Contacts of the helix formed by residues 48 - 77 (chain A) in PDB entry 1LB3
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 LEU 48 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.0 28.6 + - + +
46A VAL* 3.8 11.9 - - + +
47A ALA* 1.3 81.5 - - - +
49A GLU* 1.3 66.0 + - - +
50A GLY 3.3 2.5 - - - -
51A VAL* 3.1 15.8 + - + +
52A GLY 3.0 18.2 + - - -
96A THR* 3.4 13.2 - - - +
175A GLU* 3.4 37.0 - - + +
176A TYR* 4.6 13.2 - - + -
179A GLU* 3.8 29.4 - - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 4.1 14.6 - - - +
47A ALA 3.8 3.4 + - - -
48A LEU* 1.3 72.4 - - - +
50A GLY* 1.4 58.3 + - - +
52A GLY* 3.2 1.7 + - - -
53A HIS* 2.9 30.7 + - + +
179A GLU* 3.4 9.6 + - - +
180A ARG* 4.4 12.4 + - - +
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 1.4 73.6 - - - +
51A VAL* 1.3 57.4 + - - +
53A HIS* 3.5 3.5 + - - +
54A PHE* 3.0 27.9 + - - +
179A GLU* 2.7 26.5 + - - -
183A LEU* 3.8 21.6 - - - +
184A LYS* 4.3 19.5 + - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.5 30.5 - - + -
48A LEU* 3.1 20.1 + - + +
50A GLY* 1.3 74.3 - - - +
52A GLY* 1.3 65.8 + - - +
54A PHE* 3.2 4.0 + - + +
55A PHE* 3.1 44.9 + - + -
96A THR* 3.7 31.2 - - + +
100A MET* 5.7 1.3 - - + -
178A PHE* 5.6 0.7 - - + -
179A GLU* 4.0 9.8 - - + +
183A LEU* 3.6 20.9 - - + -
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 3.7 25.0 - - - -
41A PHE* 3.6 9.4 - - - +
42A ASP* 4.3 9.0 - - - -
48A LEU 3.0 12.2 + - - -
49A GLU 3.2 2.9 + - - -
51A VAL* 1.3 77.9 - - - +
53A HIS* 1.3 56.6 + - - +
55A PHE 3.3 0.3 + - - -
56A ARG* 2.9 36.0 + - - +
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 5.3 0.2 + - - -
49A GLU* 2.9 20.3 + - + +
50A GLY* 3.9 7.0 - - - +
52A GLY* 1.3 73.2 - - - +
54A PHE* 1.3 66.2 + - - +
56A ARG* 4.4 8.1 - - + +
57A GLU* 2.9 55.9 + - + +
184A LYS* 4.9 17.7 - - - -
721A CD 2.2 31.3 - - - -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 3.0 18.8 + - - +
51A VAL* 3.5 7.2 - - - +
53A HIS* 1.3 79.5 - - - +
55A PHE* 1.3 79.7 + + - +
57A GLU* 3.5 16.2 + - - +
58A LEU* 3.3 48.5 + - + +
100A MET* 3.6 30.7 - - + -
144A LEU* 4.8 2.2 - - + -
147A LYS* 4.1 17.5 - - + -
148A MET* 4.5 11.0 - - + -
151A HIS* 3.8 27.1 - + - -
183A LEU* 4.3 18.8 - - + -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.3 45.1 - + + +
37A LEU* 3.7 20.6 - - + -
38A GLY 3.8 7.2 - - - +
41A PHE* 3.9 17.7 - + - -
51A VAL* 3.1 42.6 + - + +
52A GLY 3.9 0.7 - - - +
54A PHE* 1.3 100.7 - + - +
56A ARG* 1.3 60.5 + - - +
58A LEU* 3.1 2.9 + - + -
59A ALA 2.9 23.2 + - - -
96A THR* 5.4 0.4 - - + -
99A ALA* 4.2 21.3 - - + -
100A MET* 4.2 13.5 - - + -
103A ALA* 3.8 21.3 - - + -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR 4.8 0.2 - - - -
35A LEU* 4.1 17.8 - - - +
38A GLY* 4.0 16.8 - - - -
39A PHE* 3.3 34.0 - - - -
42A ASP* 4.6 8.0 + - - +
52A GLY 2.9 23.8 + - - +
53A HIS* 3.4 10.7 + - - +
55A PHE* 1.3 75.3 - - - +
57A GLU* 1.3 62.7 + - - +
59A ALA* 3.1 17.9 + - - +
60A GLU* 3.3 12.0 + - - +
189A GOL 2.8 48.1 + - - -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 2.9 39.5 + - + +
54A PHE* 3.5 17.4 - - - +
56A ARG* 1.3 75.7 - - - +
58A LEU* 1.3 64.5 + - + +
60A GLU* 3.1 13.7 + - - +
