Contacts of the helix formed by residues 45 - 71 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 4.0 10.1 - - - -
146J ASP* 3.0 35.6 + - + -
67N LYS* 5.0 4.9 + - - -
37R PHE 4.6 1.6 - - - -
38R ASP* 3.4 36.2 + - - -
43R ALA* 3.3 15.3 + - - -
44R LEU* 1.3 68.8 - - - +
46R ASN* 1.3 63.7 - - - +
48R ALA* 3.5 6.9 - - - +
49R GLU* 3.1 30.7 + - - +
167R ASP* 3.6 4.0 + - - +
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Residues in contact with ASN 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R HIS* 1.3 77.5 - - - +
47R VAL* 1.3 66.2 + - - +
49R GLU* 3.3 8.6 + - - +
50R PHE 3.0 17.5 + - - -
167R ASP* 2.9 46.7 + - - +
168R LYS* 4.4 11.1 - - - +
171R VAL* 3.2 28.2 - - + +
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Residues in contact with VAL 47 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 3.9 20.9 - - + -
44R LEU* 3.5 18.6 - - + +
45R HIS 3.3 0.2 - - - -
46R ASN* 1.3 76.4 - - - +
48R ALA* 1.3 61.6 + - - +
50R PHE* 3.2 8.9 + - - +
51R PHE* 3.2 45.2 + - + -
92R THR* 4.1 26.7 - - + +
96R MET* 4.6 4.3 - - + -
163R GLU 5.8 0.2 - - - +
166R PHE* 4.3 13.2 - - + -
167R ASP* 3.1 22.6 + - + +
171R VAL* 4.6 4.7 - - + -
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Residues in contact with ALA 48 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R TYR* 3.2 40.2 - - + +
37R PHE* 3.7 24.8 - - + +
38R ASP* 4.1 4.3 - - + +
44R LEU 3.0 14.2 + - - +
45R HIS* 3.5 15.5 - - - +
47R VAL* 1.3 78.9 - - - +
49R GLU* 1.3 57.8 + - - +
51R PHE* 3.4 2.1 + - - -
52R LYS 3.0 20.8 + - - -
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Residues in contact with GLU 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67N LYS* 5.7 1.9 - - - -
34R TYR* 3.6 23.0 + - - -
45R HIS* 3.1 18.6 + - + +
46R ASN* 3.3 11.2 + - - +
48R ALA* 1.3 74.0 - - - +
50R PHE* 1.3 61.3 + - - +
52R LYS* 3.6 24.7 + - - +
53R GLU* 2.9 39.4 + - - +
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Residues in contact with PHE 50 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 5.9 0.4 - + - -
46R ASN 3.0 13.8 + - - +
47R VAL* 3.2 11.0 + - - +
49R GLU* 1.3 76.7 - - - +
51R PHE* 1.3 93.1 + + - +
53R GLU* 3.5 9.0 + - + +
54R HIS* 3.2 54.8 + + - -
96R MET* 4.0 20.9 - - + -
143R ARG* 3.9 17.7 - - - -
144R ILE* 4.5 11.7 - - + -
147R PHE* 3.7 29.2 - + - -
171R VAL* 3.7 20.2 - - + +
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Residues in contact with PHE 51 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 3.6 48.4 - + + +
33R MET* 3.8 28.9 - - + -
34R TYR 4.0 5.4 - - - +
37R PHE* 3.7 23.1 - + - -
47R VAL* 3.2 36.4 + - + -
48R ALA 3.9 4.9 - - - +
50R PHE* 1.3 99.1 - + - +
52R LYS* 1.3 59.8 + - - +
54R HIS* 3.2 5.5 + - + +
55R SER* 2.9 23.9 + - - -
92R THR 5.7 0.2 - - - -
95R ALA* 4.1 11.4 - - + -
96R MET* 3.7 24.5 - - + -
99R ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N GLU* 3.7 24.7 + - - +
34R TYR* 3.7 37.9 + - + +
48R ALA 3.0 17.8 + - - +
49R GLU* 3.6 33.1 + - - +
50R PHE 3.3 0.2 - - - -
51R PHE* 1.3 76.8 - - - +
53R GLU* 1.3 64.1 + - + +
55R SER* 3.2 20.1 + - - +
56R HIS* 3.3 29.7 + - + +
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Residues in contact with GLU 53 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R GLU* 2.9 26.2 + - + +
50R PHE* 3.6 8.9 - - + +
52R LYS* 1.3 78.7 - - + +
54R HIS* 1.3 61.9 + - + +
56R HIS* 3.3 10.7 + - - +
57R GLU* 3.1 35.7 + - - +
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Residues in contact with HIS 54 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 3.9 23.3 - + + -
50R PHE* 3.2 41.4 + + - +
51R PHE* 3.2 10.7 + - - +
53R GLU* 1.3 82.3 - - + +
