Contacts of the helix formed by residues 45 - 71 (chain W) 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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K LYS* 5.0 5.3 + - - -
142P LYS* 4.0 2.9 - - - -
146P ASP* 3.1 33.7 + - + -
150P ASN* 5.9 0.4 - - - -
37W PHE 4.6 1.1 - - - -
38W ASP* 3.4 44.9 + - - -
43W ALA* 3.3 15.0 + - - -
44W LEU* 1.3 69.6 - - - +
46W ASN* 1.3 65.4 + - - +
48W ALA* 3.5 6.7 - - - +
49W GLU* 3.1 30.6 + - + +
167W ASP* 3.6 3.8 + - - +
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Residues in contact with ASN 46 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W HIS* 1.3 78.0 - - - +
47W VAL* 1.3 65.8 + - - +
49W GLU* 3.3 9.3 + - - +
50W PHE 3.0 18.0 + - - -
167W ASP* 3.0 46.2 + - - +
168W LYS* 4.4 10.5 - - - +
171W VAL* 3.2 27.9 - - + +
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Residues in contact with VAL 47 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W PHE* 3.9 19.7 - - + -
44W LEU* 3.5 18.4 - - + +
46W ASN* 1.3 76.5 - - - +
48W ALA* 1.3 62.0 + - - +
50W PHE* 3.2 8.7 + - - +
51W PHE* 3.2 46.0 + - + -
92W THR* 4.1 26.0 - - + +
96W MET* 4.6 4.5 - - + -
163W GLU 5.8 0.2 - - - +
166W PHE* 4.3 13.9 - - + -
167W ASP* 3.1 21.7 + - + +
171W VAL* 4.6 4.7 - - + -
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Residues in contact with ALA 48 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W TYR* 3.2 39.9 - - + +
37W PHE* 3.7 23.8 - - + +
38W ASP* 4.1 4.0 - - + +
44W LEU 3.0 15.1 + - - +
45W HIS* 3.5 15.0 - - - +
46W ASN 3.2 0.2 - - - -
47W VAL* 1.3 77.6 - - - +
49W GLU* 1.3 57.5 + - - +
51W PHE* 3.4 2.5 + - - -
52W LYS 3.0 21.1 + - - -
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Residues in contact with GLU 49 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K LYS* 5.8 1.6 - - - -
34W TYR* 3.6 23.0 + - - -
45W HIS* 3.1 19.0 + - + +
46W ASN* 3.3 10.7 + - - +
48W ALA* 1.3 74.0 - - - +
50W PHE* 1.3 62.1 + - - +
52W LYS* 3.6 24.0 + - - +
53W GLU* 2.9 39.6 + - - +
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Residues in contact with PHE 50 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W TYR* 5.9 0.4 - + - -
46W ASN 3.0 13.6 + - - +
47W VAL* 3.2 10.5 + - - +
49W GLU* 1.3 76.3 - - - +
51W PHE* 1.3 93.6 + + - +
53W GLU* 3.5 8.8 + - - +
54W HIS* 3.2 54.9 + + - -
96W MET* 4.0 20.6 - - + -
143W ARG* 3.9 17.9 - - - -
144W ILE* 4.5 12.8 - - + -
147W PHE* 3.7 28.5 - + - -
171W VAL* 3.7 20.2 - - + -
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Residues in contact with PHE 51 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W TYR* 3.6 50.5 - + + +
33W MET* 3.8 30.5 - - + -
34W TYR 4.0 4.9 - - - +
37W PHE* 3.7 22.2 - + - -
47W VAL* 3.2 36.6 + - + -
48W ALA* 3.9 5.4 - - - +
50W PHE* 1.3 99.4 - + - +
52W LYS* 1.3 59.4 + - - +
54W HIS* 3.2 4.9 + - + +
55W SER* 2.9 24.3 + - - -
92W THR 5.7 0.2 - - - -
