Contacts of the helix formed by residues 10 - 38 (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 SER 10 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ARG* 4.0 3.9 + - - +
8R TYR 3.7 1.8 + - - -
9R HIS* 1.3 84.0 + - - +
11R ASP* 1.3 65.3 + - - +
13R GLU* 3.4 19.7 + - - +
14R ALA* 3.1 22.5 + - - +
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Residues in contact with ASP 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R HIS* 2.8 23.8 + - + +
10R SER* 1.3 74.2 - - - +
12R CYS* 1.3 62.4 + - - +
14R ALA* 3.4 6.6 + - - +
15R ALA* 2.9 28.8 + - - +
18R ARG* 4.6 2.1 + - - -
116R LEU* 3.6 21.7 - - + +
120R LYS* 3.1 22.6 + - - +
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Residues in contact with CYS 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R TYR* 4.1 10.3 - - + -
9R HIS* 3.1 25.2 + - + +
11R ASP* 1.3 79.3 - - - +
13R GLU* 1.3 57.5 + - - +
15R ALA* 3.1 3.2 + - - +
16R VAL* 2.9 35.4 + - - +
113R LEU* 4.3 1.0 - - - +
116R LEU* 4.0 24.7 - - - -
117R ALA* 4.3 7.6 - - - -
120R LYS* 4.1 15.7 - - - -
122R ASP* 5.0 5.2 - - - -
125R LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ARG* 2.7 34.8 + - - -
8R TYR* 3.7 21.2 + - + -
9R HIS 3.1 8.9 + - - +
10R SER* 3.5 18.2 + - - +
12R CYS* 1.3 78.6 - - - +
14R ALA* 1.3 62.5 + - - +
16R VAL 3.3 0.5 + - - -
17R ASN* 3.1 22.2 + - - +
69R GLN* 3.2 27.1 + - - +
74R GLY* 3.8 2.5 - - - -
75R ARG* 2.9 32.7 + - - +
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Residues in contact with ALA 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R SER 3.1 16.1 + - - +
11R ASP* 3.7 8.1 - - - +
12R CYS 3.3 0.2 - - - -
13R GLU* 1.3 78.4 - - - +
15R ALA* 1.3 62.4 + - - +
17R ASN* 3.5 10.1 + - - +
18R ARG* 3.1 38.7 + - - +
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Residues in contact with ALA 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R ASP 2.9 17.3 + - - +
12R CYS 3.1 1.5 + - - +
14R ALA* 1.3 74.7 - - - +
16R VAL* 1.3 60.5 + - - +
18R ARG* 3.3 25.7 + - - +
19R MET* 2.9 28.6 + - - +
113R LEU* 3.5 27.8 - - + +
116R LEU* 3.7 11.4 - - + -
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Residues in contact with VAL 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R TYR* 3.6 14.6 - - - +
12R CYS 2.9 20.4 + - - +
13R GLU 3.6 5.4 - - - +
15R ALA* 1.3 76.5 - - - +
17R ASN* 1.3 56.7 + - - +
19R MET* 3.2 7.6 + - - +
20R LEU* 2.9 29.9 + - + +
65R PHE* 3.9 33.7 - - + +
68R TYR* 4.6 5.2 - - + -
69R GLN* 3.5 21.8 - - + +
113R LEU* 4.3 12.3 - - + -
125R LEU* 4.3 23.1 - - + -
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Residues in contact with ASN 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R GLU* 3.1 15.4 + - - +
14R ALA* 3.6 12.4 - - - +
16R VAL* 1.3 76.7 - - - +
18R ARG* 1.3 62.1 + - - +
20R LEU* 3.5 17.1 - - - +
21R ASN* 3.4 19.2 + - - +
69R GLN* 3.4 12.7 + - - +
75R ARG 3.2 19.0 + - - -
76R VAL* 3.3 10.2 - - - -
77R VAL* 3.1 46.2 + - + +
79R GLN* 4.6 9.6 + - - +
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Residues in contact with ARG 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R ASP 4.6 2.8 + - - -
