Contacts of the helix formed by residues 10 - 38 (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 SER 10 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W ARG* 4.0 4.1 + - - +
8W TYR 3.7 1.6 + - - -
9W HIS* 1.3 83.4 + - - +
11W ASP* 1.3 65.2 + - - +
13W GLU* 3.4 19.6 + - - +
14W ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W HIS* 2.8 24.1 + - + +
10W SER* 1.3 72.5 - - - +
12W CYS* 1.3 61.9 + - - +
14W ALA* 3.4 7.3 + - - +
15W ALA* 2.9 28.6 + - - +
18W ARG* 4.6 2.1 + - - -
116W LEU* 3.6 22.5 - - + +
120W LYS* 3.1 22.2 + - - +
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Residues in contact with CYS 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W TYR* 4.1 9.6 - - + -
9W HIS* 3.1 25.0 + - + +
11W ASP* 1.3 78.8 - - - +
13W GLU* 1.3 58.0 - - - +
15W ALA* 3.1 2.9 + - - +
16W VAL* 2.9 36.0 + - - +
113W LEU* 4.3 0.8 - - - +
116W LEU* 4.0 24.9 - - - -
117W ALA* 4.3 8.5 - - - -
120W LYS* 4.1 15.7 - - - -
122W ASP* 5.0 4.7 - - - -
125W LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W ARG* 2.7 35.2 + - - -
8W TYR* 3.7 20.8 + - + -
9W HIS 3.1 8.5 + - - +
10W SER* 3.5 17.6 + - - +
12W CYS* 1.3 78.4 - - - +
14W ALA* 1.3 62.7 + - - +
16W VAL 3.3 0.5 + - - -
17W ASN* 3.1 22.5 + - - +
69W GLN* 3.2 26.4 + - - +
74W GLY* 3.8 2.2 - - - -
75W ARG* 2.9 32.7 + - - +
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Residues in contact with ALA 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W SER 3.1 17.4 + - - +
11W ASP* 3.7 7.9 - - - +
13W GLU* 1.3 78.1 - - - +
15W ALA* 1.3 61.2 + - - +
17W ASN* 3.5 9.2 + - - +
18W ARG* 3.1 39.4 + - - +
79W GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W ASP 2.9 17.7 + - - +
12W CYS 3.1 1.1 + - - +
14W ALA* 1.3 75.3 - - - +
16W VAL* 1.3 60.2 + - - +
18W ARG* 3.3 24.6 + - - +
19W MET* 2.9 28.8 + - - +
113W LEU* 3.5 27.9 - - + +
116W LEU* 3.7 11.0 - - + -
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Residues in contact with VAL 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W TYR* 3.6 14.4 - - - +
12W CYS 2.9 19.5 + - - +
13W GLU 3.6 5.2 - - - +
15W ALA* 1.3 77.0 - - - +
17W ASN* 1.3 56.4 + - - +
19W MET* 3.2 7.2 + - - +
20W LEU* 2.9 29.5 + - + +
65W PHE* 3.9 33.4 - - + +
68W TYR* 4.6 4.7 - - + -
69W GLN* 3.5 22.4 - - + +
113W LEU* 4.3 12.8 - - + -
125W LEU* 4.3 23.3 - - + -
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Residues in contact with ASN 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13W GLU* 3.1 14.8 + - - +
14W ALA* 3.6 12.4 - - - +
15W ALA 3.3 0.2 - - - -
16W VAL* 1.3 76.6 - - - +
18W ARG* 1.3 60.9 + - - +
20W LEU* 3.5 16.1 - - - +
21W ASN* 3.4 19.6 + - - +
69W GLN* 3.4 12.1 + - - +
75W ARG 3.2 19.0 + - - -
76W VAL* 3.3 10.7 - - - -
77W VAL* 3.1 46.3 + - + +
79W GLN* 4.6 10.0 + - - +
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Residues in contact with ARG 18 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W ASP 4.6 2.8 + - - -
14W ALA* 3.1 21.9 + - - +
15W ALA* 3.4 33.4 - - - +
17W ASN* 1.3 79.8 - - - +
