Contacts of the helix formed by residues 48 - 76 (chain Q) in PDB entry 2HM2
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 48 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q LEU* 6.3 1.1 - - - -
24Q LYS* 4.9 1.1 - - - +
46Q GLN 4.1 7.2 - - - +
47Q LEU* 1.3 76.2 - - - +
49Q ILE* 1.3 59.8 + - + +
50Q VAL* 2.7 15.9 + - + +
51Q ASP* 3.0 14.4 + - - +
52Q LEU* 2.4 37.6 + - - +
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Residues in contact with ILE 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q LEU* 3.2 12.7 - - + +
12Q LEU* 3.2 43.5 - - + +
13Q GLU* 3.9 30.5 - - + +
15Q LEU 5.7 1.6 - - - +
20Q LEU* 4.5 34.5 - - + +
23Q PHE* 6.0 0.4 - - + -
48Q ASP* 1.3 73.4 - - + +
50Q VAL* 1.3 56.8 - - + +
52Q LEU* 4.0 10.0 - - + +
53Q THR* 2.3 37.4 + - - -
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Residues in contact with VAL 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ARG* 5.8 4.3 - - - +
9Q LEU* 4.1 22.6 - - + +
48Q ASP* 2.7 9.7 + - + -
49Q ILE* 1.3 79.3 - - + +
51Q ASP* 1.3 64.9 + - - +
53Q THR* 3.1 5.2 + - - -
54Q ASP* 2.7 34.8 + - + +
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Residues in contact with ASP 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q LEU* 3.7 26.1 - - + +
48Q ASP* 3.0 16.6 + - - +
50Q VAL* 1.3 85.7 - - - +
52Q LEU* 1.3 56.7 + - - +
54Q ASP* 3.6 9.2 - - - +
55Q LYS* 2.6 37.1 + - - +
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Residues in contact with LEU 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q LEU* 5.8 0.2 - - + -
20Q LEU* 4.2 8.5 - - + -
23Q PHE* 3.9 17.9 - - + -
24Q LYS* 3.3 42.6 - - + +
27Q LEU* 4.6 6.3 - - + -
39Q ILE* 5.1 9.6 - - + -
43Q ALA 4.5 14.8 - - - +
44Q LEU* 5.7 0.7 - - - -
47Q LEU* 3.4 15.8 - - + +
48Q ASP 2.4 36.8 + - - +
49Q ILE* 4.0 6.7 - - + -
51Q ASP* 1.3 67.9 - - - +
53Q THR* 1.3 57.0 + - - +
55Q LYS* 3.6 0.5 + - - +
56Q LEU* 3.0 55.2 + - + +
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Residues in contact with THR 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ARG* 4.0 20.4 - - + -
8Q ILE* 3.8 16.6 - - + -
9Q LEU* 3.5 13.0 - - + +
12Q LEU* 3.1 21.8 - - - +
49Q ILE 2.3 26.6 + - - -
50Q VAL 3.3 4.0 - - - +
52Q LEU* 1.3 75.2 - - - +
54Q ASP* 1.3 55.6 + - - +
56Q LEU* 3.0 7.4 + - - -
57Q VAL* 2.5 58.5 + - + +
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Residues in contact with ASP 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ARG* 6.0 2.5 - - - -
50Q VAL* 2.7 21.4 + - + +
51Q ASP* 3.6 10.8 - - - +
53Q THR* 1.3 74.2 - - - +
55Q LYS* 1.3 52.2 + - - +
57Q VAL* 4.3 6.0 - - - +
58Q ALA* 2.4 53.9 + - - +
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Residues in contact with LYS 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ARG 5.3 0.4 + - - -
39Q ILE* 3.4 22.7 - - + +
40Q PRO* 3.3 39.0 - - - +
43Q ALA* 4.5 6.3 - - + -
47Q LEU* 3.5 24.7 - - + -
51Q ASP 2.6 22.1 + - - +
52Q LEU* 3.8 2.9 - - + +
54Q ASP* 1.3 74.7 + - - +
56Q LEU* 1.3 52.0 + - - +
58Q ALA* 4.3 4.0 - - + -
59Q SER* 2.4 61.2 + - - -
60Q TYR* 5.2 1.6 + - - -
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Residues in contact with LEU 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q LEU* 5.1 2.0 - - + -
23Q PHE* 3.6 33.4 - - + -
27Q LEU* 3.4 31.6 - - + -
39Q ILE* 4.0 9.2 - - + -
52Q LEU* 3.0 42.6 + - + +
53Q THR* 3.4 7.0 - - - +
55Q LYS* 1.3 75.0 - - - +
57Q VAL* 1.3 58.3 + - + +
59Q SER* 3.0 4.0 + - - -
60Q TYR* 2.7 59.8 + - + +
65Q ALA* 4.2 7.2 - - + -
68Q LEU* 4.2 2.9 - - + -
69Q VAL* 5.1 9.4 - - + -
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Residues in contact with VAL 57 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ARG* 4.8 11.9 - - + -
8Q ILE* 3.8 23.6 - - + -
53Q THR* 2.5 42.8 + - + +
