Contacts of the helix formed by residues 43 - 72 (chain C) in PDB entry 4NE1
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 SER 43 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 1.3 76.5 - - - +
44C LYS* 1.3 65.1 + - - +
45C GLN* 3.2 17.1 + - - +
46C THR* 3.0 20.1 + - - -
47C ILE* 3.1 13.2 + - - +
64D ARG* 4.0 20.6 - - - +
65D VAL 2.3 39.0 + - - +
66D ASP* 3.5 11.1 - - - -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C HIS* 5.2 9.4 - - + +
42C PHE 3.8 1.2 + - - -
43C SER* 1.3 71.2 - - - +
45C GLN* 1.3 60.7 + - + +
47C ILE* 3.2 11.1 + - + +
48C ALA* 2.6 42.3 + - + +
64D ARG* 5.0 2.4 - - - +
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Residues in contact with GLN 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER* 3.1 21.3 + - - +
44C LYS* 1.3 78.9 + - + +
46C THR* 1.3 55.7 + - - +
48C ALA* 3.7 6.0 - - - +
49C ALA* 2.7 37.5 + - - +
66D ASP* 3.4 25.4 + - - +
67D VAL* 3.3 35.5 - - + +
70D LEU* 4.6 0.4 - - - -
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.6 19.7 - - + -
43C SER* 3.0 14.0 + - - -
45C GLN* 1.3 71.5 - - - +
47C ILE* 1.3 60.8 + - - +
49C ALA 3.3 0.7 + - - -
50C ILE* 2.8 56.1 + - + +
53D GLY* 4.8 2.0 - - - -
65D VAL* 2.9 39.7 + - + +
66D ASP 3.8 2.4 + - - -
67D VAL 5.1 0.2 - - - +
70D LEU* 3.3 30.3 - - + +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C HIS* 3.8 20.6 - - + +
27C VAL* 4.7 1.5 - - + +
28C GLY* 4.5 20.6 - - - +
31C CYS* 3.7 20.4 - - + -
32C GLU* 5.5 5.2 - - + +
42C PHE* 3.4 37.7 - - + +
43C SER 3.1 15.4 + - - +
44C LYS* 3.3 12.3 - - + +
46C THR* 1.3 76.1 - - - +
48C ALA* 1.3 62.4 + - - +
50C ILE* 3.2 5.9 + - - +
51C SER* 3.1 29.6 + - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C HIS* 3.7 18.8 + - + -
44C LYS* 2.6 26.0 + - + +
45C GLN* 3.9 6.3 - - - +
47C ILE* 1.3 73.7 - - - +
49C ALA* 1.3 59.8 + - - +
51C SER* 4.0 1.6 - - - -
52C GLU* 3.3 36.3 + - - +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN 2.7 22.8 + - - +
48C ALA* 1.3 71.6 - - - +
50C ILE* 1.3 63.2 + - - +
52C GLU* 4.3 11.6 - - - +
53C LEU* 3.7 19.9 + - - +
56C ARG* 5.7 0.5 + - - -
67D VAL* 4.7 11.0 - - + -
70D LEU* 3.4 20.0 - - + -
71D GLU* 5.5 1.6 - - + +
74D LEU* 4.3 19.2 - - + +
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Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 3.5 20.4 - - + -
31C CYS* 3.5 25.8 - - - -
42C PHE* 4.1 1.8 - - + -
46C THR* 2.8 47.9 + - + +
47C ILE* 3.2 4.2 + - - +
49C ALA* 1.3 76.5 - - - +
51C SER* 1.3 62.1 + - - +
53C LEU* 3.7 8.2 + - + +
54C THR* 3.4 21.2 + - - +
45D PHE* 4.9 1.0 - - + -
46D VAL* 4.2 8.1 - - + +
49D ALA* 3.8 25.4 - - + -
50D ALA* 3.8 16.8 - - - +
70D LEU* 3.8 16.8 - - + -
74D LEU* 5.7 1.1 - - + -
----------------------------------------------------------
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS* 4.7 4.4 - - - +
23C VAL* 3.4 12.7 - - - +
24C HIS* 3.1 56.3 + - - -
27C VAL* 3.6 16.3 - - - +
47C ILE* 3.1 12.0 + - - +
48C ALA 4.0 2.7 - - - -
49C ALA 3.4 0.2 - - - -
50C ILE* 1.3 73.0 - - - +
52C GLU* 1.3 65.3 + - - +
53C LEU 3.2 1.6 - - - -
54C THR 3.2 1.6 + - - -
55C PHE* 3.2 21.5 + - - +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS* 6.3 4.5 - - + -
48C ALA* 3.3 24.8 + - - +
49C ALA* 4.3 9.9 - - - +
51C SER* 1.3 76.9 - - - +
53C LEU* 1.3 57.0 + - - +
55C PHE* 3.6 7.1 + - - +
56C ARG* 3.0 56.3 + - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 3.7 11.2 + - - +
50C ILE* 3.7 11.6 + - + +
51C SER 3.2 0.6 - - - -
52C GLU* 1.3 78.4 - - - +
