Contacts of the helix formed by residues 45 - 71 (chain C) in PDB entry 1MFR
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 HIS 45 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE 4.6 1.6 - - - -
38C ASP* 3.4 37.3 + - - -
43C ALA* 3.3 15.8 + - + -
44C LEU* 1.3 68.2 - - - +
46C ASN* 1.3 64.8 + - - +
48C ALA* 3.5 6.7 - - - +
49C GLU* 3.1 30.4 + - + +
167C ASP* 3.6 3.4 + - - +
142F LYS* 4.0 9.9 - - - -
146F ASP* 3.0 33.7 + - + -
67O LYS* 5.1 4.2 + - - -
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Residues in contact with ASN 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C HIS* 1.3 77.5 - - - +
47C VAL* 1.3 66.2 - - - +
49C GLU* 3.3 8.6 + - - +
50C PHE 3.0 17.8 + - - -
167C ASP* 2.9 46.2 + - - +
168C LYS* 4.4 10.9 - - - +
171C VAL* 3.2 27.4 - - + +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.9 20.2 - - + -
44C LEU* 3.5 18.6 - - + +
45C HIS 3.3 0.2 - - - -
46C ASN* 1.3 76.6 - - - +
48C ALA* 1.3 62.6 + - - +
50C PHE* 3.2 8.5 + - - +
51C PHE* 3.2 44.9 + - + -
92C THR* 4.1 25.6 - - + +
96C MET* 4.6 5.2 - - + -
163C GLU 5.8 0.2 - - - +
166C PHE* 4.3 14.1 - - + -
167C ASP* 3.1 23.1 + - + +
171C VAL* 4.4 4.7 - - + +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.2 39.9 - - + +
37C PHE* 3.7 23.3 - - + +
38C ASP* 4.1 4.7 - - + +
44C LEU 3.0 14.7 + - - +
45C HIS* 3.5 14.8 - - - +
47C VAL* 1.3 77.6 - - - +
49C GLU* 1.3 57.7 + - - +
51C PHE* 3.4 2.1 + - - -
52C LYS 3.0 21.3 + - - -
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.6 23.4 + - - -
45C HIS* 3.1 18.5 + - + +
46C ASN* 3.3 11.0 + - - +
48C ALA* 1.3 74.5 - - - +
50C PHE* 1.3 61.3 + - - +
52C LYS* 3.6 24.4 + - - +
53C GLU* 2.9 39.8 + - - +
67O LYS* 5.8 1.6 - - - -
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Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 5.9 0.2 - + - -
46C ASN 3.0 13.8 + - - +
47C VAL* 3.2 10.5 + - - +
49C GLU* 1.3 77.1 - - - +
51C PHE* 1.3 92.2 - + - +
53C GLU* 3.5 8.4 + - + +
54C HIS* 3.2 55.4 + + - -
96C MET* 4.0 20.2 - - + -
143C ARG* 3.9 17.9 - - - -
144C ILE* 4.5 11.4 - - + -
147C PHE* 3.7 29.6 - + - -
171C VAL* 3.7 20.6 - - + +
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.6 51.1 - + + +
33C MET* 3.8 30.5 - - + -
34C TYR 4.0 4.9 - - - +
37C PHE* 3.7 21.8 - + - -
47C VAL* 3.2 37.9 + - + -
48C ALA 3.9 4.9 - - - +
49C GLU 3.2 0.2 - - - -
50C PHE* 1.3 98.4 - + - +
52C LYS* 1.3 59.2 + - - +
54C HIS* 3.2 5.5 + - + +
55C SER* 2.9 23.7 + - - -
95C ALA* 4.1 11.9 - - + -
96C MET* 3.7 24.5 - - + -
99C ALA* 4.2 8.1 - - + -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.7 37.8 + - + +
48C ALA 3.0 17.1 + - - +
49C GLU* 3.6 33.3 + - - +
50C PHE 3.3 0.2 - - - -
51C PHE* 1.3 76.8 - - - +
53C GLU* 1.3 62.2 + - + +
55C SER* 3.2 21.6 + - - +
56C HIS* 3.3 30.3 + - + +
63O GLU* 3.7 24.9 - - - +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 2.9 25.9 + - + +
50C PHE* 3.6 9.1 - - + +
51C PHE 3.2 0.2 - - - -
52C LYS* 1.3 77.9 - - + +
54C HIS* 1.3 62.1 + - + +
56C HIS* 3.3 10.1 + - - +
57C GLU* 3.1 36.1 + - - +
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Residues in contact with HIS 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.9 23.7 - + + -
50C PHE* 3.2 41.0 + + - +
51C PHE* 3.2 11.0 + - - +
53C GLU* 1.3 82.9 - - + +
55C SER* 1.3 63.8 + - - +
57C GLU* 3.6 18.4 + - - +
58C GLU* 3.2 32.2 + - - +
103C GLU* 3.6 17.7 + - - -
140C ASP* 3.7 25.8 - - + -
