Contacts of the strand formed by residues 40 - 72 (chain m) in PDB entry 5MQF
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 LEU 40 (chain m).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6l PRO* 5.1 3.5 - - - +
33m ALA 3.4 6.3 - - - +
34m PHE* 4.7 2.7 - - + +
38m MET 3.4 6.9 + - - +
39m ASN* 1.3 73.5 - - - +
41m ILE* 1.3 62.6 + - - +
42m LEU* 4.0 4.3 + - + +
70m VAL 3.6 0.9 - - - +
71m LEU* 3.2 7.5 - - - +
72m LEU* 2.8 45.8 + - + +
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Residues in contact with ILE 41 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6l PRO* 5.1 8.7 - - + +
30m THR 3.4 0.7 - - - +
31m PHE* 3.8 3.1 - - - -
32m LYS* 2.9 35.2 + - + -
33m ALA* 2.9 36.3 + - + +
40m LEU* 1.3 74.4 - - - +
42m LEU* 1.3 58.6 + - - +
43m CYS 4.1 0.4 - - - -
70m VAL 3.5 4.7 - - - +
71m LEU* 4.7 3.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 42 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27m PHE* 6.2 3.8 - - + -
29m GLY* 4.4 11.2 - - - +
30m THR 3.3 6.7 - - - +
31m PHE* 5.5 0.9 - - - -
40m LEU* 4.0 5.1 - - + +
41m ILE* 1.3 72.5 - - - +
43m CYS* 1.3 60.8 + - - +
45m CYS* 3.6 17.4 - - + +
68m GLY 3.3 6.2 - - - +
69m LEU* 4.7 0.4 - - - -
70m VAL* 2.8 45.0 + - + +
72m LEU* 6.3 1.8 - - + +
----------------------------------------------------------
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Residues in contact with CYS 43 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78l LYS* 5.6 10.1 - - + -
29m GLY* 3.5 0.5 - - - -
30m THR* 2.7 50.9 + - - +
32m LYS* 5.2 8.2 - - + +
41m ILE 4.1 0.8 - - - -
42m LEU* 1.3 68.7 - - - +
44m ASP* 1.3 71.7 + - + +
45m CYS 3.2 3.8 + - - -
68m GLY 4.2 0.9 - - - -
69m LEU* 4.6 7.6 - - + +
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Residues in contact with ASP 44 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W THR* 3.6 31.0 - - - -
28m ILE 3.9 5.7 - - - +
29m GLY* 4.0 2.8 - - - -
30m THR* 4.8 3.1 + - - +
43m CYS* 1.3 75.4 - - + +
45m CYS* 1.3 62.1 + - - +
46m ASP* 3.9 1.2 + - - +
68m GLY* 3.4 14.5 + - - -
69m LEU* 4.8 0.4 - - - +
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Residues in contact with CYS 45 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27m PHE* 5.9 3.8 - - + -
28m ILE 3.3 10.5 - - - +
29m GLY* 3.9 2.2 - - - -
42m LEU* 3.6 28.0 - - + +
44m ASP* 1.3 72.9 - - - +
46m ASP* 1.3 60.7 + - - +
66m VAL* 4.0 0.9 - - - -
67m LEU* 2.9 27.1 + - + +
68m GLY 2.8 27.6 + - - +
70m VAL* 4.1 11.4 - - + -
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Residues in contact with ASP 46 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20W ARG 4.9 8.5 - - - +
26m ILE 3.8 0.2 - - - +
27m PHE* 3.6 4.5 - - - +
28m ILE* 2.9 36.5 + - + +
44m ASP 3.9 1.5 + - - +
45m CYS* 1.3 74.4 - - - +
47m GLU* 1.3 62.7 + - - +
48m PHE 4.3 0.2 + - - -
64m LYS* 5.7 4.7 - - + -
65m ARG 3.2 15.7 - - - +
66m VAL* 4.7 3.6 - - - -
67m LEU* 4.3 2.0 - - - +