95W ALA* 4.1 12.1 - - + -
96W MET* 3.7 24.7 - - + -
99W ALA* 4.2 8.1 - - + -
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Residues in contact with LYS 52 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K GLU* 3.6 25.3 + - - +
34W TYR* 3.7 38.0 + - + +
48W ALA 3.0 17.6 + - - +
49W GLU* 3.6 32.5 + - - +
50W PHE 3.3 0.2 - - - -
51W PHE* 1.3 76.6 - - - +
53W GLU* 1.3 63.4 + - + +
55W SER* 3.2 22.2 + - - +
56W HIS* 3.3 28.0 + - + +
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Residues in contact with GLU 53 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W GLU* 2.9 26.8 + - + +
50W PHE* 3.6 8.5 - - + +
52W LYS* 1.3 77.5 - - + +
54W HIS* 1.3 61.1 + - + +
56W HIS* 3.3 12.2 + - - +
57W GLU* 3.1 36.1 + - - +
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Residues in contact with HIS 54 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W TYR* 3.9 23.2 - + + -
50W PHE* 3.2 40.4 + + - +
51W PHE* 3.2 11.0 + - - +
53W GLU* 1.3 82.4 - - + +
55W SER* 1.3 63.8 + - - +
57W GLU* 3.4 17.5 + - - +
58W GLU* 3.2 33.1 + - - +
103W GLU* 3.6 18.0 + - - -
140W ASP* 3.7 26.7 - - + -
143W ARG* 3.1 26.5 + - - -
144W ILE* 4.9 5.2 - - + -
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Residues in contact with SER 55 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K GLU* 4.4 5.5 + - - -
27W SER* 2.9 47.0 + - - +
30W TYR* 3.7 14.6 - - - +
31W SER* 3.8 14.7 + - - -
51W PHE 2.9 9.6 + - - -
52W LYS* 3.2 16.1 + - - +
53W GLU 3.3 0.4 - - - -
54W HIS* 1.3 74.8 - - - +
56W HIS* 1.3 77.3 + - - +
58W GLU 3.4 1.0 + - - -
59W ARG* 3.1 12.4 + - - +
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Residues in contact with HIS 56 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K ARG* 6.0 3.3 - - + +
63K GLU* 3.1 28.1 + - - -
52W LYS* 3.3 34.1 + - + +
53W GLU* 3.3 11.9 + - - +
54W HIS 3.2 0.4 - - - -
55W SER* 1.3 91.0 + - - +
57W GLU* 1.3 56.8 + - - +
59W ARG* 3.5 7.2 + - + +
60W GLU* 3.1 26.7 + - - +
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Residues in contact with GLU 57 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53W GLU* 3.1 22.3 + - - +
54W HIS* 3.6 25.6 + - - +
55W SER 3.2 0.4 - - - -
56W HIS* 1.3 75.7 - - - +
58W GLU* 1.3 64.1 + - + +
60W GLU* 3.2 6.5 + - - +
61W HIS* 2.9 46.5 + - + +
140W ASP* 4.1 17.3 - - - +
143W ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W GLU* 2.7 31.2 - - - +
26W ALA* 4.2 10.0 - - + +
27W SER* 3.8 12.1 - - - +
30W TYR* 4.0 16.4 - - + -
54W HIS* 3.2 20.1 + - - +
55W SER 3.4 0.2 + - - -
57W GLU* 1.3 80.7 - - - +
59W ARG* 1.3 57.1 + - - +
61W HIS* 3.1 12.1 + - - +
62W ALA* 3.0 25.8 + - - +
103W GLU* 3.4 15.4 - - - +
106W VAL* 4.9 1.1 - - - +
176W MG 2.0 33.0 - - - -
177W MG 2.6 24.3 - - - -
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Residues in contact with ARG 59 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K HIS* 6.0 3.1 - - + +