19W MET* 1.3 64.6 + - - +
21W ASN* 3.4 7.4 + - - +
22W LEU* 3.1 20.4 + - - +
79W GLN* 4.8 16.1 - - - +
116W LEU* 5.4 2.4 - - - +
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Residues in contact with MET 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15W ALA 2.9 16.2 + - - +
16W VAL* 3.5 5.8 - - - +
18W ARG* 1.3 75.3 - - - +
20W LEU* 1.3 64.0 + - - +
22W LEU* 3.2 14.2 + - - +
23W GLU* 2.9 28.0 + - + +
65W PHE* 3.4 30.7 - - + -
106W VAL* 4.6 3.4 - - - +
109W ALA* 3.1 50.7 - - + +
110W LEU* 3.5 21.8 - - + +
113W LEU* 3.7 19.7 - - + -
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Residues in contact with LEU 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W VAL* 2.9 16.4 + - + +
17W ASN* 3.5 19.7 - - - +
19W MET* 1.3 78.2 - - - +
21W ASN* 1.3 62.8 + - + +
23W GLU* 3.4 8.8 + - - +
24W LEU* 3.1 40.9 + - + +
62W ALA* 3.7 16.7 - - - +
65W PHE* 4.2 13.2 - - + +
66W MET* 3.8 36.6 - - + +
69W GLN* 5.8 0.4 - - + +
76W VAL* 4.0 19.1 - - + -
77W VAL 5.6 0.7 - - - +
78W LEU* 3.7 17.3 - - + -
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Residues in contact with ASN 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K TYR* 4.4 4.8 + - - +
17W ASN 3.4 7.4 + - - +
18W ARG 3.6 8.3 - - - +
19W MET 3.2 0.4 - - - -
20W LEU* 1.3 81.4 - - + +
22W LEU* 1.3 61.2 + - - +
24W LEU* 3.1 8.5 + - - +
25W TYR* 2.8 30.3 + - - +
79W GLN* 3.5 42.6 + - - +
80W ASP 3.2 27.5 + - - +
81W ILE* 4.3 7.7 - - - +
82W LYS 5.6 0.9 + - - -
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Residues in contact with LEU 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W ARG 3.1 14.2 + - - +
19W MET* 3.2 16.1 + - - +
21W ASN* 1.3 77.2 + - - +
23W GLU* 1.3 57.3 + - - +
25W TYR* 3.2 24.2 + - + +
26W ALA* 2.9 26.0 + - - +
102W LEU* 5.4 1.8 - - + -
105W THR* 4.4 16.2 - - + +
106W VAL* 3.9 30.7 - - + +
109W ALA* 3.7 30.7 - - + -
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Residues in contact with GLU 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W MET* 2.9 19.9 + - + +
20W LEU 3.4 9.0 - - - +
21W ASN 3.2 0.2 - - - -
22W LEU* 1.3 76.5 - - - +
24W LEU* 1.3 57.6 + - - +
26W ALA* 3.3 4.6 + - - +
27W SER* 2.9 28.1 + - - -
58W GLU* 2.7 20.6 - - - +
61W HIS* 3.4 18.7 + - + +
62W ALA* 3.8 14.6 - - + +
65W PHE* 4.1 19.1 - - + -
106W VAL* 4.0 15.6 - - + +
110W LEU* 4.9 2.6 - - - +
133W TYR* 3.7 14.7 - - - -
176W MG 2.4 31.3 - - - -
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Residues in contact with LEU 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K TYR* 3.6 38.4 - - + +
20W LEU* 3.1 31.9 + - + +
21W ASN* 3.1 10.1 + - - +
23W GLU* 1.3 75.5 - - - +
25W TYR* 1.3 56.7 + - - +
27W SER* 3.5 6.0 - - - +
28W TYR* 3.0 27.5 + - - +
59W ARG* 4.9 17.5 - - + -
62W ALA* 3.7 18.4 - - + -
63W GLU* 6.4 0.2 - - + -
66W MET* 5.1 6.7 - - + -
78W LEU* 4.8 0.2 - - + -
81W ILE* 3.7 23.5 - - + +
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Residues in contact with TYR 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W ASN* 2.8 17.2 + - - +