54Q ASP* 3.9 4.7 - - - +
56Q LEU* 1.3 73.9 - - + +
58Q ALA* 1.3 55.8 + - - +
61Q TYR* 2.5 34.0 + - - -
62Q GLU* 3.3 32.1 - - + +
65Q ALA* 3.9 12.6 - - + -
69Q VAL* 6.2 0.4 - - + -
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Residues in contact with ALA 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q ASP* 2.4 50.1 + - - +
55Q LYS* 4.2 4.3 - - + +
57Q VAL* 1.3 72.3 - - - +
59Q SER* 1.3 60.0 + - - +
61Q TYR* 3.9 11.8 - - - -
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Residues in contact with SER 59 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q PHE* 4.7 4.0 - - - -
55Q LYS* 2.4 48.4 + - - -
58Q ALA* 1.3 79.2 - - - +
60Q TYR* 1.3 91.2 + - - +
61Q TYR* 3.4 17.1 + - - -
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Residues in contact with TYR 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q LEU 5.6 0.9 + - - -
32Q LEU* 3.5 29.8 - - + +
36Q PHE* 4.1 19.7 - + + -
37Q GLU 2.4 30.1 + - - -
38Q ARG* 3.7 13.5 + - - -
39Q ILE* 4.0 11.5 + - + +
55Q LYS* 5.4 0.8 + - - -
56Q LEU* 2.7 35.9 + - + +
59Q SER* 1.3 101.1 - - - +
61Q TYR* 1.3 85.2 + - - +
64Q TYR* 3.2 21.3 - + + +
65Q ALA* 3.9 16.6 - - - +
68Q LEU* 3.7 27.1 - - + -
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Residues in contact with TYR 61 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q PHE* 3.5 38.8 - + - -
57Q VAL 2.5 24.6 + - - -
58Q ALA 3.9 10.8 - - - -
59Q SER 3.4 16.8 + - - -
60Q TYR* 1.3 75.2 - - - +
62Q GLU* 1.3 53.7 + - - +
63Q ASP* 3.2 11.0 - - + +
64Q TYR* 4.5 8.1 - - + +
65Q ALA* 2.7 41.7 + - - +
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Residues in contact with GLU 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q GLY* 4.4 17.2 - - - -
3Q THR 4.8 0.7 + - - -
4Q LYS* 3.2 46.0 + - + +
5Q ARG* 4.7 6.3 + - + +
8Q ILE* 4.7 1.1 - - - +
57Q VAL* 3.3 28.8 + - + -
61Q TYR* 1.3 73.7 - - - +
63Q ASP* 1.3 64.9 + - - +
65Q ALA* 4.3 1.6 - - - -
66Q ALA* 3.3 13.0 + - - +
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Residues in contact with ASP 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q LYS* 3.6 21.1 + - - +
61Q TYR* 3.2 6.9 - - + +
62Q GLU* 1.3 82.6 + - - +
64Q TYR* 1.3 65.2 + - - +
67Q GLU* 3.4 23.0 + - - +
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Residues in contact with TYR 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q PRO 5.1 4.0 + - - -
32Q LEU* 4.1 23.1 - - + +
33Q ARG* 3.5 44.8 + - + +
36Q PHE* 5.2 8.3 - + + -
60Q TYR* 3.2 32.8 + + + +
61Q TYR* 3.6 9.1 + - + +
63Q ASP* 1.3 76.9 - - - +
65Q ALA* 1.3 53.7 + - - +
67Q GLU* 3.0 16.8 + - + +
68Q LEU* 2.7 41.1 + - + +
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Residues in contact with ALA 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q ILE* 4.8 0.9 - - + -
56Q LEU* 3.9 11.2 - - + +
57Q VAL* 3.9 26.2 - - + -
60Q TYR* 3.5 9.5 + - + -
61Q TYR 2.7 24.5 + - - +
62Q GLU 4.1 2.2 - - - +
64Q TYR* 1.3 77.0 - - - +
66Q ALA* 1.3 52.4 + - - +
68Q LEU* 2.5 12.1 + - - +
69Q VAL* 2.4 44.4 + - + +
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Residues in contact with ALA 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q LYS* 2.9 41.5 - - + +
8Q ILE* 4.5 10.2 - - + +
62Q GLU 3.3 5.7 + - - +
65Q ALA* 1.3 77.7 - - - +
67Q GLU* 1.3 54.3 + - + +
69Q VAL* 3.7 8.7 - - - +
70Q VAL* 2.7 43.3 + - + +
85Q LEU* 4.6 15.7 - - + +
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Residues in contact with GLU 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q LYS* 5.6 1.1 - - - +
63Q ASP 3.4 15.7 + - - +
64Q TYR* 3.0 27.8 + - + +
65Q ALA 3.0 0.8 - - - -
66Q ALA* 1.3 77.9 - - + +
68Q LEU* 1.3 61.5 + - - +
70Q VAL* 3.7 10.4 - - - +
71Q ALA* 3.3 23.4 + - - +
86Q GLN* 5.5 11.5 + - - +