143C ARG* 3.1 28.2 + - - -
144C ILE* 4.9 4.7 - - + -
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER* 2.9 47.1 + - - +
30C TYR* 3.7 14.6 - - - +
31C SER* 3.8 15.0 + - - -
34C TYR* 5.8 0.2 - - - +
51C PHE 2.9 9.6 + - - -
52C LYS* 3.2 16.6 + - - +
53C GLU 3.3 0.4 - - - -
54C HIS* 1.3 74.4 - - - +
56C HIS* 1.3 76.4 + - - +
58C GLU 3.4 1.0 + - - -
59C ARG* 3.1 12.0 + - - +
63O GLU* 4.5 4.9 + - - -
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Residues in contact with HIS 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LYS* 3.3 35.1 + - + +
53C GLU* 3.3 12.1 + - - +
54C HIS 3.2 0.4 - - - -
55C SER* 1.3 89.6 + - - +
57C GLU* 1.3 56.5 + - - +
59C ARG* 3.5 8.0 + - + +
60C GLU* 3.1 26.0 + - - +
59O ARG* 6.1 3.1 - - + +
63O GLU* 3.1 29.6 + - - -
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLU* 3.1 21.3 + - - +
54C HIS* 3.6 25.8 + - - +
55C SER 3.2 0.2 - - - -
56C HIS* 1.3 75.6 - - - +
58C GLU* 1.3 63.1 + - + +
60C GLU* 3.2 7.2 + - + +
61C HIS* 3.0 46.1 + - + +
140C ASP* 4.1 17.5 - - - +
143C ARG* 5.8 1.7 + - - -
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 2.7 31.3 - - - +
26C ALA* 4.2 9.4 - - + +
27C SER* 3.8 13.2 - - - +
30C TYR* 4.0 16.6 - - + -
54C HIS* 3.2 21.4 + - - +
55C SER 3.4 0.2 + - - -
57C GLU* 1.3 80.3 - - - +
59C ARG* 1.3 58.4 + - - +
61C HIS* 3.1 10.8 + - - +
62C ALA* 3.0 25.8 + - - +
103C GLU* 3.4 14.3 - - - +
106C VAL* 4.9 0.8 - - - +
176C MG 2.0 32.6 - - - -
177C MG 2.6 25.0 - - - -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 4.9 12.3 - - + +
27C SER* 3.6 14.3 + - - +
55C SER 3.1 18.0 + - - +
56C HIS* 3.6 9.6 - - + +
57C GLU 3.1 0.2 - - - -
58C GLU* 1.3 74.6 - - - +
60C GLU* 1.3 62.9 + - - +
62C ALA* 3.2 8.4 + - - +
63C GLU* 3.1 35.8 + - + +
56O HIS* 6.1 2.7 - - + +
59O ARG* 5.7 9.2 - - + -
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS 3.1 15.1 + - - +
57C GLU* 3.2 10.5 + - - +
59C ARG* 1.3 75.8 - - - +
61C HIS* 1.3 61.0 + - + +
63C GLU* 3.5 12.6 + - - +
64C LYS* 3.1 33.2 + - - +
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Residues in contact with HIS 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 3.4 15.5 + - - +
57C GLU* 3.0 30.2 + - + +
58C GLU* 3.1 17.7 + - - +
59C ARG 3.2 0.2 - - - -
60C GLU* 1.3 77.9 - - + +
62C ALA* 1.3 65.1 + - - +
64C LYS* 3.4 17.9 + - - -
65C PHE* 3.3 12.7 + - - -
132C GLU 4.6 6.8 + - - -
133C TYR* 3.0 40.7 + + + -
136C GLU* 5.1 13.9 - - + +
137C GLN* 5.1 0.9 - - - -
140C ASP* 5.6 0.4 - - - -
176C MG 2.7 24.3 - - - -
177C MG 4.3 10.1 - - - -
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.7 16.7 - - + +
23C GLU* 3.8 9.6 - - + +
24C LEU* 3.7 35.4 - - + -
58C GLU 3.0 12.5 + - - +
59C ARG 3.2 8.7 + - - +
61C HIS* 1.3 76.3 - - - +
63C GLU* 1.3 63.9 + - + +
65C PHE* 3.3 8.9 + - - +
66C MET* 3.1 26.6 + - + +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 6.4 0.4 - - + -
59C ARG* 3.1 24.5 + - + +
60C GLU* 3.8 12.0 - - - +
61C HIS 3.3 0.2 - - - -
62C ALA* 1.3 76.6 - - + +
64C LYS* 1.3 63.7 + - - +
66C MET* 3.2 24.4 + - + +
67C LYS* 3.1 24.6 + - - +
31O SER* 4.9 5.0 + - - +
34O TYR* 5.1 10.9 - - + -
52O LYS* 3.7 20.1 + - - +
55O SER* 4.4 4.9 + - - -
56O HIS* 3.0 34.7 + - - -
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLU* 3.1 20.1 + - - +
61C HIS* 3.6 17.0 + - - +
62C ALA 3.3 0.4 - - - -
63C GLU* 1.3 76.3 - - - +
65C PHE* 1.3 57.4 + - - +
67C LYS* 3.5 7.9 + - - +