54C THR* 1.3 54.3 + - - +
56C ARG* 3.6 29.0 - - + +
57C GLN* 2.6 41.2 + - - +
45D PHE* 4.0 13.7 - - + -
49D ALA* 5.5 0.9 - - + -
74D LEU* 4.0 18.4 - - + -
77D LEU* 3.4 39.0 - - + -
78D LEU* 3.3 32.3 - - + -
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL* 3.5 26.5 - - + -
27C VAL* 3.5 1.7 - - - +
50C ILE 3.4 10.7 + - - -
51C SER 3.2 3.3 + - - -
53C LEU* 1.3 72.8 - - - +
55C PHE* 1.3 60.1 + - - +
57C GLN* 3.3 2.1 + - - +
58C CYS* 3.0 45.1 + - - -
10D PHE* 3.9 25.1 - - + -
42D LEU* 4.3 10.5 - - + +
45D PHE* 3.4 14.7 - - - -
46D VAL* 3.3 22.3 - - + +
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Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 3.7 36.6 - - + -
19C LEU* 3.9 24.5 - - + -
20C LYS* 3.7 50.5 - - + -
23C VAL* 3.9 9.1 - - + +
51C SER 3.2 9.7 + - - +
52C GLU* 3.7 10.1 - - - +
54C THR* 1.3 78.6 - - - +
56C ARG* 1.3 69.3 + - + +
58C CYS* 3.3 21.6 + - - +
59C GLU* 3.9 3.5 + - - +
18D LEU* 3.9 20.2 - - + -
21D LEU* 5.2 1.1 - - + -
22D HIS* 6.2 0.4 - + - -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 5.7 0.4 + - - -
52C GLU* 3.0 46.5 + - - +
53C LEU* 3.7 29.6 - - + +
55C PHE* 1.3 84.4 - - + +
57C GLN* 1.3 59.8 + - - +
59C GLU* 3.5 25.3 - - - +
60C ASN* 4.0 8.8 + - - -
78D LEU* 5.4 6.5 - - - +
----------------------------------------------------------
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 2.6 23.8 + - - +
54C THR 3.7 4.5 - - - +
56C ARG* 1.3 71.3 - - - +
58C CYS* 1.3 62.6 + - - +
59C GLU 3.1 3.8 + - - -
60C ASN* 3.4 12.6 + - - +
61C PHE* 3.3 52.3 + - + +
42D LEU* 5.4 0.9 - - + -
45D PHE* 3.9 24.0 - - + -
78D LEU* 4.3 17.5 - - - +
81D PHE* 3.1 44.3 + - - +
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Residues in contact with CYS 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 3.0 26.7 + - - -
55C PHE* 3.3 11.4 + - - +
57C GLN* 1.3 76.8 - - - +
59C GLU* 1.3 60.2 + - - +
61C PHE* 4.1 7.2 - - - +
62C ALA* 3.2 25.8 + - - +
15D VAL* 6.0 0.4 - - - -
18D LEU* 3.6 47.9 - - + +
19D LEU* 4.1 8.5 - - + +
42D LEU* 3.8 28.0 - - - -
----------------------------------------------------------
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PHE 3.9 4.1 + - - +
56C ARG* 3.5 18.3 + - - +
57C GLN 3.1 0.4 - - - -
58C CYS* 1.3 76.7 - - - +
60C ASN* 1.3 79.2 + - - +
62C ALA* 3.3 5.1 + - - +
63C LYS* 3.0 55.7 + - + +
22D HIS* 4.7 20.6 + - + +
----------------------------------------------------------
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Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG 4.0 10.5 + - - -
57C GLN* 3.4 13.6 + - - +
59C GLU* 1.3 100.2 + - - +
61C PHE* 1.3 61.4 + - - +
63C LYS* 4.5 5.5 - - - +
64C ASP* 2.9 38.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN* 3.3 50.3 + - + +
58C CYS* 4.1 6.5 - - - +
59C GLU 3.3 0.4 - - - -
60C ASN* 1.3 74.7 - - + +
62C ALA* 1.3 55.3 + - - +
64C ASP* 4.7 0.7 - - - -
65C LEU* 2.8 42.0 + - - +
85C LEU* 3.7 40.7 - - + +
19D LEU* 4.7 4.5 - - + -
38D MET* 3.9 18.8 - - + -
41D LEU* 4.4 16.6 - - + -
42D LEU* 3.8 31.2 - - + -
45D PHE* 5.1 2.7 - + - -
81D PHE* 4.1 26.7 - + - -
----------------------------------------------------------
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C CYS 3.2 17.4 + - - +
59C GLU* 3.7 4.0 - - - +
61C PHE* 1.3 77.9 - - - +
63C LYS* 1.3 58.5 + - - +
65C LEU* 3.4 2.7 + - - +
66C GLU* 2.8 29.5 + - - +
18D LEU 4.9 0.7 - - - +
19D LEU* 3.4 45.4 - - + +
22D HIS* 4.8 5.8 - - + +
23D PHE* 3.5 14.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 3.0 39.4 + - + +
