Contacts of the helix formed by residues 45 - 71 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 5.1 4.9 + - - -
37O PHE 4.6 1.8 - - - -
38O ASP* 3.4 44.1 + - - -
43O ALA* 3.3 15.2 + - + -
44O LEU* 1.3 69.8 - - - +
46O ASN* 1.3 63.7 + - - +
48O ALA* 3.5 6.1 - - - +
49O GLU* 3.1 30.9 + - + +
167O ASP* 3.6 3.2 + - - +
142R LYS* 4.0 2.9 - - - -
146R ASP* 3.1 33.0 + - + -
150R ASN* 5.8 0.2 - - - -
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Residues in contact with ASN 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O HIS* 1.3 77.5 - - - +
47O VAL* 1.3 65.0 + - - +
49O GLU* 3.3 9.1 + - - +
50O PHE 3.0 18.0 + - - -
167O ASP* 3.0 46.0 + - - +
168O LYS* 4.4 10.5 - - - +
171O VAL* 3.2 28.2 - - + +
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Residues in contact with VAL 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O PHE* 3.9 20.9 - - + -
44O LEU* 3.5 18.4 - - + +
46O ASN* 1.3 76.8 - - - +
48O ALA* 1.3 60.8 + - - +
50O PHE* 3.2 9.0 + - - +
51O PHE* 3.2 45.4 + - + -
92O THR* 4.1 26.9 - - + +
96O MET* 4.6 4.0 - - + -
163O GLU 5.8 0.4 - - - +
166O PHE* 4.3 13.0 - - + -
167O ASP* 3.1 22.9 + - + +
171O VAL* 4.6 5.2 - - + -
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Residues in contact with ALA 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O TYR* 3.2 40.1 - - + +
37O PHE* 3.7 24.0 - - + +
38O ASP* 4.1 4.5 - - + +
44O LEU 3.0 14.3 + - - +
45O HIS* 3.5 15.0 - - - +
47O VAL* 1.3 78.6 - - - +
49O GLU* 1.3 58.9 + - - +
51O PHE* 3.4 1.9 + - - -
52O LYS 3.0 21.3 + - - -
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Residues in contact with GLU 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 5.8 1.2 - - - -
34O TYR* 3.6 23.4 + - - -
45O HIS 3.1 18.2 + - - +
46O ASN* 3.3 11.9 + - - +
48O ALA* 1.3 74.0 - - - +
50O PHE* 1.3 60.7 + - - +
52O LYS* 3.6 24.7 + - - +
53O GLU* 2.9 39.2 + - - +
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Residues in contact with PHE 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 5.9 0.4 - + - -
46O ASN 3.0 13.8 + - - +
47O VAL* 3.2 10.1 + - - +
49O GLU* 1.3 76.5 - - - +
51O PHE* 1.3 92.8 + + - +
53O GLU* 3.5 8.6 + - + +
54O HIS* 3.2 54.3 + + - -
96O MET* 4.0 20.6 - - + -
143O ARG* 3.9 17.9 - - - -
144O ILE* 4.5 12.3 - - + -
147O PHE* 3.7 28.7 - + - -
171O VAL* 3.7 21.1 - - + +
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Residues in contact with PHE 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.6 48.6 - + + +
33O MET* 3.8 28.9 - - + -
34O TYR 4.0 4.5 - - - +
37O PHE* 3.7 22.9 - + - -
47O VAL* 3.2 36.5 + - + -
48O ALA* 3.9 5.2 - - - +
50O PHE* 1.3 98.3 - + - +
52O LYS* 1.3 59.8 + - - +
54O HIS* 3.2 5.5 + - + +
55O SER* 2.9 24.1 + - - -
92O THR 5.7 0.2 - - - -
95O ALA* 4.1 12.6 - - + -
96O MET* 3.7 23.1 - - + -
99O ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 3.7 24.6 + - - +
34O TYR* 3.7 39.0 + - + +
48O ALA 3.0 18.0 + - - +
49O GLU* 3.6 33.5 + - - +
50O PHE 3.3 0.2 - - - -
51O PHE* 1.3 76.1 - - - +
53O GLU* 1.3 64.2 + - + +
55O SER* 3.2 20.1 + - - +
56O HIS* 3.3 30.0 + - + +
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Residues in contact with GLU 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O GLU* 2.9 26.4 + - + +
50O PHE* 3.6 9.3 - - + +
52O LYS* 1.3 77.3 - - + +
54O HIS* 1.3 63.8 + - + +
56O HIS* 3.3 10.7 + - - +
57O GLU* 3.1 35.5 + - - +
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Residues in contact with HIS 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.9 22.6 - + + -
50O PHE* 3.2 41.4 + + - +
51O PHE* 3.2 10.1 + - - +
53O GLU* 1.3 82.3 - - + +
55O SER* 1.3 64.1 + - - +
57O GLU* 3.6 18.6 + - - +
58O GLU* 3.2 33.1 + - - +
103O GLU* 3.6 17.5 + - - -
140O ASP* 3.7 26.9 - - + -