59K ARG* 5.8 8.5 - - + -
24W LEU* 4.9 11.7 - - + -
27W SER* 3.6 13.4 + - - +
55W SER 3.1 17.5 + - - +
56W HIS* 3.6 9.4 - - + +
58W GLU* 1.3 73.9 - - - +
60W GLU* 1.3 63.4 + - - +
62W ALA* 3.2 8.7 + - - +
63W GLU* 3.1 36.5 + - + +
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Residues in contact with GLU 60 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W HIS 3.1 15.3 + - - +
57W GLU* 3.2 10.1 + - - +
59W ARG* 1.3 75.7 - - - +
61W HIS* 1.3 60.9 + - + +
63W GLU* 3.5 12.2 + - - +
64W LYS* 3.1 33.3 + - - +
----------------------------------------------------------
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Residues in contact with HIS 61 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W GLU* 3.4 15.7 + - - +
57W GLU* 2.9 31.4 + - + +
58W GLU* 3.1 17.5 + - - +
59W ARG 3.2 0.2 - - - -
60W GLU* 1.3 77.8 - - + +
62W ALA* 1.3 64.6 + - - +
64W LYS* 3.4 17.9 + - - +
65W PHE* 3.3 12.7 + - - -
132W GLU 4.6 7.0 + - - -
133W TYR* 3.0 41.0 + + + -
136W GLU* 5.1 13.9 - - + +
137W GLN* 5.1 1.3 - - - -
140W ASP* 5.6 0.4 - - - -
176W MG 2.7 24.4 - - - -
177W MG 4.3 9.9 - - - -
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Residues in contact with ALA 62 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20W LEU* 3.7 16.6 - - + +
23W GLU* 3.8 10.7 - - + +
24W LEU* 3.7 34.5 - - + -
58W GLU 3.0 11.9 + - - +
59W ARG 3.2 9.4 + - - +
61W HIS* 1.3 76.7 - - - +
63W GLU* 1.3 64.0 + - + +
65W PHE* 3.3 8.1 + - - +
66W MET* 3.1 26.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 63 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K SER* 4.8 5.5 + - - +
34K TYR* 5.1 11.3 + - + -
52K LYS* 3.6 20.9 - - - +
55K SER* 4.4 5.4 + - - -
56K HIS* 3.1 34.9 + - - -
24W LEU* 6.4 0.2 - - + -
59W ARG* 3.1 26.0 + - + +
60W GLU* 3.8 12.2 - - - +
62W ALA* 1.3 76.1 - - + +
64W LYS* 1.3 64.4 + - - +
66W MET* 3.2 24.9 + - + +
67W LYS* 3.1 24.4 + - - +
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Residues in contact with LYS 64 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60W GLU* 3.1 20.8 + - - +
61W HIS* 3.6 17.8 + - - +
62W ALA 3.3 0.4 - - - -
63W GLU* 1.3 75.5 - - - +
65W PHE* 1.3 58.2 + - - +
67W LYS* 3.5 7.7 + - - +
68W TYR* 2.9 27.4 + - - +
128W PHE* 3.7 9.5 - - + -
132W GLU* 2.9 51.5 + - + +
133W TYR* 3.2 21.8 - - + +
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Residues in contact with PHE 65 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W VAL* 3.9 30.2 - - + +
19W MET* 3.4 32.8 - - + -
20W LEU* 4.2 19.1 - - + -
23W GLU* 4.1 14.4 - - + -
61W HIS 3.3 17.3 + - - -
62W ALA 3.3 8.6 + - - +
63W GLU 3.2 0.4 - - - -
64W LYS* 1.3 77.8 - - - +
66W MET* 1.3 62.5 + - - +
68W TYR* 3.5 3.6 - - + +
69W GLN* 3.0 24.9 + - - +
110W LEU* 4.0 11.0 - - + -
113W LEU* 4.5 8.1 - - + -
125W LEU* 5.3 0.2 - - + -
128W PHE* 3.5 24.5 - + - -