14R ALA* 3.1 22.3 + - - +
15R ALA* 3.4 33.9 - - - +
17R ASN* 1.3 79.6 - - - +
19R MET* 1.3 64.3 + - - +
21R ASN* 3.4 7.5 + - - +
22R LEU* 3.1 20.3 + - - +
79R GLN* 4.8 17.0 - - - +
116R LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R ALA 2.9 16.0 + - - +
16R VAL* 3.5 5.4 - - - +
18R ARG* 1.3 75.4 - - - +
20R LEU* 1.3 64.6 + - - +
22R LEU* 3.2 13.0 + - - +
23R GLU* 2.9 27.5 + - - +
65R PHE* 3.4 30.5 - - + -
106R VAL* 4.6 3.6 - - - +
109R ALA* 3.1 50.7 - - + +
110R LEU* 3.5 21.5 - - + +
113R LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N TYR* 5.1 0.2 - - - +
16R VAL* 2.9 15.6 + - + +
17R ASN* 3.5 19.1 - - - +
19R MET* 1.3 78.0 - - - +
21R ASN* 1.3 63.5 + - + +
23R GLU* 3.4 9.1 + - - +
24R LEU* 3.1 42.1 + - + +
62R ALA* 3.7 17.3 - - + +
65R PHE* 4.2 13.2 - - + +
66R MET* 3.8 35.9 - - + +
69R GLN* 5.8 0.4 - - - +
76R VAL* 4.0 19.1 - - + -
77R VAL 5.6 0.9 - - - +
78R LEU* 3.7 16.4 - - + -
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Residues in contact with ASN 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N TYR* 4.4 4.4 + - - +
17R ASN 3.4 7.6 + - - +
18R ARG 3.6 8.3 - - - +
19R MET 3.2 0.2 - - - -
20R LEU* 1.3 82.5 - - + +
22R LEU* 1.3 61.1 + - - +
24R LEU* 3.1 8.8 + - - +
25R TYR* 2.8 30.1 + - - +
79R GLN* 3.5 43.6 + - - +
80R ASP 3.2 28.1 + - - +
81R ILE* 4.3 7.4 - - - +
82R LYS 5.6 0.7 + - - -
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Residues in contact with LEU 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R ARG 3.1 13.7 + - - +
19R MET* 3.2 15.2 + - - +
21R ASN* 1.3 78.1 + - - +
23R GLU* 1.3 57.5 + - - +
25R TYR* 3.2 24.1 + - + -
26R ALA* 2.9 26.9 + - - +
102R LEU* 5.4 1.3 - - + -
105R THR* 4.4 17.0 - - + +
106R VAL* 3.9 30.7 - - + +
109R ALA* 3.7 29.8 - - + -
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Residues in contact with GLU 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R MET* 2.9 19.3 + - + +
20R LEU 3.4 9.2 - - - +
21R ASN 3.2 0.2 - - - -
22R LEU* 1.3 76.1 - - - +
24R LEU* 1.3 58.0 + - - +
26R ALA* 3.3 5.4 + - - +
27R SER* 2.9 28.1 + - - -
58R GLU* 2.7 20.6 - - - +
61R HIS* 3.4 18.4 - - + +
62R ALA* 3.8 13.5 - - + +
65R PHE* 4.1 18.8 - - + -
106R VAL* 4.0 14.7 - - - +
110R LEU* 4.9 2.8 - - - +
133R TYR* 3.7 15.1 - - - -
176R MG 2.4 31.1 - - - -
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Residues in contact with LEU 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N TYR* 3.6 39.3 - - + +
20R LEU* 3.1 30.8 + - + +
21R ASN* 3.5 9.0 - - - +
23R GLU* 1.3 76.6 - - - +
25R TYR* 1.3 57.4 + - - +
27R SER* 3.5 6.6 - - - +
28R TYR* 3.0 27.0 + - - +
59R ARG* 4.9 17.5 - - + +
62R ALA* 3.7 19.3 - - + -
63R GLU* 6.4 0.2 - - + -
66R MET* 5.1 6.1 - - + -
81R ILE* 3.7 25.4 - - + +
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Residues in contact with TYR 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R ASN* 2.8 16.7 + - - +
22R LEU* 3.4 28.3 - - + +
24R LEU* 1.3 72.8 - - - +