143O ARG* 3.2 27.6 + - - -
144O ILE* 4.9 4.3 - - + -
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Residues in contact with SER 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 4.4 5.0 + - - -
27O SER* 2.9 48.2 + - - +
30O TYR* 3.7 14.3 - - - +
31O SER* 3.8 14.7 + - - -
34O TYR* 5.8 0.2 - - - +
51O PHE 2.9 9.6 + - - -
52O LYS* 3.2 16.5 + - - +
53O GLU 3.3 0.4 - - - -
54O HIS* 1.3 74.4 - - - +
56O HIS* 1.3 75.6 + - - +
57O GLU 3.3 0.2 + - - -
58O GLU 3.4 1.0 + - - -
59O ARG* 3.1 11.8 + - - +
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Residues in contact with HIS 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 6.1 2.9 - - + +
63C GLU* 3.0 35.0 + - - -
52O LYS* 3.4 29.3 + - + +
53O GLU* 3.3 12.1 + - - +
54O HIS 3.2 0.4 - - - -
55O SER* 1.3 90.8 + - - +
57O GLU* 1.3 56.8 + - - +
59O ARG* 3.5 8.4 + - + +
60O GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O GLU* 3.1 21.5 + - - +
54O HIS* 3.6 25.6 + - - +
55O SER 3.2 0.2 - - - -
56O HIS* 1.3 75.6 - - - +
58O GLU* 1.3 65.4 + - + +
60O GLU* 3.2 7.6 + - + +
61O HIS* 2.9 46.3 + - + +
140O ASP* 4.1 17.7 - - - +
143O ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLU* 2.7 30.9 - - - +
26O ALA* 4.2 9.4 - - + +
27O SER* 3.8 12.1 - - - +
30O TYR* 4.0 17.0 - - + -
54O HIS* 3.2 21.0 + - - +
57O GLU* 1.3 79.9 - - - +
59O ARG* 1.3 58.6 + - - +
61O HIS* 3.1 10.9 + - - +
62O ALA* 3.0 26.0 + - - +
103O GLU* 3.4 15.1 - - - +
106O VAL* 5.7 0.7 - - - -
176O MG 2.0 33.2 - - - -
177O MG 2.6 24.2 - - - -
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Residues in contact with ARG 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS* 6.1 2.9 - - + +
59C ARG* 5.7 9.2 - - + -
24O LEU* 4.9 11.9 - - + -
27O SER* 3.6 13.8 + - - +
55O SER 3.1 17.0 + - - +
56O HIS* 3.6 9.4 - - + +
57O GLU 3.1 0.2 - - - -
58O GLU* 1.3 75.2 - - - +
60O GLU* 1.3 64.0 + - - +
62O ALA* 3.2 8.4 + - - +
63O GLU* 3.1 36.2 + - + +
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Residues in contact with GLU 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56O HIS 3.1 14.7 + - - +
57O GLU* 3.2 10.3 + - - +
59O ARG* 1.3 75.5 - - - +
61O HIS* 1.3 60.6 + - + +
63O GLU* 3.5 12.4 + - - +
64O LYS* 3.1 33.2 + - - +
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Residues in contact with HIS 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLU* 3.4 15.5 - - - +
57O GLU* 2.9 31.4 + - + +
58O GLU* 3.1 17.7 + - - +
59O ARG 3.2 0.2 - - - -
60O GLU* 1.3 77.7 - - + +
62O ALA* 1.3 64.8 + - - +
64O LYS* 3.4 18.4 + - - +
65O PHE* 3.3 12.9 + - - -
132O GLU 4.6 6.6 + - - -
133O TYR* 3.0 40.3 + + + -
136O GLU* 5.1 14.1 - - + +
137O GLN* 5.1 1.1 - - - -
140O ASP* 5.6 0.2 - - - -
176O MG 2.7 23.6 - - - -
177O MG 4.3 10.8 - - - -
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Residues in contact with ALA 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O LEU* 3.7 16.4 - - + +
23O GLU* 3.8 10.9 - - + +
24O LEU* 3.7 34.5 - - + -
58O GLU 3.0 11.9 + - - +
59O ARG 3.2 9.2 + - - +
61O HIS* 1.3 75.8 - - - +
63O GLU* 1.3 64.3 + - + +
65O PHE* 3.3 8.9 + - - +
66O MET* 3.1 26.2 + - + +
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Residues in contact with GLU 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 4.9 5.2 + - - +
34C TYR* 5.2 10.1 - - + -
52C LYS* 3.7 20.7 - - - +
55C SER* 4.5 5.2 + - - -
56C HIS* 3.1 33.8 + - - -
24O LEU* 6.4 0.7 - - + -
59O ARG* 3.1 23.2 + - + +
60O GLU* 3.8 12.3 - - - +
62O ALA* 1.3 75.9 - - + +
64O LYS* 1.3 64.6 + - - +
66O MET* 3.2 25.3 + - + +
67O LYS* 3.1 24.6 + - - +
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Residues in contact with LYS 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O GLU* 3.1 20.6 + - - +
61O HIS* 3.6 18.0 + - - +
