Contacts of the helix formed by residues 45 - 71 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 4.1 2.7 - - - -
146B ASP* 3.1 33.3 + - + -
67E LYS* 5.0 5.1 + - - -
37I PHE 4.6 1.6 - - - -
38I ASP* 3.4 43.8 + - - -
43I ALA* 3.3 15.5 + - + -
44I LEU* 1.3 69.0 - - - +
46I ASN* 1.3 65.1 + - - +
48I ALA* 3.5 6.7 + - - +
49I GLU* 3.1 30.6 + - + +
167I ASP* 3.6 3.4 + - - +
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Residues in contact with ASN 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I HIS* 1.3 77.1 - - - +
47I VAL* 1.3 66.3 + - - +
49I GLU* 3.3 8.3 + - - +
50I PHE 3.0 18.0 + - - -
167I ASP* 3.0 46.0 + - - +
168I LYS* 4.4 10.1 - - - +
171I VAL* 3.2 27.6 - - + +
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Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 3.9 20.6 - - + -
44I LEU* 3.5 18.4 - - + +
46I ASN* 1.3 77.7 - - - +
48I ALA* 1.3 61.2 + - - +
50I PHE* 3.2 8.8 + - - +
51I PHE* 3.2 45.5 + - + -
92I THR* 4.1 25.8 - - + +
96I MET* 4.6 4.5 - - + -
163I GLU 5.8 0.2 - - - +
166I PHE* 4.3 13.7 - - + -
167I ASP* 3.1 22.5 + - + +
171I VAL* 4.4 4.5 - - + +
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Residues in contact with ALA 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I TYR* 3.2 39.0 - - + +
37I PHE* 3.7 24.6 - - + +
38I ASP* 4.1 4.3 - - + +
44I LEU 3.0 14.3 + - - +
45I HIS* 3.5 15.5 - - - +
46I ASN 3.2 0.2 - - - -
47I VAL* 1.3 77.8 - - - +
49I GLU* 1.3 57.6 + - - +
51I PHE* 3.4 2.1 + - - -
52I LYS 3.0 21.3 + - - -
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Residues in contact with GLU 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LYS* 5.8 1.7 - - - -
34I TYR* 3.6 23.6 + - - -
45I HIS* 3.1 18.2 + - + +
46I ASN* 3.3 11.0 + - - +
48I ALA* 1.3 74.9 - - - +
50I PHE* 1.3 61.9 + - - +
51I PHE 3.2 0.2 - - - -
52I LYS* 3.6 24.4 + - - +
53I GLU* 2.9 40.0 + - - +
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Residues in contact with PHE 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I TYR* 5.9 0.2 - + - -
46I ASN 3.0 14.0 + - - +
47I VAL* 3.2 11.2 + - - +
49I GLU* 1.3 76.0 - - - +
51I PHE* 1.3 93.2 + + - +
53I GLU* 3.5 8.7 + - + +
54I HIS* 3.2 54.6 + + - -
96I MET* 4.0 20.2 - - + -
143I ARG* 3.9 17.3 - - - -
144I ILE* 4.5 12.6 - - + -
147I PHE* 3.7 30.1 - + - -
171I VAL* 3.7 20.8 - - + +
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Residues in contact with PHE 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I TYR* 3.6 50.2 - + + +
33I MET* 3.8 29.8 - - + -
34I TYR 4.0 4.7 - - - +
37I PHE* 3.7 22.2 - + - -
47I VAL* 3.2 38.1 + - + -
48I ALA* 3.9 5.6 - - - +
50I PHE* 1.3 99.4 - + - +
52I LYS* 1.3 59.1 + - - +
54I HIS* 3.2 5.3 + - + +
55I SER* 2.9 23.9 + - - -
95I ALA* 4.1 12.6 - - + -
96I MET* 3.7 24.5 - - + -
99I ALA* 4.2 8.7 - - + -
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Residues in contact with LYS 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E GLU* 3.6 24.7 + - - +
34I TYR* 3.7 39.4 + - + +
48I ALA 3.0 18.2 + - - +
49I GLU* 3.6 33.1 + - - +
50I PHE 3.3 0.2 - - - -
51I PHE* 1.3 76.8 - - - +
53I GLU* 1.3 62.1 + - + +
55I SER* 3.2 21.1 + - - +
56I HIS* 3.3 30.7 + - + +
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Residues in contact with GLU 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLU* 2.9 26.1 + - + +
50I PHE* 3.6 9.2 - - + +
52I LYS* 1.3 77.9 - - + +
54I HIS* 1.3 62.2 + - + +
56I HIS* 3.3 9.5 + - - +
57I GLU* 3.1 35.5 + - - +
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Residues in contact with HIS 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I TYR* 3.9 23.2 - + + -
50I PHE* 3.2 42.1 + + - +
51I PHE* 3.2 10.5 + - - +
53I GLU* 1.3 82.1 - - + +
55I SER* 1.3 62.8 + - - +