129W LEU* 4.0 12.1 - - + -
133W TYR* 3.4 30.5 - + - -
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Residues in contact with MET 66 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K TYR* 5.6 0.2 - - + -
31K SER* 3.4 40.4 - - - +
34K TYR* 4.5 15.9 - - + -
35K ALA* 4.2 13.2 - - + -
20W LEU* 3.8 30.1 - - + -
24W LEU* 5.1 7.4 - - + -
62W ALA* 3.1 20.5 + - + +
63W GLU* 3.2 22.9 + - + +
65W PHE* 1.3 76.3 - - - +
67W LYS* 1.3 61.2 + - - +
69W GLN* 3.4 4.2 - - - +
70W ASN* 3.3 28.2 + - - -
76W VAL* 3.9 21.6 - - + +
78W LEU* 4.7 8.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 67 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 5.9 1.0 - - - +
34K TYR* 3.4 28.0 + - - +
38K ASP* 3.1 33.5 + - - +
45K HIS* 5.0 5.1 + - - -
49K GLU* 5.8 1.3 - - - -
63W GLU 3.1 9.5 + - - +
64W LYS* 3.6 11.4 - - - +
66W MET* 1.3 78.6 - - - +
68W TYR* 1.3 58.9 + - - +
70W ASN* 3.5 3.8 + - - +
71W LYS* 3.0 44.0 + - + +
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Residues in contact with TYR 68 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 5.4 0.4 - - - -
8W TYR* 3.9 18.6 - + - -
16W VAL* 4.6 7.6 - - + -
64W LYS 2.9 18.3 + - - +
65W PHE* 3.5 6.7 - - - +
66W MET 3.2 0.4 - - - -
67W LYS* 1.3 74.7 - - - +
69W GLN* 1.3 67.1 + - - +
71W LYS* 3.1 17.6 + - + +
72W ARG* 2.8 52.5 + - + +
124W HIS* 2.8 41.7 + + - -
125W LEU* 3.2 36.3 - - + +
128W PHE* 3.6 43.1 - + + -
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Residues in contact with GLN 69 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W TYR* 3.0 35.9 + - - -
13W GLU* 3.2 28.3 + - - +
16W VAL* 3.5 13.7 - - + +
17W ASN* 3.4 19.4 + - - +
20W LEU* 5.8 0.9 - - + +
65W PHE 3.0 13.6 + - - +
66W MET* 3.4 7.0 - - - +
68W TYR* 1.3 84.2 - - - +
70W ASN* 1.3 61.7 - - - +
72W ARG* 3.2 4.9 + - - +
73W GLY 3.1 3.6 + - - -
74W GLY* 2.9 43.5 + - - -
75W ARG 4.0 6.5 - - - -
76W VAL* 3.7 24.0 - - + +
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Residues in contact with ASN 70 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 3.3 17.4 - - - +
35K ALA* 3.1 29.2 + - - +
38K ASP* 3.1 39.2 + - - +
39K ARG* 3.3 28.1 - - - +
40K ASP* 4.9 3.5 + - - +
4W VAL* 4.5 1.0 - - - +
66W MET 3.3 13.3 + - - +
67W LYS 3.9 3.4 - - - +
69W GLN* 1.3 77.6 - - - +
71W LYS* 1.3 65.4 + - - +
73W GLY* 3.2 10.2 + - - -
74W GLY 3.9 11.7 - - - +
75W ARG* 4.0 1.8 + - - +
76W VAL* 4.6 9.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 2.8 37.4 + - - +
138D VAL* 4.2 26.4 - - + +
139D LYS* 4.6 11.8 - - - +
142D LYS* 4.1 27.2 - - + +
4W VAL* 3.4 17.5 - - - +
67W LYS* 3.0 30.3 + - + +
68W TYR* 3.1 23.2 + - + +
70W ASN* 1.3 76.3 - - - +
72W ARG* 1.3 63.1 + - + +
128W PHE* 6.2 2.4 - - - -
----------------------------------------------------------
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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