55R SER* 1.3 63.3 + - - +
57R GLU* 3.6 16.9 + - - +
58R GLU* 3.2 32.8 + - - +
103R GLU* 3.6 17.5 + - - -
140R ASP* 3.7 26.5 - - + -
143R ARG* 3.1 27.3 + - - -
144R ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N GLU* 4.4 5.5 + - - -
27R SER* 2.9 47.9 + - - +
30R TYR* 3.7 13.9 - - - +
31R SER* 3.8 14.8 - - - -
51R PHE 2.9 10.0 + - - -
52R LYS* 3.2 16.5 + - - +
53R GLU 3.3 0.4 - - - -
54R HIS* 1.3 75.0 - - - +
56R HIS* 1.3 76.6 + - - +
58R GLU 3.4 0.9 + - - -
59R ARG* 3.1 12.0 + - - +
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Residues in contact with HIS 56 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N ARG* 6.0 2.9 - - + +
63N GLU* 3.0 35.4 + - - -
52R LYS* 3.3 29.8 + - + +
53R GLU* 3.3 11.9 + - - +
54R HIS 3.2 0.2 - - - -
55R SER* 1.3 90.5 + - - +
57R GLU* 1.3 56.9 + - - +
59R ARG* 3.5 7.7 + - + +
60R GLU* 3.1 26.0 + - - +
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Residues in contact with GLU 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R GLU* 3.1 21.5 + - - +
54R HIS* 3.6 24.6 + - - +
55R SER 3.2 0.2 - - - -
56R HIS* 1.3 75.3 - - - +
58R GLU* 1.3 64.3 + - + +
60R GLU* 3.2 6.3 + - - +
61R HIS* 2.9 46.1 + - + +
140R ASP* 4.1 17.7 - - - +
143R ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R GLU* 2.7 30.2 - - - +
26R ALA* 4.2 9.4 - - + -
27R SER* 3.8 12.1 - - - +
30R TYR* 4.0 17.0 - - + -
54R HIS* 3.2 21.3 + - - +
57R GLU* 1.3 80.7 - - - +
59R ARG* 1.3 57.6 + - - +
61R HIS* 3.1 10.8 + - - +
62R ALA* 3.0 26.3 + - - +
103R GLU* 3.4 15.5 - - - +
106R VAL* 4.9 0.8 - - - +
140R ASP* 4.4 0.2 - - - +
176R MG 2.0 32.2 - - - -
177R MG 2.6 24.8 - - - -
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Residues in contact with ARG 59 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N HIS* 6.0 2.5 - - + +
59N ARG* 5.6 9.9 - - + -
24R LEU* 4.9 11.4 - - + -
27R SER* 3.6 14.1 + - - +
55R SER 3.1 17.8 + - - +
56R HIS* 3.6 10.3 - - + +
58R GLU* 1.3 74.3 - - - +
60R GLU* 1.3 64.5 + - - +
62R ALA* 3.2 8.9 + - - +
63R GLU* 3.1 37.2 + - + +
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Residues in contact with GLU 60 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R HIS 3.1 15.5 + - - +
57R GLU* 3.2 11.2 + - + +
59R ARG* 1.3 75.5 - - - +
61R HIS* 1.3 60.9 + - + +
63R GLU* 3.5 12.4 + - - +
64R LYS* 3.1 32.5 + - - +
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Residues in contact with HIS 61 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R GLU* 3.4 15.7 - - - +
57R GLU* 2.9 30.4 + - + +
58R GLU* 3.1 18.1 + - - +
59R ARG 3.2 0.2 - - - -
60R GLU* 1.3 76.9 - - + +
62R ALA* 1.3 63.1 + - - +
64R LYS* 3.4 19.2 + - - +
65R PHE* 3.3 13.2 + - - -
132R GLU 4.6 6.8 + - - -
133R TYR* 3.0 40.1 + + + -
136R GLU* 5.1 14.1 - - + +
137R GLN* 5.1 0.9 - - - -
140R ASP* 5.6 0.2 - - - -
176R MG 2.7 24.5 - - - -
177R MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R LEU* 3.7 16.6 - - + +
23R GLU* 3.8 10.3 - - + +
24R LEU* 3.7 34.8 - - + -
58R GLU 3.0 12.2 + - - +
59R ARG 3.2 8.9 + - - +
61R HIS* 1.3 75.6 - - - +
63R GLU* 1.3 64.2 + - + +
65R PHE* 3.3 8.6 + - - +
66R MET* 3.1 26.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 63 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N SER* 4.9 5.2 + - - +
34N TYR* 5.1 9.9 - - + -
52N LYS* 3.6 20.3 - - - +
55N SER* 4.4 5.7 + - - -
56N HIS* 3.0 36.0 + - - -
24R LEU* 6.4 0.4 - - + -
59R ARG* 3.1 23.8 + - + +
60R GLU* 3.8 12.4 - - - +
61R HIS 3.3 0.2 - - - -
62R ALA* 1.3 75.2 - - + +
64R LYS* 1.3 64.0 - - - +
66R MET* 3.2 24.3 + - + +
67R LYS* 3.1 24.4 + - - +
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Residues in contact with LYS 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R GLU* 3.1 20.2 + - - +