57I GLU* 3.4 17.7 + - - +
58I GLU* 3.2 32.4 + - - +
103I GLU* 3.6 17.7 + - - -
140I ASP* 3.7 26.7 - - + -
143I ARG* 3.1 27.7 + - - -
144I ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E GLU* 4.4 5.2 + - - -
27I SER* 2.9 46.9 + - - +
30I TYR* 3.7 14.8 - - - +
31I SER* 3.8 15.2 + - - -
51I PHE 2.9 9.1 + - - -
52I LYS* 3.2 16.8 + - - +
53I GLU 3.3 0.6 - - - -
54I HIS* 1.3 75.1 - - - +
56I HIS* 1.3 75.2 + - - +
58I GLU 3.4 1.4 + - - -
59I ARG* 3.1 11.8 + - - +
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Residues in contact with HIS 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ARG* 6.0 3.3 - - + +
63E GLU* 3.1 29.2 + - - -
52I LYS* 3.3 35.0 + - + +
53I GLU* 3.3 12.3 + - - +
54I HIS 3.2 0.4 - - - -
55I SER* 1.3 90.5 + - - +
57I GLU* 1.3 56.3 + - - +
59I ARG* 3.5 7.8 + - + +
60I GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I GLU* 3.1 21.5 + - - +
54I HIS* 3.6 26.0 + - - +
55I SER 3.2 0.4 - - - -
56I HIS* 1.3 75.6 - - - +
58I GLU* 1.3 64.7 + - + +
60I GLU* 3.2 7.7 + - + +
61I HIS* 2.9 44.6 + - + +
140I ASP* 4.1 18.0 - - - +
143I ARG* 5.8 1.9 + - - -
----------------------------------------------------------
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Residues in contact with GLU 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLU* 2.7 30.6 - - - +
26I ALA* 4.2 9.4 - - + -
27I SER* 3.8 12.8 - - - +
30I TYR* 4.0 16.8 - - + -
54I HIS* 3.2 21.4 + - - +
57I GLU* 1.3 79.7 - - - +
59I ARG* 1.3 58.4 + - - +
61I HIS* 3.1 11.8 + - - +
62I ALA* 3.0 25.5 + - - +
103I GLU* 3.4 14.9 - - - +
106I VAL* 4.9 1.2 - - - +
140I ASP* 4.4 0.2 - - - +
176I MG 2.0 32.0 - - - -
177I MG 2.6 24.9 - - - -
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Residues in contact with ARG 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E HIS* 6.0 3.1 - - + +
59E ARG* 5.7 8.7 - - + -
24I LEU* 4.9 12.3 - - + +
27I SER* 3.6 13.6 + - - +
55I SER 3.1 17.8 + - - +
56I HIS* 3.6 10.3 - - + +
57I GLU 3.1 0.2 - - - -
58I GLU* 1.3 75.2 - - - +
60I GLU* 1.3 62.6 + - - +
62I ALA* 3.2 8.4 + - - +
63I GLU* 3.1 35.4 + - + +
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Residues in contact with GLU 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I HIS 3.1 15.1 + - - +
57I GLU* 3.2 10.9 + - + +
59I ARG* 1.3 74.9 - - - +
61I HIS* 1.3 61.0 + - + +
63I GLU* 3.5 11.6 + - - +
64I LYS* 3.1 32.4 + - - +
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Residues in contact with HIS 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLU* 3.4 16.4 + - - +
57I GLU* 2.9 30.6 + - + +
58I GLU* 3.1 18.6 + - - +
59I ARG 3.2 0.2 - - - -
60I GLU* 1.3 76.6 - - + +
62I ALA* 1.3 63.9 + - - +
64I LYS* 3.4 19.2 + - - +
65I PHE* 3.3 12.9 + - - -
132I GLU 4.6 6.7 + - - -
133I TYR* 3.0 39.2 + + + -
136I GLU* 5.1 14.6 - - + +
137I GLN* 5.1 1.1 - - - -
140I ASP* 5.6 0.7 - - - -
176I MG 2.7 24.5 - - - -
177I MG 4.3 9.6 - - - -
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Residues in contact with ALA 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 3.7 16.5 - - + +
23I GLU* 3.8 9.8 - - + +
24I LEU* 3.7 35.2 - - + +
58I GLU 3.0 11.9 + - - +
59I ARG 3.5 9.0 - - - +
61I HIS* 1.3 76.2 - - - +
63I GLU* 1.3 63.7 + - - +
65I PHE* 3.3 9.1 + - - +
66I MET* 3.1 26.1 + - + +
----------------------------------------------------------
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Residues in contact with GLU 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E SER* 4.9 5.1 + - - +
34E TYR* 5.1 10.6 - - + -
52E LYS* 3.6 20.2 + - - +
55E SER* 4.4 5.4 + - - -
56E HIS* 3.1 34.3 + - - -
24I LEU* 6.4 0.2 - - + -
59I ARG* 3.1 24.7 + - + +
60I GLU* 3.8 12.2 - - - +
62I ALA* 1.3 75.7 - - - +
64I LYS* 1.3 64.1 + - - +