60C ASN* 4.5 4.9 - - - +
62C ALA* 1.3 76.9 - - - +
64C ASP* 1.3 55.9 + - - +
66C GLU* 3.5 7.3 + - - +
67C MET* 2.9 47.1 + - + +
22D HIS* 2.8 57.6 + - - +
23D PHE 4.7 0.2 - - - -
24D LYS* 3.2 55.9 - - + +
----------------------------------------------------------
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASN* 2.9 28.3 + - - +
61C PHE 4.0 0.2 - - - +
63C LYS* 1.3 69.5 - - - +
65C LEU* 1.3 60.4 + - - +
67C MET* 3.4 22.4 + - - +
68C PHE* 2.9 45.8 + - + -
85C LEU* 3.7 18.0 - - + +
87C ARG* 3.4 22.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE 2.8 26.5 + - - +
62C ALA 3.5 4.5 - - - +
64C ASP* 1.3 71.4 - - - +
66C GLU* 1.3 52.0 + - - +
68C PHE* 3.3 7.1 + - + +
69C ALA* 2.8 35.7 + - - +
77C ILE* 3.6 28.7 - - + +
81C ASP* 3.7 40.6 - - + +
82C VAL* 3.8 7.2 - - + +
85C LEU* 3.6 15.5 - - + +
19D LEU* 3.8 33.9 - - + -
30D VAL* 5.2 0.7 - - + -
38D MET* 3.9 18.8 - - + -
----------------------------------------------------------
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA 2.8 20.4 + - - +
63C LYS* 3.5 13.4 - - - +
65C LEU* 1.3 70.6 - - - +
67C MET* 1.3 65.6 + - - +
69C ALA 3.1 0.3 + - - -
70C ARG* 2.8 45.2 + - + +
77C ILE* 4.5 0.6 - - - +
23D PHE* 4.1 8.5 - - + -
24D LYS* 2.8 38.7 + - - +
25D ASP* 3.0 27.4 + - + +
28D THR* 3.4 32.9 + - - +
----------------------------------------------------------
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Residues in contact with MET 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LYS* 2.9 42.8 + - + +
64C ASP* 3.4 24.9 + - - +
66C GLU* 1.3 85.5 - - - +
68C PHE* 1.3 56.5 - - + +
70C ARG* 5.2 1.8 - - - -
71C HIS* 2.6 38.7 + - - +
24D LYS* 5.7 3.6 - - + +
----------------------------------------------------------
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ASP* 2.9 33.9 + - + +
65C LEU* 3.5 7.0 - - - +
67C MET* 1.3 83.5 - - + +
69C ALA* 1.3 61.7 + - - +
71C HIS* 3.4 8.3 + + + +
72C ALA* 3.2 23.6 + - - +
81C ASP* 3.4 39.2 - - - +
84C LEU* 4.0 28.3 - - + -
85C LEU* 3.5 25.1 - - + -
87C ARG* 3.6 26.5 - - - -
71G HIS* 5.6 6.7 - - - -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU 2.8 20.4 + - - +
66C GLU* 3.1 4.7 + - - +
68C PHE* 1.3 71.1 - - - +
70C ARG* 1.3 60.4 - - - +
72C ALA* 3.5 6.1 + - - +
74C ARG* 3.0 35.7 + - - +
75C THR 5.1 1.3 - - - +
76C THR 4.3 4.3 - - - -
77C ILE* 3.6 32.1 - - + +
81C ASP* 3.6 11.9 - - - +
28D THR* 4.5 5.8 - - + +
----------------------------------------------------------
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLU* 2.8 28.6 + - + +
67C MET* 4.9 2.0 - - - +
69C ALA* 1.3 72.7 - - - +
71C HIS* 1.3 62.6 - - - +
72C ALA 3.2 0.9 - - - -
73C LYS* 3.3 14.7 + - - +
74C ARG 3.9 8.3 - - - +
25D ASP* 2.4 41.5 + - + +
27D LYS* 2.8 33.7 - - - +
28D THR* 5.6 2.0 + - - +
----------------------------------------------------------
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C MET 2.6 25.5 + - - +
68C PHE* 3.6 10.8 - + - +
69C ALA 3.3 0.4 - - - -
70C ARG* 1.3 79.1 - - - +
72C ALA* 1.3 54.4 + - - +
73C LYS* 3.5 12.5 + - - -
71G HIS* 5.9 5.2 - + - -
----------------------------------------------------------
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE 3.2 11.1 + - - +
69C ALA 3.5 0.6 + - - +
70C ARG 3.2 0.6 - - - -
71C HIS* 1.3 77.6 - - - +
73C LYS* 1.3 74.5 + - - +
74C ARG* 3.3 40.5 + - - +
81C ASP* 5.5 0.4 - - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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