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Residues in contact with GLU 47 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25m ARG* 5.9 4.9 - - + -
26m ILE 3.4 7.2 - - - +
27m PHE* 5.4 2.5 - - + -
46m ASP* 1.3 75.0 - - - +
48m PHE* 1.3 61.5 + - - +
63m GLU 3.5 1.4 - - - +
64m LYS* 3.2 7.0 - - - +
65m ARG* 2.8 46.1 + - + +
67m LEU* 5.3 4.9 - - + +
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Residues in contact with PHE 48 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25m ARG* 4.0 4.2 - - - +
26m ILE* 2.8 46.7 + - + +
47m GLU* 1.3 75.3 - - - +
49m ARG* 1.3 65.4 + - - +
63m GLU 3.3 8.7 - - - +
64m LYS* 5.3 3.6 - - + -
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Residues in contact with ARG 49 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24m GLY 5.5 2.9 - - - +
25m ARG* 5.5 7.0 - - + +
26m ILE* 5.3 0.9 - - - +
48m PHE* 1.3 78.4 - - - +
63m GLU* 3.3 30.3 + - + +
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Residues in contact with GLU 63 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47m GLU 3.5 1.2 - - - +
48m PHE* 3.3 7.5 - - - -
49m ARG* 3.3 46.2 + - + +
64m LYS* 1.3 60.9 + - - +
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Residues in contact with LYS 64 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46m ASP* 5.7 5.4 - - + -
47m GLU 3.2 7.0 - - - +
48m PHE* 4.7 4.0 - - + +
63m GLU* 1.3 75.7 - - - +
65m ARG* 1.3 60.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 65 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46m ASP* 3.2 6.9 - - - +
47m GLU* 2.8 44.5 + - + +
64m LYS* 1.3 76.5 - - - +
66m VAL* 1.3 63.2 + - - +
67m LEU* 3.6 1.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W VAL 4.4 1.8 - - - +
20W ARG* 2.4 48.9 - - + +
45m CYS 4.3 2.5 - - - -
46m ASP* 4.5 2.0 - - - +
65m ARG* 1.3 73.0 - - - +
67m LEU* 1.3 61.0 + - - +
68m GLY 5.4 0.2 - - - +
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Residues in contact with LEU 67 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72l ILE* 4.9 16.1 - - + +
45m CYS* 2.9 21.8 + - + +
46m ASP* 4.9 2.7 - - - -
47m GLU* 5.3 3.8 - - + +
65m ARG* 3.6 4.4 + - + +
66m VAL* 1.3 74.8 - - - +
68m GLY* 1.3 61.4 + - - +
69m LEU 4.1 2.3 + - - -
70m VAL* 5.2 8.1 - - + -
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Residues in contact with GLY 68 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75l ASP* 6.5 0.4 - - - -
42m LEU 3.3 2.3 - - - +
44m ASP* 3.4 9.9 + - - -
45m CYS* 2.8 44.7 + - - +
66m VAL* 5.4 0.6 - - - +
67m LEU* 1.3 77.3 - - - +
69m LEU* 1.3 61.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72l ILE* 3.5 6.3 - - - +
73l LEU* 3.0 38.0 + - + +
74l PRO 3.6 25.6 - - - +
75l ASP* 4.6 10.2 - - + +
77l LEU* 6.4 0.2 - - + -
78l LYS* 5.6 7.4 - - + +
42m LEU 3.6 4.7 - - - -
43m CYS* 4.6 7.4 - - + +
44m ASP 4.8 0.2 - - - +
67m LEU* 4.1 1.2 + - - -
68m GLY* 1.3 70.3 - - - -
70m VAL* 1.3 57.9 + - - +