66I MET* 3.2 24.9 + - + +
67I LYS* 3.1 24.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I GLU* 3.1 20.6 + - - +
61I HIS* 3.6 17.8 + - - +
62I ALA 3.3 0.2 - - - -
63I GLU* 1.3 76.1 - - - +
65I PHE* 1.3 58.2 + - - +
67I LYS* 3.5 7.9 + - - +
68I TYR* 2.9 26.9 + - - +
128I PHE* 3.7 9.5 - - + -
132I GLU* 2.9 52.8 + - + +
133I TYR* 3.2 21.5 - - + +
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Residues in contact with PHE 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I VAL* 3.9 29.4 - - + +
19I MET* 3.4 32.5 - - + -
20I LEU* 4.2 18.1 - - + +
23I GLU* 4.1 14.8 - - + -
61I HIS 3.3 16.9 + - - -
62I ALA 3.3 8.0 + - - +
63I GLU 3.2 0.8 - - - -
64I LYS* 1.3 77.2 - - - +
66I MET* 1.3 64.3 + - - +
68I TYR* 3.5 3.0 - - + +
69I GLN* 3.0 25.1 + - - +
110I LEU* 4.0 10.5 - - + -
113I LEU* 4.5 7.6 - - + -
125I LEU* 5.3 0.2 - - + -
128I PHE* 3.5 26.2 - + - -
129I LEU* 4.0 11.9 - - + -
133I TYR* 3.4 30.7 - + - -
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Residues in contact with MET 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 5.5 0.2 - - + -
31E SER* 3.3 39.5 - - - +
34E TYR* 4.5 15.0 - - + -
35E ALA* 4.3 13.2 - - + -
20I LEU* 3.8 30.3 - - + +
24I LEU* 5.1 7.6 - - + -
62I ALA* 3.1 21.9 + - + +
63I GLU* 3.2 22.9 + - + +
65I PHE* 1.3 74.7 - - - +
67I LYS* 1.3 61.1 + - - +
69I GLN* 3.4 4.9 - - - +
70I ASN* 3.3 26.8 + - - -
76I VAL* 3.9 21.2 - - + +
78I LEU* 4.7 8.1 - - + -
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Residues in contact with LYS 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.4 28.5 + - - +
38E ASP* 3.2 32.5 + - - +
45E HIS* 5.1 4.6 + - - -
49E GLU* 5.8 1.1 - - - -
63I GLU 3.1 9.1 + - - +
64I LYS* 3.6 11.2 - - - +
66I MET* 1.3 79.4 - - - +
68I TYR* 1.3 57.1 + - - +
70I ASN* 3.5 3.3 + - - +
71I LYS* 3.0 44.5 + - + +
142W LYS* 6.0 0.8 - - - +
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Residues in contact with TYR 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I TYR* 3.9 18.4 - + - -
16I VAL* 4.6 8.1 - - + -
64I LYS 2.9 18.1 + - - +
65I PHE* 3.5 6.7 - - - +
67I LYS* 1.3 74.5 - - - +
69I GLN* 1.3 67.5 + - - +
71I LYS* 3.1 17.2 + - + +
72I ARG* 2.8 51.6 + - + +
124I HIS* 2.8 42.2 + + - -
125I LEU* 3.2 35.9 - - + -
128I PHE* 3.6 43.1 - + + -
135W GLU* 5.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLN 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I TYR* 3.0 36.7 + - - -
13I GLU* 3.2 27.1 + - - +
16I VAL* 3.5 14.6 - - + +
17I ASN* 3.4 19.2 + - - -
20I LEU* 5.8 1.1 - - + +
65I PHE 3.0 13.9 + - - +
66I MET 3.4 6.7 - - - +
68I TYR* 1.3 83.3 - - - +
70I ASN* 1.3 61.3 + - - +
72I ARG* 3.2 5.0 + - - +
73I GLY 3.1 3.6 + - - -
74I GLY* 2.9 42.9 + - - -
75I ARG 4.0 6.7 - - - -
76I VAL* 3.7 23.8 - - + +
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Residues in contact with ASN 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ALA* 3.1 29.1 + - - +
38E ASP* 3.2 39.1 + - - +
39E ARG* 3.3 27.9 - - - +
40E ASP* 4.9 3.6 + - - +
4I VAL* 4.5 1.0 - - - +
66I MET* 3.3 13.7 + - - +
67I LYS 3.9 3.1 - - - +
69I GLN* 1.3 77.0 - - - +
71I LYS* 1.3 66.0 + - - +
73I GLY* 3.2 9.9 + - - -
74I GLY 3.9 12.4 - - - +
75I ARG* 4.0 1.6 + - - +
76I VAL* 4.6 9.2 + - - +
142W LYS* 3.4 17.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 3.4 17.3 - - - +
67I LYS* 3.0 30.1 + - + +
68I TYR* 3.1 22.8 + - + +
70I ASN* 1.3 75.9 - - - +
72I ARG* 1.3 63.2 + - + +
124I HIS* 5.4 0.2 - - + -
128I PHE* 6.2 2.6 - - - -
135W GLU* 2.8 37.5 + - - +
138W VAL* 4.2 25.5 - - + +
139W LYS* 4.6 11.2 - - - +
142W LYS* 4.2 27.7 - - + +
----------------------------------------------------------
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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