22W LEU* 3.4 28.5 - - + +
23W GLU 3.2 0.2 - - - -
24W LEU* 1.3 72.8 - - - +
26W ALA* 1.3 64.7 + - - +
28W TYR* 3.2 4.1 + - + +
29W THR* 2.9 47.5 + - + +
81W ILE* 4.0 10.7 - - + +
82W LYS* 3.4 37.7 - - + +
83W LYS 3.8 12.3 + - - -
84W PRO* 4.1 0.9 - - + -
85W GLU* 3.8 25.6 + - - +
102W LEU* 4.1 16.8 - - + -
105W THR* 6.5 0.2 - - + -
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Residues in contact with ALA 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W LEU 2.9 13.4 + - - +
23W GLU* 3.5 9.6 - - - +
25W TYR* 1.3 76.2 - - - +
27W SER* 1.3 64.2 + - - +
29W THR* 3.3 3.2 + - - -
30W TYR* 3.1 31.2 + - + -
58W GLU* 4.2 15.7 - - + -
102W LEU* 4.0 25.4 - - + -
103W GLU* 6.5 0.4 - - - -
106W VAL* 4.2 19.5 - - + -
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Residues in contact with SER 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W GLU 2.9 16.9 + - - -
24W LEU* 3.5 11.3 - - - +
26W ALA* 1.3 76.3 - - - +
28W TYR* 1.3 62.7 + - - +
30W TYR 3.1 2.9 + - - -
31W SER* 3.0 18.6 + - - -
55W SER* 2.9 40.2 + - - +
58W GLU* 3.8 12.9 - - - +
59W ARG* 3.6 16.6 - - - +
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Residues in contact with TYR 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 5.2 0.2 - - - +
21K ASN* 4.4 2.9 + - - +
24K LEU* 3.6 27.6 - - + +
66K MET* 5.6 0.4 - - + -
78K LEU* 3.5 36.3 - - + +
79K GLN 3.0 30.6 + - - -
81K ILE* 3.7 22.0 - - + +
24W LEU 3.0 19.0 + - - +
25W TYR* 3.2 6.9 + - - +
27W SER* 1.3 77.8 + - - +
29W THR* 1.3 59.9 + - - +
31W SER* 3.2 15.9 - - - -
32W SER* 3.2 18.4 + - - -
81W ILE* 4.0 12.6 - - + -
82W LYS 3.6 17.9 - - - +
83W LYS* 4.0 3.8 - - - -
84W PRO* 3.7 17.7 - - + +
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Residues in contact with THR 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W TYR* 2.9 31.4 + - + +
26W ALA 3.6 8.3 - - - -
28W TYR* 1.3 75.0 - - - +
30W TYR* 1.3 61.7 + - - +
32W SER* 3.2 6.8 + - - -
33W MET* 3.2 39.3 + - + +
84W PRO* 3.4 21.8 - - + +
85W GLU* 5.0 0.8 + - - +
89W TRP* 4.0 15.3 - - + -
102W LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W ALA* 3.1 23.5 + - + -
27W SER 3.1 6.5 + - - +
29W THR* 1.3 73.8 - - - +
31W SER* 1.3 59.9 + - - +
33W MET* 3.2 12.2 + - + +
34W TYR* 2.8 28.9 + - - +
50W PHE* 5.9 0.4 - + - -
51W PHE* 3.6 47.8 - + - +
54W HIS* 3.9 29.1 + + + -
55W SER* 3.7 7.0 - - - -
58W GLU* 4.0 13.2 - - + -
99W ALA* 3.9 24.5 + - + +
102W LEU* 3.9 17.9 - - + +
103W GLU* 2.8 42.1 + - - +
144W ILE* 4.3 2.6 - - + +
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Residues in contact with SER 31 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K LEU* 6.0 0.5 - - - +
63K GLU* 4.8 6.6 + - - +
66K MET* 3.3 30.9 - - - +
78K LEU* 4.8 1.1 - - - -
27W SER 3.0 12.5 + - - -
28W TYR* 3.2 24.4 - - - -
30W TYR* 1.3 75.4 - - - +
32W SER* 1.3 62.8 + - - +
34W TYR* 3.4 12.3 + - - +
35W ALA* 3.1 22.5 + - - +
55W SER* 3.8 12.9 + - - -
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Residues in contact with SER 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 3.3 17.6 - - - +
