Contacts of the helix formed by residues 56 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE* 1.3 87.2 - - + +
57A PRO* 1.3 66.4 - - - +
58A GLN* 2.4 49.9 + - - +
59A GLY* 2.9 18.4 + - - -
2B GLU* 2.9 15.9 + - - +
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.0 12.3 - - + +
40A LYS* 3.7 23.3 - - + +
41A GLU* 3.6 10.1 - - + -
42A THR* 3.1 33.4 - - - +
55A PHE 2.7 15.9 - - - +
56A ASP* 1.3 84.0 - - - +
58A GLN* 1.3 61.0 + - - +
60A GLY* 3.2 11.4 + - - -
61A LEU* 3.3 17.9 + - + +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP* 2.4 41.2 + - - +
57A PRO* 1.3 78.3 - - - +
59A GLY* 1.3 80.2 + - - +
61A LEU* 3.7 15.8 - - + +
62A GLN* 2.9 56.9 + - - +
5B LYS* 5.7 0.2 - - - +
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.9 0.2 - - - -
55A PHE* 4.6 3.4 - - - -
56A ASP 2.9 8.5 + - - -
58A GLN* 1.3 98.3 - - - +
60A GLY* 1.3 60.6 + - - +
62A GLN* 3.1 3.4 - - - +
63A ASN* 3.1 6.4 + - - +
5B LYS* 2.3 50.8 + - - -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.7 36.7 - - - -
35A VAL* 4.6 4.3 - - - -
37A LEU* 4.8 2.2 - - - -
55A PHE* 4.1 6.7 - - - -
57A PRO 3.2 7.4 + - - -
58A GLN 3.2 0.2 - - - -
59A GLY* 1.3 74.6 - - - +
61A LEU* 1.3 64.5 + - - +
63A ASN* 3.1 3.6 + - - +
64A ILE* 3.1 28.2 + - - +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 5.1 1.1 - - + +
36A ASP 4.8 1.6 - - - +
37A LEU* 3.5 44.8 - - + +
40A LYS* 3.5 39.9 - - + -
57A PRO* 3.3 17.2 + - + +
58A GLN* 3.7 14.1 - - + +
60A GLY* 1.3 74.4 - - - +
62A GLN* 1.3 62.3 + - - +
64A ILE* 3.2 19.1 + - + +
65A ALA* 3.3 12.5 + - - +
68A LYS* 5.5 0.2 + - - -
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 2.9 43.7 + - - +
59A GLY* 3.1 7.8 - - - +
61A LEU* 1.3 78.3 - - - +
63A ASN* 1.3 57.3 + - - +
65A ALA* 3.6 8.1 - - - +
66A VAL* 3.3 23.9 + - + +
5B LYS* 3.1 22.4 + - - +
7B LYS* 4.8 12.3 + - - +
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Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY 4.0 1.2 + - - -
12A SER* 2.9 29.5 + - - +
23A TYR* 3.8 7.4 - - + -
59A GLY 3.1 5.9 + - - +
60A GLY 3.1 6.9 + - - +
62A GLN* 1.3 75.4 - - - +
64A ILE* 1.3 61.8 + - - +
65A ALA 3.2 0.4 - - - -
66A VAL* 3.2 7.6 + - - +
67A VAL* 2.8 33.7 + - - +
5B LYS* 2.7 35.5 + - - +
6B ALA 3.4 9.7 + - - +
7B LYS* 3.9 6.6 - - - +
8B ALA* 3.9 13.4 + - - +
37B PHE* 3.8 19.8 - - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 4.6 10.1 - - - -
13A VAL 3.9 13.0 - - - +
14A TYR* 3.9 21.8 - - + -
21A GLY* 4.5 0.2 - - - -
22A GLN 3.9 24.2 - - - +
23A TYR* 4.3 5.2 - - + -
37A LEU* 3.9 35.9 - - + -
60A GLY 3.1 13.8 + - - +
61A LEU* 3.2 9.1 + - + +
63A ASN* 1.3 73.9 - - - +
65A ALA* 1.3 56.7 + - - +
67A VAL* 3.4 3.7 - - + +
68A LYS* 2.5 52.3 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU 3.3 8.2 + - - +
62A GLN* 3.6 13.9 - - - +
64A ILE* 1.3 78.6 - - - +
66A VAL* 1.3 52.9 + - + +
68A LYS* 3.3 19.2 - - - +
69A HIS* 2.7 34.5 + - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.3 20.4 - - + +
63A ASN* 3.5 10.8 - - - +
64A ILE 3.2 0.6 - - - -
65A ALA* 1.3 73.4 - - + +
67A VAL* 1.3 57.3 + - - +
69A HIS* 2.9 6.6 + - - +
70A ASN* 2.7 51.8 + - - +
8B ALA* 3.2 41.5 - - + +
9B ASN 3.8 8.1 - - - +
10B LYS* 4.1 20.0 - - + +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 3.1 42.8 - - - +
14A TYR* 3.5 24.7 - - + +
63A ASN* 2.8 27.8 + - - +
64A ILE* 3.5 7.0 - - + +
66A VAL* 1.3 75.7 - - + +
68A LYS* 1.3 62.9 + - - +
70A ASN* 3.7 1.8 - - - +
71A LEU* 3.0 24.4 + - - +
8B ALA* 5.0 2.7 - - + -
35B TYR* 3.2 35.5 - - + -
37B PHE* 4.7 6.7 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 2.9 52.9 - - + +
19A ASP* 4.2 7.6 - - - +
61A LEU 5.5 0.2 + - - -
64A ILE* 2.5 33.6 + - - +
65A ALA* 3.3 28.7 - - - +
