -
71E LEU* 1.3 78.7 - - - +
73E VAL* 1.3 49.7 + - - +
75E THR* 2.9 11.1 - - - -
76E LYS* 2.7 56.6 + - - +
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Residues in contact with VAL 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 HIS* 3.4 32.0 + - + +
70E ASN 3.5 6.3 - - - +
71E LEU 2.9 0.6 + - - -
72E GLY* 1.3 73.3 - - - +
74E LEU* 1.3 50.7 + - - +
76E LYS* 2.7 23.2 + - - +
77E ARG* 2.6 66.6 + - - +
11F ALA* 4.1 15.9 - - + +
12F VAL 3.7 2.2 - - - +
13F ASP 3.9 12.1 - - - +
14F GLY* 3.3 22.7 - - - -
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Residues in contact with LEU 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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70E ASN 3.2 18.2 - - - +
71E LEU 3.1 2.9 + - - +
73E VAL* 1.3 80.0 - - + +
75E THR* 1.3 63.3 + - - +
77E ARG* 3.5 29.9 - - - +
78E SER* 2.8 29.5 + - - -
11F ALA* 4.4 1.6 - - + -
35F TYR* 4.1 5.6 - - + -
58F TYR* 3.5 32.3 - - + -
63F TYR* 3.3 60.8 - - + +
79F LEU* 3.8 15.9 - - + -
83F ASP* 4.3 0.7 - - - +
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Residues in contact with THR 75 (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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16E SER* 5.1 4.9 + - - +
71E LEU* 2.4 48.0 + - - +
72E GLY* 2.9 16.6 - - - -
74E LEU* 1.3 76.1 - - - +
76E LYS* 1.3 66.1 + - + +
78E SER* 2.9 5.9 + - - -
80E SER* 3.3 25.6 + - - +
33F PHE* 4.4 34.5 - - + +
58F TYR* 3.3 11.3 + - - +
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Residues in contact with LYS 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 GLY* 2.7 40.6 + - - +
73E VAL* 2.7 20.7 + - + +
75E THR* 1.3 72.8 - - - +
77E ARG* 1.3 55.0 + - - +
78E SER 2.3 15.9 + - - -
79E ASN* 2.8 13.5 + - - -
80E SER* 4.1 4.7 + - - +
307E NAG 5.1 2.8 - - - +
13F ASP 5.3 1.6 - - - +
14F GLY 3.9 10.5 - - - +
15F GLY 4.5 3.4 - - - +
16F GLY* 3.3 25.9 - - - +
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Residues in contact with ARG 77 (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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73E VAL* 2.6 46.3 + - + +
74E LEU* 3.8 16.2 - - - +
76E LYS* 1.3 69.4 - - - +
78E SER* 1.3 52.5 + - - -
11F ALA* 3.8 3.8 - - - +
12F VAL* 3.5 15.4 + - - +
14F GLY* 3.9 6.9 - - - +
16F GLY* 3.3 5.4 - - - +
17F GLY* 2.4 36.8 - - - +
19F LEU* 3.2 15.3 - - + +
63F TYR* 4.3 0.8 - - - -
79F LEU* 2.6 52.4 + - + +
82F PRO* 3.6 15.9 - - + +
83F ASP* 2.5 41.9 + - - -
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Residues in contact with SER 78 (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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74E LEU 2.8 17.9 + - - -
75E THR 3.4 3.8 - - - -
76E LYS 2.3 17.0 + - - -
77E ARG* 1.3 69.6 - - - +
79E ASN* 1.3 60.7 + - - +
80E SER 2.9 5.0 + - - -
81E THR* 2.6 30.8 + - - -
17F GLY 3.7 1.1 - - - -
19F LEU* 4.3 14.7 - - - +
58F TYR* 3.4 28.3 + - - -
79F LEU* 4.9 10.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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