61A GLU* 3.0 19.9 + - - +
721A CD 2.0 32.7 - - - -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.7 28.0 - - + -
54A PHE* 3.3 35.8 + - + +
55A PHE* 3.1 8.5 + - + +
57A GLU* 1.3 77.6 - - + +
59A ALA* 1.3 67.3 + - - +
61A GLU* 3.7 14.0 - - + +
62A LYS* 2.9 29.9 + - - +
144A LEU* 3.7 30.1 - - + -
148A MET* 3.6 29.6 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 2.8 42.5 + - - +
34A TYR* 3.5 15.0 - - + +
35A LEU* 3.9 17.3 - - + +
55A PHE 2.9 8.6 + - - +
56A ARG* 3.1 13.9 + - - +
58A LEU* 1.3 77.4 - - - +
60A GLU* 1.3 63.5 + - - +
63A ARG* 3.1 18.8 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG 3.3 7.2 + - - +
57A GLU* 3.1 10.9 + - - +
59A ALA* 1.3 76.8 - - - +
61A GLU* 1.3 59.7 - - - +
63A ARG* 3.3 28.2 + - - +
64A GLU* 2.9 47.4 + - + +
718A CD 2.2 28.2 - - - -
723A CD 2.7 28.5 - - - -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU 3.0 13.1 + - - +
58A LEU* 3.2 18.8 + - + +
60A GLU* 1.3 76.8 - - - +
62A LYS* 1.4 75.3 + - - +
64A GLU* 3.3 13.4 + - - +
65A GLY* 3.0 20.1 + - - -
140A LYS* 3.2 39.5 + - + +
144A LEU* 6.1 0.9 - - + -
722A CD 3.3 19.2 - - - -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.6 37.1 + - + +
30A ALA* 3.9 5.8 - - + -
31A SER* 3.6 9.4 - - - +
34A TYR* 3.6 19.7 - - + -
58A LEU* 2.9 21.4 + - - +
61A GLU* 1.4 89.6 - - - +
63A ARG* 1.3 63.3 + - - +
65A GLY* 3.2 2.9 + - - -
66A ALA 3.0 17.3 + - - -
107A GLU* 2.9 26.6 + - - +
110A LEU* 3.7 20.6 - - + +
141A GLU* 2.8 30.7 + - - -
144A LEU* 4.1 10.4 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.6 14.8 - - + -
31A SER* 3.7 15.8 + - - +
59A ALA* 3.1 27.0 + - - +
60A GLU* 3.6 33.1 + - - +
62A LYS* 1.3 75.0 - - - +
64A GLU* 1.3 65.2 + - - +
66A ALA* 3.1 8.5 + - - +
67A GLU* 2.9 47.3 + - + +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 2.9 32.9 + - + +
61A GLU* 3.6 15.1 - - - +
62A LYS 3.3 0.2 - - - -
63A ARG* 1.3 78.4 - - + +
65A GLY* 1.3 55.4 + - - +
67A GLU* 3.2 16.5 + - - +
68A ARG* 2.9 32.7 + - - +
140A LYS* 5.9 0.2 + - - -
718A CD 2.2 21.8 - - - -
722A CD 2.3 22.6 - - - -
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 4.1 11.2 - - - -
61A GLU* 3.0 15.4 + - - -
62A LYS 3.2 4.9 + - - -
64A GLU* 1.3 76.3 - - - +
66A ALA* 1.3 60.2 + - - +
68A ARG* 4.6 2.5 - - - -
69A LEU* 3.1 11.3 + - - +
137A TYR* 2.7 39.0 + - - -
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.9 11.0 - - + +
27A HIS* 3.8 20.7 - - + +
28A LEU* 3.7 32.1 - - + -
62A LYS 3.0 8.1 + - - +
63A ARG 3.4 8.5 - - - +
65A GLY* 1.3 76.7 - - - +
67A GLU* 1.3 63.2 + - + +
69A LEU* 3.2 9.0 + - - +
70A LEU* 3.0 28.2 + - + +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 6.2 0.4 - - + -
63A ARG* 2.9 44.0 + - + +
64A GLU* 3.7 16.8 - - - +
66A ALA* 1.3 76.4 - - + +
68A ARG* 1.3 59.0 + - - +
70A LEU* 3.2 15.6 + - + +
71A GLU* 3.0 27.6 + - - +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 2.9 16.4 + - - +
65A GLY* 4.6 1.6 - - - -
67A GLU* 1.3 78.2 - - - +
69A LEU* 1.3 60.7 + - - +
71A GLU* 3.3 17.3 + - - +
72A PHE* 3.0 21.8 + - - +
132A PHE* 3.7 14.1 - - + -
136A HIS* 3.5 55.4 + - - +
137A TYR* 3.3 19.5 - - - +