26R ALA* 1.3 62.6 + - - +
28R TYR* 3.2 3.5 + - - +
29R THR* 2.9 49.2 + - - -
81R ILE* 4.0 9.8 - - + +
82R LYS* 3.4 37.7 - - + +
83R LYS 3.8 12.3 + - - -
84R PRO* 4.1 1.3 - - + -
85R GLU* 3.8 26.0 + - - +
102R LEU* 4.1 17.7 - - + -
105R THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R LEU 2.9 14.2 + - - +
23R GLU* 3.5 9.9 - - - +
25R TYR* 1.3 75.8 - - - +
27R SER* 1.3 62.8 + - - +
29R THR* 3.3 3.0 + - - -
30R TYR* 3.1 30.8 + - + -
58R GLU* 4.2 15.7 - - + -
102R LEU* 4.0 25.8 - - + -
103R GLU* 6.2 0.4 - - - +
106R VAL* 4.2 19.5 - - + -
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Residues in contact with SER 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R GLU 2.9 15.8 + - - -
24R LEU* 3.5 11.7 - - - +
26R ALA* 1.3 75.2 - - - +
28R TYR* 1.3 62.9 + - - +
30R TYR 3.1 2.9 + - - -
31R SER* 3.0 18.9 + - - -
55R SER* 2.9 39.5 + - - +
58R GLU* 3.8 12.7 - - - +
59R ARG* 3.6 16.6 - - - +
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Residues in contact with TYR 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 5.1 0.2 - - - +
21N ASN* 4.4 2.9 + - - +
24N LEU* 3.6 28.2 - - + +
78N LEU* 3.4 39.8 - - + +
79N GLN 3.0 30.6 + - - -
81N ILE* 3.8 22.5 - - + +
24R LEU 3.0 19.0 + - - +
25R TYR* 3.5 5.8 - - - +
27R SER* 1.3 77.4 + - - +
29R THR* 1.3 60.5 + - - +
31R SER* 3.2 16.4 - - - -
32R SER* 3.2 18.2 + - - -
81R ILE* 4.0 12.3 - - + -
82R LYS 3.6 19.1 - - - +
83R LYS* 4.0 3.1 - - - -
84R PRO* 3.7 15.5 - - + +
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Residues in contact with THR 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R TYR* 2.9 30.7 + - + +
26R ALA 3.6 7.9 - - - -
27R SER 3.2 0.2 - - - -
28R TYR* 1.3 76.2 - - - +
30R TYR* 1.3 63.0 + - - +
32R SER* 3.2 6.4 + - - -
33R MET* 3.2 39.5 + - + +
84R PRO* 3.4 20.5 - - - +
85R GLU 5.0 0.4 + - - +
89R TRP* 4.0 15.3 - - + -
102R LEU* 3.7 25.8 - - + -
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Residues in contact with TYR 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R ALA* 3.1 23.2 + - + -
27R SER 3.1 6.9 + - - +
29R THR* 1.3 73.0 - - - +
31R SER* 1.3 60.3 + - - +
33R MET* 3.2 12.6 + - + +
34R TYR* 2.8 28.8 + - - +
51R PHE* 3.6 47.2 - + - +
54R HIS* 3.9 28.0 - + + -
55R SER* 3.7 7.2 - - - -
58R GLU* 4.0 13.5 - - + -
99R ALA* 3.9 24.5 + - + +
102R LEU* 3.9 17.8 - - + +
103R GLU* 2.8 41.0 + - - +
144R ILE* 4.3 4.0 - - + +
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Residues in contact with SER 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N LEU* 6.1 0.3 - - - +
63N GLU* 4.9 6.4 + - - +
66N MET* 3.3 34.0 - - - +
78N LEU* 4.8 1.3 - - - -
27R SER* 3.0 12.3 + - - -
28R TYR* 3.2 24.4 - - - -
30R TYR* 1.3 75.8 - - - +
32R SER* 1.3 60.7 + - - +
34R TYR* 3.4 12.5 + - - +
35R ALA* 3.1 23.0 + - - +
55R SER* 3.8 12.7 + - - -
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Residues in contact with SER 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N VAL* 6.3 0.2 - - - -
78N LEU* 3.3 18.0 - - - +
28R TYR 3.2 5.7 + - - -
29R THR 3.2 11.3 + - - -