61R HIS* 3.6 17.4 + - - +
62R ALA 3.3 0.2 - - - -
63R GLU* 1.3 75.9 - - - +
65R PHE* 1.3 57.4 + - - +
67R LYS* 3.5 7.5 + - - +
68R TYR* 2.9 27.7 + - - +
128R PHE* 3.7 10.0 - - + -
132R GLU* 2.9 52.7 + - + +
133R TYR* 3.2 21.5 - - + +
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Residues in contact with PHE 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R VAL* 3.9 29.8 - - + +
19R MET* 3.4 32.8 - - + -
20R LEU* 4.2 18.6 - - + -
23R GLU* 4.1 14.8 - - + -
61R HIS 3.3 17.4 + - - -
62R ALA 3.3 8.2 + - - +
63R GLU 3.2 0.2 - - - -
64R LYS* 1.3 78.2 - - - +
66R MET* 1.3 64.5 + - - +
68R TYR* 3.5 3.0 - - + +
69R GLN* 3.0 24.4 + - - +
110R LEU* 4.0 12.1 - - + -
113R LEU* 4.5 7.6 - - + -
125R LEU* 5.3 0.2 - - + -
128R PHE* 3.5 25.4 - + - -
129R LEU* 4.0 12.1 - - + -
133R TYR* 3.4 31.4 - + - -
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Residues in contact with MET 66 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N TYR* 5.5 0.2 - - + -
31N SER* 3.3 40.6 - - - +
34N TYR* 4.5 15.3 - - + -
35N ALA* 4.3 12.3 - - + -
20R LEU* 3.8 29.6 - - + +
24R LEU* 5.1 7.6 - - + -
62R ALA* 3.1 21.5 + - + +
63R GLU* 3.5 24.2 - - + +
65R PHE* 1.3 75.8 - - - +
67R LYS* 1.3 62.1 + - - +
69R GLN* 3.4 4.5 - - - +
70R ASN* 3.3 26.6 + - - -
76R VAL* 3.9 21.6 - - + +
78R LEU* 4.7 8.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 3.3 29.4 - - - +
38N ASP* 3.1 33.8 + - - +
45N HIS* 5.0 4.4 + - - -
49N GLU* 5.7 2.0 - - - -
63R GLU 3.1 10.3 + - - +
64R LYS* 3.6 11.4 - - - +
66R MET* 1.3 78.8 - - - +
68R TYR* 1.3 58.1 + - - +
70R ASN* 3.5 3.3 + - - +
71R LYS* 3.0 44.0 + - + +
142S LYS* 6.0 0.4 - - - +
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Residues in contact with TYR 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R TYR* 3.9 18.2 - + - -
16R VAL* 4.6 8.5 - - + -
64R LYS 2.9 17.9 + - - +
65R PHE* 3.5 6.7 - - - +
66R MET 3.2 0.2 - - - -
67R LYS* 1.3 75.2 - - - +
69R GLN* 1.3 68.2 + - - +
71R LYS* 3.1 17.3 + - + +
72R ARG* 2.8 51.5 + - + +
124R HIS* 2.8 42.8 + + - -
125R LEU* 3.2 35.8 - - + -
128R PHE* 3.6 44.2 - + + -
135S GLU* 5.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLN 69 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R TYR* 3.0 36.4 + - - -
13R GLU* 3.2 27.2 + - - +
16R VAL* 3.5 15.0 - - + +
17R ASN* 3.4 19.2 + - - -
20R LEU* 5.8 0.6 - - + +
65R PHE 3.0 14.0 + - - +
66R MET 3.4 6.5 - - - +
68R TYR* 1.3 82.9 - - - +
70R ASN* 1.3 60.7 + - - +
72R ARG* 3.2 4.9 + - - +
73R GLY 3.1 3.6 + - - -
74R GLY* 2.9 42.8 + - - -
75R ARG 4.0 6.1 - - - -
76R VAL* 3.7 23.8 - - + +
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Residues in contact with ASN 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 6.2 0.2 - - - -
35N ALA* 3.0 29.9 + - - +
38N ASP* 3.1 40.4 + - - +
39N ARG* 3.3 27.6 - - - +
40N ASP* 4.9 3.3 + - - +
4R VAL* 4.5 0.9 - - - +
66R MET 3.3 13.1 + - - -
67R LYS 3.9 3.4 - - - +
69R GLN* 1.3 76.3 - - - +
71R LYS* 1.3 65.9 + - - +
73R GLY* 3.2 10.0 + - - -
74R GLY 3.9 11.8 - - - +
75R ARG* 4.0 1.6 + - - +
76R VAL* 4.6 8.6 + - - +
142S LYS* 3.3 16.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 3.4 17.5 - - - +
67R LYS* 3.0 30.1 + - + +
68R TYR* 3.3 22.1 - - + +
70R ASN* 1.3 76.7 - - - +
72R ARG* 1.3 63.6 + - + +
128R PHE* 6.2 2.4 - - - -
135S GLU* 2.8 35.6 + - - +
138S VAL* 4.3 25.1 - - + +
139S LYS* 4.6 11.6 - - - +
142S LYS* 4.1 28.3 - - + +
----------------------------------------------------------
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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