62O ALA 3.3 0.4 - - - -
63O GLU* 1.3 75.9 - - - +
65O PHE* 1.3 59.1 + - - +
67O LYS* 3.5 8.1 + - - +
68O TYR* 2.9 27.2 + - - +
128O PHE* 3.7 10.3 - - + -
132O GLU* 2.9 53.4 + - + +
133O TYR* 3.2 22.2 - - + +
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Residues in contact with PHE 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O VAL* 3.9 30.0 - - + +
19O MET* 3.4 32.5 - - + -
20O LEU* 4.2 19.9 - - + +
23O GLU* 4.1 14.8 - - + -
61O HIS 3.3 16.7 + - - -
62O ALA 3.3 8.2 + - - +
63O GLU 3.2 0.4 - - - -
64O LYS* 1.3 76.7 - - - +
66O MET* 1.3 64.1 + - - +
68O TYR* 3.5 3.2 - - + +
69O GLN* 3.0 25.1 + - - +
110O LEU* 4.0 10.3 - - + -
113O LEU* 4.5 8.1 - - + -
125O LEU* 5.3 0.2 - - + -
128O PHE* 3.5 24.9 - + - -
129O LEU* 4.0 12.6 - - + -
133O TYR* 3.4 31.2 - + - -
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Residues in contact with MET 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 5.5 0.2 - - + -
31C SER* 3.4 39.0 - - - +
34C TYR* 4.6 16.4 - - + -
35C ALA* 4.4 13.0 - - + -
20O LEU* 3.8 29.1 - - + +
24O LEU* 5.1 8.3 - - + -
62O ALA* 3.1 21.5 + - + +
63O GLU* 3.2 23.3 + - + +
65O PHE* 1.3 75.6 - - - +
67O LYS* 1.3 62.6 + - - +
69O GLN* 3.4 4.7 - - - +
70O ASN* 3.3 26.9 + - - -
76O VAL* 3.9 21.4 - - + +
78O LEU* 4.7 7.6 - - + -
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Residues in contact with LYS 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.3 28.7 - - - +
38C ASP* 3.2 34.4 + - - +
45C HIS* 5.1 4.8 + - - -
49C GLU* 5.8 1.3 - - - -
142F LYS* 6.0 0.8 - - - +
63O GLU 3.1 9.4 + - - +
64O LYS* 3.6 11.7 - - - +
66O MET* 1.3 78.1 - - - +
68O TYR* 1.3 58.3 + - - +
70O ASN* 3.5 3.5 + - - +
71O LYS* 3.0 45.2 + - + +
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Residues in contact with TYR 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLU* 5.6 0.2 - - - -
8O TYR* 3.9 18.2 - + - -
16O VAL* 4.6 7.2 - - + -
64O LYS 2.9 18.8 + - - +
65O PHE* 3.5 6.7 - - - +
67O LYS* 1.3 74.5 - - - +
69O GLN* 1.3 68.3 + - - +
71O LYS* 3.1 17.2 + - + +
72O ARG* 2.8 53.1 + - + +
124O HIS* 2.8 41.6 + + - -
125O LEU* 3.2 36.3 - - + -
128O PHE* 3.6 43.3 - + + -
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Residues in contact with GLN 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O TYR* 3.0 36.1 + - - -
13O GLU* 3.2 28.3 + - - +
16O VAL* 3.5 14.5 - - + +
17O ASN* 3.4 18.2 + - - -
20O LEU* 6.0 0.4 - - + -
65O PHE 3.0 13.7 + - - +
66O MET* 3.4 7.0 - - - +
68O TYR* 1.3 84.4 - - - +
70O ASN* 1.3 61.0 + - - +
72O ARG* 3.2 4.7 + - - +
73O GLY 3.1 3.3 + - - -
74O GLY* 2.9 42.7 + - - -
75O ARG 4.0 6.7 - - - -
76O VAL* 3.7 24.7 - - + +
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Residues in contact with ASN 70 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 6.3 0.4 - - - -
35C ALA* 3.1 30.1 + - - +
38C ASP* 3.1 38.8 + - - +
39C ARG* 3.4 27.5 - - - +
40C ASP* 5.0 3.5 + - - +
142F LYS* 3.3 16.3 - - - +
4O VAL* 4.5 1.0 - - - +
66O MET 3.3 12.9 + - - -
67O LYS 3.9 3.6 - - - +
69O GLN* 1.3 76.9 - - - +
71O LYS* 1.3 65.6 + - - +
73O GLY* 3.2 10.4 + - - -
74O GLY 3.9 11.8 - - - +
75O ARG* 4.0 1.9 + - - +
76O VAL* 4.6 9.5 + - - +
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Residues in contact with LYS 71 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLU* 2.8 37.4 + - - +
138F VAL* 4.2 25.4 - - + +
139F LYS* 4.6 11.8 - - - +
142F LYS* 4.1 28.3 - - + +
4O VAL* 3.4 18.0 - - - +
67O LYS* 3.0 29.0 + - + +
68O TYR* 3.1 22.6 + - + +
70O ASN* 1.3 76.1 - - - +
72O ARG* 1.3 62.2 + - + +
128O PHE* 6.2 2.6 - - - -
----------------------------------------------------------
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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