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Residues in contact with LEU 68 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q LEU* 3.6 33.9 - - + +
30Q VAL* 4.2 25.8 - - + -
32Q LEU* 4.6 15.5 - - + -
39Q ILE* 5.9 0.2 - - + -
56Q LEU* 4.2 2.9 - - + -
60Q TYR* 3.7 41.5 - - + +
64Q TYR* 2.7 22.0 + - + +
65Q ALA* 2.5 16.4 + - - +
67Q GLU* 1.3 71.5 - - - +
69Q VAL* 1.3 66.2 + - + +
71Q ALA* 3.5 2.9 + - - +
72Q VAL* 3.1 31.9 + - + +
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Residues in contact with VAL 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q ILE* 4.6 20.0 - - + -
12Q LEU* 4.1 23.8 - - + -
23Q PHE* 4.2 17.3 - - + -
27Q LEU* 5.3 0.4 - - - -
56Q LEU* 5.1 12.3 - - + -
57Q VAL* 6.2 0.4 - - + -
65Q ALA* 2.4 37.8 + - + +
66Q ALA* 3.7 7.9 - - - +
68Q LEU* 1.3 76.5 - - + +
70Q VAL* 1.3 66.6 + - - +
72Q VAL* 3.0 16.6 + - - +
73Q LEU* 3.1 14.0 + - + +
85Q LEU* 3.7 21.1 - - + -
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Residues in contact with VAL 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q ALA* 2.7 30.6 + - + +
67Q GLU* 3.7 12.8 - - - +
69Q VAL* 1.3 73.6 - - - +
71Q ALA* 1.3 66.8 + - + +
72Q VAL 3.0 1.6 + - - -
73Q LEU* 3.0 1.3 + - - -
74Q ARG* 3.0 62.8 + - - +
82Q ALA* 3.5 17.0 - - + +
85Q LEU* 3.4 35.4 - - + -
86Q GLN* 4.3 9.6 - - + +
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Residues in contact with ALA 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q VAL* 5.0 19.3 - - + +
67Q GLU 3.3 13.9 + - - +
68Q LEU* 4.0 3.8 - - - +
70Q VAL* 1.3 83.0 - - + +
72Q VAL* 1.3 62.3 + - - +
74Q ARG* 3.4 15.5 - - - +
75Q ASP* 3.1 21.0 + - - +
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Residues in contact with VAL 72 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q PHE* 3.6 31.4 - - + +
26Q LYS* 4.0 26.7 - - + +
27Q LEU* 3.9 23.8 - - + -
30Q VAL* 4.1 21.8 - - + -
68Q LEU* 3.1 16.8 - - + +
69Q VAL* 3.0 8.8 + - - +
71Q ALA* 1.3 74.7 - - - +
73Q LEU* 1.3 68.9 + - + +
75Q ASP* 2.8 23.6 + - - +
76Q MET* 3.2 10.9 + - + +
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Residues in contact with LEU 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q VAL* 3.6 30.1 - - + -
12Q LEU* 4.6 0.9 - - + -
15Q LEU* 3.9 22.9 - - + -
23Q PHE* 3.9 25.8 - - + -
69Q VAL* 3.4 13.7 - - + +
70Q VAL 3.0 4.9 + - - +
72Q VAL* 1.3 74.7 - - - +
74Q ARG* 1.3 58.6 + - - +
76Q MET* 2.8 31.5 + - + +
78Q MET* 3.1 31.4 + - + +
81Q GLU* 5.3 2.2 - - + -
82Q ALA* 4.0 16.8 - - + +
85Q LEU* 3.7 21.8 - - + -
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Residues in contact with ARG 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q VAL* 3.0 42.1 + - - +
71Q ALA* 3.4 16.4 - - - +
73Q LEU* 1.3 75.9 - - - +
75Q ASP* 1.3 62.3 + - - +
77Q ARG* 3.2 14.6 + - - -
78Q MET 3.7 10.9 + - - +
79Q LEU* 4.2 34.3 + - + +
82Q ALA* 3.5 19.1 + - + +
83Q ALA* 5.3 3.4 - - - +
86Q GLN* 3.4 27.5 - - - +
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Residues in contact with ASP 75 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q LYS* 3.2 34.0 + - + +
29Q THR* 5.5 3.3 + - - -
71Q ALA 3.1 12.0 + - - +
72Q VAL* 2.8 15.1 + - - +
74Q ARG* 1.3 72.2 - - - +
76Q MET* 1.3 50.3 + - + +
77Q ARG* 2.7 41.3 + - - -
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Residues in contact with MET 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q LEU* 3.8 21.1 - - + -
19Q GLU* 3.8 52.5 - - + +
22Q LYS* 4.1 10.8 - - - -
23Q PHE* 4.3 8.1 - - + -
26Q LYS* 3.7 28.7 - - + -
72Q VAL* 3.4 14.1 - - + +
73Q LEU* 2.8 23.7 + - + +
75Q ASP* 1.3 74.3 - - - +
77Q ARG* 1.3 89.7 + - - +
78Q MET* 3.2 12.2 + - + +
----------------------------------------------------------
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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