30R TYR 3.2 0.4 - - - -
31R SER* 1.3 73.7 - - - +
33R MET* 1.3 61.3 + - - +
35R ALA* 3.2 7.5 + - - +
36R PHE* 2.9 28.4 + - - +
84R PRO* 3.2 28.6 - - - +
86R ARG 4.0 6.6 + - - -
87R ASP* 5.1 6.6 + - - +
89R TRP* 3.4 17.6 + - - -
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Residues in contact with MET 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R THR* 3.2 33.3 + - + +
30R TYR* 3.2 16.1 + - + +
32R SER* 1.3 76.4 - - - +
34R TYR* 1.3 64.9 + - - +
36R PHE* 3.3 0.9 + - - +
37R PHE* 3.0 33.1 + - + -
51R PHE* 3.8 42.8 - - + -
89R TRP* 3.7 44.2 - - + -
95R ALA* 3.8 23.3 - - + +
98R ALA* 4.0 7.4 - - + -
99R ALA* 4.2 9.2 - - - +
102R LEU* 5.2 0.7 - - + -
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Residues in contact with TYR 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N GLU* 5.1 11.0 - - + -
66N MET* 4.5 22.9 - - + -
67N LYS* 3.3 38.2 - - + +
70N ASN* 6.3 0.2 - - - -
30R TYR 2.8 13.6 + - - +
31R SER* 3.4 15.3 - - - +
33R MET* 1.3 78.2 - - - +
35R ALA* 1.3 72.0 + - - +
37R PHE 3.4 0.3 + - - -
38R ASP* 3.2 29.6 + - + +
48R ALA* 3.2 37.4 - - + +
49R GLU* 3.6 20.1 + - - -
51R PHE* 4.0 2.8 - - - +
52R LYS* 3.7 42.2 + - + +
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Residues in contact with ALA 35 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N MET* 4.3 14.4 - - + -
70N ASN* 3.0 28.0 + - - +
76N VAL* 4.1 32.3 - - + +
31R SER 3.1 11.0 + - - +
32R SER* 3.6 9.0 - - - +
34R TYR* 1.3 84.7 - - - +
36R PHE* 1.3 62.5 + - - +
38R ASP* 4.4 0.9 - - - -
39R ARG* 3.5 9.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R SER 2.9 17.0 + - - +
33R MET 3.5 4.5 - - - +
34R TYR 3.1 0.2 - - - -
35R ALA* 1.3 78.1 - - - +
37R PHE* 1.3 86.6 + + - +
39R ARG* 3.3 52.4 - - - +
42R VAL* 3.3 36.4 - - + +
87R ASP 4.5 3.6 - - - +
88R GLU* 3.8 12.3 - - + -
89R TRP* 3.6 32.5 - - + -
90R GLY* 3.5 42.0 - - - -
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Residues in contact with PHE 37 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R MET* 3.0 27.5 + - + +
34R TYR 3.4 0.4 + - - -
36R PHE* 1.3 90.5 - + - +
38R ASP* 1.3 60.8 + - - +
39R ARG 3.2 0.4 - - - -
42R VAL* 3.5 22.9 - - + -
43R ALA* 3.5 7.1 + - - -
44R LEU* 3.2 50.2 + - + +
45R HIS* 4.3 0.5 + - - -
47R VAL* 3.9 11.4 - - + -
48R ALA* 3.7 15.2 - - + +
51R PHE* 3.7 19.5 - + - -
89R TRP* 4.8 0.4 - - + -
91R ASN* 3.5 24.0 - - - -
92R THR* 3.6 28.0 - - - -
95R ALA* 3.7 22.4 - - + -
----------------------------------------------------------
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Residues in contact with ASP 38 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 2.9 31.4 + - - -
67N LYS* 3.1 45.0 + - - +
70N ASN* 3.2 32.5 + - - +
34R TYR* 3.2 29.1 + - + +
35R ALA* 4.3 1.3 - - - -
36R PHE 3.2 0.6 - - - -
37R PHE* 1.3 74.6 - - - +
39R ARG* 1.3 61.2 + - - +
45R HIS* 3.4 23.3 + - - -
48R ALA* 4.1 2.5 - - + +
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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).
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