67A VAL* 1.3 75.7 - - - +
69A HIS* 1.3 66.4 + - - +
71A LEU* 3.3 11.6 + - - +
72A GLY* 3.5 3.5 + - - -
48C GLU* 6.3 3.6 - - + -
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 2.7 17.7 + - - +
66A VAL* 2.9 10.7 + - - +
68A LYS* 1.3 75.7 - - - +
70A ASN* 1.3 73.3 - - - +
71A LEU 2.8 2.1 + - - -
72A GLY* 3.0 11.3 + - - -
73A VAL* 3.4 31.6 + - + +
76A LYS* 6.5 0.2 - - - -
10B LYS* 4.1 28.9 - - + +
11B ALA 3.8 13.6 + - - -
13B ASP* 5.5 2.5 + - - -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 2.7 29.4 + - - +
67A VAL 3.7 0.2 - - - +
69A HIS* 1.3 73.2 - - - +
71A LEU* 1.3 61.8 + - - +
73A VAL* 3.5 4.2 - - - +
74A LEU* 3.1 26.9 + - - +
8B ALA* 5.2 1.0 - - - +
9B ASN 2.7 24.2 + - - -
10B LYS* 3.4 8.7 - - - -
11B ALA* 3.3 33.9 + - + +
35B TYR* 3.2 38.5 + - + +
56B TYR* 4.3 6.7 - - - -
63B TYR* 4.3 0.8 + - - -
87B TRP* 4.4 0.8 - - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 4.0 20.0 - - + +
15A GLN 4.0 0.7 - - - -
16A SER* 3.2 42.6 - - - +
67A VAL 3.0 13.9 + - - +
68A LYS 3.5 9.6 - - - +
69A HIS 2.8 4.6 + - - -
70A ASN* 1.3 70.3 - - - +
72A GLY* 1.3 62.6 + - - +
73A VAL 3.0 0.3 + - - -
74A LEU* 3.0 3.7 + - - -
75A THR* 2.4 40.7 + - - +
33B PHE* 4.0 11.0 - - + +
34B VAL 4.3 2.7 - - - -
35B TYR* 3.8 26.5 - - + +
58B TYR* 3.7 23.1 - - + -
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS 3.5 4.2 + - - -
69A HIS 3.0 7.4 + - - -
71A LEU* 1.3 77.3 - - - +
73A VAL* 1.3 52.1 + - - +
75A THR* 2.8 12.0 - - - -
76A LYS* 2.7 56.6 + - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS* 3.4 39.7 + - + +
70A ASN 3.5 7.0 - - - +
71A LEU 3.0 0.4 + - - -
72A GLY* 1.3 72.0 - - - +
74A LEU* 1.3 51.3 + - - +
76A LYS* 2.6 22.8 + - - +
77A ARG* 2.6 63.9 + - - +
11B ALA* 3.8 15.0 - - + +
12B VAL 3.5 3.6 - - - +
13B ASP 4.0 7.9 - - - +
14B GLY* 3.3 22.2 - - - -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASN 3.1 11.6 + - - +
71A LEU 3.0 7.2 + - - +
73A VAL* 1.3 76.0 - - - +
75A THR* 1.3 61.9 + - - +
77A ARG* 3.5 25.7 - - - +
78A SER* 2.8 30.3 + - - -
11B ALA* 4.3 2.9 - - + -
35B TYR* 4.4 1.8 - - + -
58B TYR* 3.5 29.4 - - + -
63B TYR* 3.1 46.7 - - + +
79B LEU* 3.2 43.5 - - + +
83B ASP* 4.1 0.7 - - - +
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER* 5.1 6.0 - - - +
71A LEU* 2.4 44.2 + - - +
72A GLY* 2.8 17.0 - - - -
73A VAL 2.8 0.2 + - - -
74A LEU* 1.3 79.6 - - - +
76A LYS* 1.3 66.9 + - + +
78A SER* 2.9 5.7 + - - -
80A SER* 3.3 29.8 + - - +
33B PHE* 4.7 22.9 - - + +
58B TYR* 3.2 15.5 + - - +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS* 6.5 0.2 - - - -
72A GLY* 2.7 35.6 + - - +
73A VAL* 2.6 16.2 + - - +
75A THR* 1.3 72.6 - - + +
77A ARG* 1.3 55.3 + - - +
78A SER 2.4 18.4 + - - -
79A ASN* 2.8 12.8 + - - -
80A SER* 5.0 4.3 - - - -
13B ASP 5.4 2.5 - - - +
14B GLY 3.7 11.9 - - - +
15B GLY 4.4 4.3 - - - +
16B GLY* 3.1 25.2 - - - +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 2.6 32.5 + - - +
74A LEU* 3.8 13.2 - - + +
76A LYS* 1.3 70.7 - - - +
78A SER* 1.3 53.4 + - - +
11B ALA* 3.6 4.2 - - - +
12B VAL* 3.2 29.5 + - - +
14B GLY* 4.0 11.8 - - - -
16B GLY* 3.2 3.2 - - - +
17B GLY* 2.5 34.3 - - - +
19B LEU* 3.0 14.5 - - + +
63B TYR* 4.0 2.0 - - - -
79B LEU* 2.7 51.0 + - + +
82B PRO* 3.6 19.5 - - + +
83B ASP* 2.4 42.6 + - - -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 2.8 17.6 + - - -
75A THR 3.4 3.6 - - - -
76A LYS 2.4 17.6 + - - -
77A ARG* 1.3 68.8 - - - +
79A ASN* 1.3 62.2 + - - +
80A SER 2.8 5.5 + - - -
81A THR* 2.7 37.0 + - - -
17B GLY 3.5 1.6 - - - -
19B LEU* 4.2 13.0 - - - +
58B TYR* 3.6 24.4 - - - -
79B LEU* 3.8 17.2 - - - +
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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