68C TYR* 2.9 27.7 + - - +
128C PHE* 3.7 9.1 - - + -
132C GLU* 2.9 52.7 + - + +
133C TYR* 3.2 21.5 - - + +
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Residues in contact with PHE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 3.9 28.9 - - + +
19C MET* 3.4 32.5 - - + -
20C LEU* 4.2 19.0 - - + +
23C GLU* 4.1 15.0 - - + -
61C HIS 3.3 16.5 + - - -
62C ALA 3.3 8.6 + - - +
63C GLU 3.2 0.4 - - - -
64C LYS* 1.3 77.8 - - - +
66C MET* 1.3 64.5 + - - +
68C TYR* 3.5 3.3 - - + +
69C GLN* 3.0 24.6 + - - +
110C LEU* 4.0 10.8 - - + -
113C LEU* 4.5 7.4 - - + -
125C LEU* 5.3 0.2 - - + -
128C PHE* 3.5 24.5 - + - -
129C LEU* 4.0 12.6 - - + -
133C TYR* 3.4 31.4 - + - -
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Residues in contact with MET 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.8 29.6 - - + +
24C LEU* 5.1 7.9 - - + -
62C ALA* 3.1 21.5 + - + +
63C GLU* 3.2 22.9 + - + +
65C PHE* 1.3 75.3 - - - +
67C LYS* 1.3 62.4 + - - +
69C GLN* 3.4 4.4 - - - +
70C ASN* 3.3 27.6 + - - -
76C VAL* 3.9 21.4 - - + +
78C LEU* 4.7 7.2 - - + -
28O TYR* 5.5 0.7 - - + -
31O SER* 3.3 39.5 - - - +
34O TYR* 4.5 15.9 - - + -
35O ALA* 4.3 12.6 - - + -
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU 3.1 9.0 + - - +
64C LYS* 3.6 11.4 - - - +
66C MET* 1.3 80.2 - - - +
68C TYR* 1.3 56.3 + - - +
70C ASN* 3.5 3.5 + - - +
71C LYS* 3.0 45.2 + - + +
34O TYR* 3.3 29.4 + - - +
38O ASP* 3.2 33.1 + - - +
45O HIS* 5.1 4.6 + - - -
49O GLU* 5.8 1.8 - - - -
142R LYS* 6.0 0.4 - - - +
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Residues in contact with TYR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 3.9 18.4 - + - -
16C VAL* 4.6 7.4 - - + -
64C LYS 2.9 18.6 + - - +
65C PHE* 3.5 6.7 - - - +
66C MET 3.2 0.2 - - - -
67C LYS* 1.3 74.3 - - - +
69C GLN* 1.3 67.4 + - - +
71C LYS* 3.1 17.0 + - + +
72C ARG* 2.8 53.1 + - + +
124C HIS* 2.8 41.8 + + - -
125C LEU* 3.2 36.3 - - + -
128C PHE* 3.6 44.2 - + + -
135R GLU* 5.7 0.4 - - - -
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 3.0 36.2 + - - -
13C GLU* 3.2 27.7 + - - +
16C VAL* 3.5 14.1 - - + +
17C ASN* 3.4 19.4 + - - -
20C LEU* 6.0 0.4 - - + -
65C PHE 3.0 13.7 + - - +
66C MET* 3.4 7.2 - - - +
68C TYR* 1.3 83.3 - - - +
70C ASN* 1.3 60.7 + - - +
72C ARG* 3.2 4.5 + - - +
73C GLY 3.1 3.3 + - - -
74C GLY* 2.9 42.6 + - - -
75C ARG 4.0 6.5 - - - -
76C VAL* 3.7 24.5 - - + +
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Residues in contact with ASN 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 4.5 0.7 - - - +
66C MET 3.3 12.7 + - - -
67C LYS 3.9 3.4 - - - +
69C GLN* 1.3 75.7 - - - +
71C LYS* 1.3 65.3 + - - +
73C GLY* 3.2 9.9 + - - -
74C GLY 3.9 12.1 - - - +
75C ARG* 4.0 1.9 + - - +
76C VAL* 4.6 9.3 + - - +
34O TYR* 6.3 0.4 - - - -
35O ALA* 3.1 30.5 + - - +
38O ASP* 3.1 38.4 + - - +
39O ARG* 3.3 27.3 - - - +
40O ASP* 4.9 3.5 + - - +
142R LYS* 3.2 17.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 3.4 17.5 - - - +
67C LYS* 3.0 29.7 + - + +
68C TYR* 3.3 22.3 - - + +
70C ASN* 1.3 76.7 - - - +
72C ARG* 1.3 64.3 + - + +
124C HIS* 5.4 0.2 - - + -
128C PHE* 6.2 2.6 - - - -
135R GLU* 2.8 34.8 + - - +
138R VAL* 4.3 23.5 - - + +
139R LYS* 4.6 12.0 - - - +
142R LYS* 4.1 28.7 - - + +
----------------------------------------------------------
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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