140A LYS* 5.0 11.7 - - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.9 30.3 - - + +
23A LEU* 3.4 45.3 - - + +
24A VAL* 3.6 13.0 - - + +
27A HIS* 3.7 22.7 - - + +
65A GLY 3.1 17.8 + - - +
66A ALA 3.2 6.5 + - - +
68A ARG* 1.3 77.9 - - - +
70A LEU* 1.3 57.2 + - - +
72A PHE* 3.2 3.6 + - + +
73A GLN* 2.9 27.9 + - - +
117A LEU* 4.8 2.5 - - + -
129A LEU* 6.1 0.2 - - + -
132A PHE* 3.8 22.2 - - + -
133A LEU* 4.9 0.9 - - + -
137A TYR* 3.4 14.4 - - + +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 4.9 3.4 - - - +
24A VAL* 3.9 23.8 - - + -
28A LEU* 5.8 1.8 - - + -
66A ALA* 3.0 20.8 + - + +
67A GLU* 3.2 18.6 + - + +
69A LEU* 1.3 72.5 - - - +
71A GLU* 1.3 65.8 + - - +
73A GLN* 3.3 7.2 + - + +
74A ASN* 3.1 26.0 + - - +
80A ALA* 3.6 22.8 - - + +
81A LEU 5.6 0.9 - - - +
82A PHE* 3.6 43.3 - - + -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU 3.0 13.3 + - - +
68A ARG* 3.7 19.4 + - - +
69A LEU 3.3 0.2 - - - -
70A LEU* 1.3 77.0 - - - +
72A PHE* 1.3 56.5 + - - +
74A ASN* 3.2 8.7 + - + +
75A ASP* 2.8 46.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 27.4 - + - -
20A VAL* 4.1 12.6 - - + -
68A ARG 3.0 13.6 + - - +
69A LEU 3.4 8.5 - - - +
71A GLU* 1.3 76.7 + - - +
73A GLN* 1.3 65.4 + - - +
75A ASP* 3.1 7.7 + - - +
76A ARG* 3.0 47.1 + - + +
128A HIS* 3.4 32.8 - + - -
129A LEU* 3.6 30.3 - - + -
132A PHE* 3.6 47.1 - + + -
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 2.7 41.7 + - - -
17A GLU* 3.0 25.0 + - - +
20A VAL* 3.7 11.2 - - + +
21A ASN* 3.0 29.6 + - - +
69A LEU 2.9 12.4 + - - +
70A LEU* 3.4 13.7 - - + +
71A GLU 3.3 0.2 - - - -
72A PHE* 1.3 77.5 - - - +
74A ASN* 1.3 62.1 + - - +
76A ARG* 3.3 1.6 + - - +
77A GLY 3.1 3.8 + - - -
78A GLY* 2.9 33.9 + - - +
79A ARG 3.9 7.9 - - - -
80A ALA* 3.7 26.0 - - + +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.6 10.2 - - - +
70A LEU 3.1 12.8 + - - +
71A GLU* 3.7 9.9 - - + +
73A GLN* 1.3 80.0 - - - +
75A ASP* 1.3 66.1 + - - +
77A GLY* 3.1 11.4 + - - -
78A GLY 3.9 13.1 - - - +
79A ARG* 5.3 2.8 - - - -
80A ALA* 4.9 11.5 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.4 15.7 - - - +
71A GLU* 2.8 45.2 + - - +
72A PHE* 3.1 9.6 + - + +
74A ASN* 1.3 74.5 - - - +
76A ARG* 1.3 64.1 + - + +
77A GLY 3.4 0.2 - - - -
128A HIS* 5.8 4.0 - - + -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.2 4.0 - - - +
9A ARG* 3.6 24.1 - - - +
10A GLN 3.1 19.6 + - - +
11A ASN* 3.0 32.5 + - - +
12A TYR* 3.6 33.9 - - + +
72A PHE* 3.0 41.6 + - + +
73A GLN 4.0 0.2 - - - +
75A ASP* 1.3 81.3 - - + +
77A GLY* 1.3 60.2 + - - +
78A GLY 3.4 0.6 + - - -
126A ASP* 2.9 30.3 + - - -
128A HIS* 3.2 39.0 + - + +
----------------------------------------------------------
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 3.7 32.5 + - - -
8A ILE* 3.7 11.3 - - - +
9A ARG* 3.8 13.3 + - - -
73A GLN 3.1 0.4 + - - -
74A ASN 3.1 12.5 + - - -
75A ASP 3.4 0.4 - - - -
76A ARG* 1.3 78.2 - - - +
78A GLY* 1.3 62.9 + - - +
79A ARG* 4.6 6.2 - - - +
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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
------------------------------------------------------------
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