28W TYR 3.2 6.0 + - - -
29W THR 3.2 11.8 + - - -
30W TYR 3.2 0.6 - - - -
31W SER* 1.3 72.9 - - - +
33W MET* 1.3 60.8 + - - +
35W ALA* 3.2 6.7 + - - +
36W PHE* 2.9 28.4 + - - +
84W PRO* 3.2 29.4 - - - +
86W ARG 4.0 6.2 + - - -
87W ASP* 5.1 7.2 + - - +
89W TRP* 3.4 17.6 + - - -
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Residues in contact with MET 33 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W THR* 3.2 34.0 + - + +
30W TYR* 3.2 15.9 + - + +
32W SER* 1.3 76.0 - - - +
34W TYR* 1.3 66.1 + - - +
36W PHE* 3.3 0.9 + - - +
37W PHE* 3.0 32.7 + - + -
51W PHE* 3.8 41.3 - - + -
89W TRP* 3.7 44.2 - - + +
95W ALA* 3.8 23.8 - - + +
98W ALA* 4.0 7.6 - - + -
99W ALA* 4.2 8.7 - - - +
102W LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K GLU* 5.1 13.4 + - + +
66K MET* 4.5 22.4 - - + -
67K LYS* 3.4 37.0 - - + +
30W TYR 2.8 13.7 + - - +
31W SER* 3.4 15.9 - - - +
32W SER 3.2 0.2 - - - -
33W MET* 1.3 77.6 - - - +
35W ALA* 1.3 72.3 + - - +
36W PHE 3.3 0.3 + - - -
37W PHE 3.4 0.5 + - - -
38W ASP* 3.2 30.3 + - + +
48W ALA* 3.2 38.3 - - + +
49W GLU* 3.6 20.3 + - - -
51W PHE* 4.0 2.2 - - - +
52W LYS* 3.7 42.4 + - + +
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Residues in contact with ALA 35 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K MET* 4.2 15.7 - - + -
70K ASN* 3.0 27.1 + - - +
76K VAL* 4.2 31.4 - - + +
31W SER 3.1 10.4 + - - +
32W SER* 3.2 9.6 + - - +
34W TYR* 1.3 86.0 - - - +
36W PHE* 1.3 64.3 + - - +
38W ASP* 4.4 0.9 - - - -
39W ARG* 3.5 9.2 + - - +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32W SER 2.9 16.8 + - - +
33W MET 3.5 5.4 - - - +
34W TYR 3.1 0.6 - - - -
35W ALA* 1.3 78.5 - - - +
37W PHE* 1.3 86.7 + + - +
39W ARG* 3.3 52.2 - - - +
42W VAL* 3.3 36.2 - - + +
87W ASP 4.5 3.8 - - - +
88W GLU* 3.8 11.9 - - + -
89W TRP* 3.6 32.5 - - + -
90W GLY* 3.5 42.0 - - - -
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Residues in contact with PHE 37 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W MET* 3.0 27.0 + - + +
34W TYR 3.4 0.4 + - - -
36W PHE* 1.3 92.0 - + - +
38W ASP* 1.3 59.8 + - - +
39W ARG 3.2 0.4 - - - -
42W VAL* 3.5 21.8 - - + -
43W ALA* 3.5 7.2 + - - -
44W LEU* 3.2 49.2 + - + +
45W HIS* 4.3 0.7 + - - -
47W VAL* 3.9 11.4 - - + -
48W ALA* 3.7 15.3 - - + -
51W PHE* 3.7 20.4 - + - -
89W TRP* 4.8 0.4 - - + -
91W ASN* 3.5 24.0 - - - -
92W THR* 3.6 27.1 - - - -
95W ALA* 3.7 22.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 38 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K LYS* 3.1 46.1 + - - +
70K ASN* 3.2 31.1 + - - +
142P LYS* 3.0 26.0 + - - -
34W TYR* 3.2 30.0 + - + +
35W ALA* 4.3 1.6 - - - -
36W PHE 3.2 0.4 - - - -
37W PHE* 1.3 74.8 - - - +
39W ARG* 1.3 66.2 + - - +
45W HIS* 3.4 22.3 + - - -
48W ALA* 4.1 2.9 - - + +
----------------------------------------------------------
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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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