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Residues in contact with VAL 70 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70l PHE* 6.0 2.7 - - + -
71l LEU 3.7 7.0 - - - +
72l ILE* 4.7 2.0 - - + +
73l LEU* 6.4 0.2 - - - -
40m LEU 3.6 0.9 - - - +
41m ILE* 3.5 3.1 - - - +
42m LEU* 2.8 50.9 + - + +
45m CYS* 4.1 15.9 - - + -
67m LEU* 5.2 8.1 - - + -
68m GLY 3.5 1.1 + - - +
69m LEU* 1.3 73.3 - - - +
71m LEU* 1.3 62.8 + - - +
72m LEU* 3.9 3.1 - - + +
----------------------------------------------------------
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Residues in contact with LEU 71 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6l PRO* 5.6 11.7 - - + +
10l LEU* 6.3 4.0 - - + -
70l PHE* 3.4 4.6 - - - +
71l LEU* 3.0 41.7 + - + +
73l LEU* 5.5 4.3 - - + +
39m ASN* 6.6 0.2 - - + -
40m LEU 3.2 7.2 - - - +
41m ILE* 4.7 2.9 - - + +
69m LEU 4.4 0.4 + - - -
70m VAL* 1.3 72.4 - - - +
72m LEU* 1.3 62.7 + - - +
73m ARG 4.1 0.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 72 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69l ARG 5.0 0.9 - - - +
70l PHE* 4.1 11.2 - - + -
38m MET 4.3 0.2 - - - +
39m ASN* 3.2 6.9 - - - +
40m LEU* 2.8 47.1 + - + +
42m LEU* 6.3 0.2 - - - +
70m VAL* 3.9 4.3 - - + -
71m LEU* 1.3 74.5 - - - +
73m ARG* 1.3 64.5 + - - +
77m LEU* 6.3 2.5 - - + -
----------------------------------------------------------
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Residues in contact with ARG 73 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 U 4.5 10.3 - - + +
65l GLY 5.7 2.0 - - - +
68l ILE* 4.0 14.6 - - + +
69l ARG* 3.4 20.0 + - - +
70l PHE* 4.6 1.0 - - - +
38m MET 4.5 0.2 - - - -
39m ASN* 4.4 6.5 - - - +
71m LEU 4.1 1.4 + - - -
72m LEU* 1.3 74.3 - - - +
74m GLY* 1.3 65.5 + - - +
75m GLU* 3.3 8.5 - - + +
76m ASN* 3.3 16.8 + - + +
77m LEU* 3.8 6.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 74 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 U 3.6 6.6 + - - -
1032 U 5.4 3.9 - - - -
37m HIS 3.4 20.2 - - - +
38m MET* 3.2 26.9 + - - +
39m ASN* 3.7 4.9 - - - +
72m LEU 3.7 0.8 + - - -
73m ARG* 1.3 67.3 - - - +
75m GLU* 1.3 65.0 + - - +
76m ASN 3.1 2.5 - - - -
77m LEU* 3.0 23.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 75 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 U 3.3 33.1 + - + +
1032 U 4.3 19.8 + - - +
66l SER 5.5 6.5 - - - +
22m GLN* 5.2 2.4 - - - +
73m ARG* 4.7 7.4 - - + +
74m GLY* 1.3 74.6 - - - +
76m ASN* 1.3 59.9 + - + +
77m LEU 3.7 3.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 76 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69l ARG* 4.7 22.7 - - + +
21m LEU* 3.3 9.7 - - + +
22m GLN* 2.9 41.4 + - + +
73m ARG* 3.3 12.1 + - + +
74m GLY 3.1 1.0 - - - -
75m GLU* 1.3 78.1 - - + +
77m LEU* 1.3 59.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20m ILE 4.0 4.3 - - - +
21m LEU* 4.8 0.9 - - - +
22m GLN* 5.1 1.5 - - - +
38m MET* 4.8 9.6 - - + +
72m LEU* 6.3 2.0 - - + -
73m ARG 3.8 3.0 + - - +
74m GLY* 3.0 26.6 + - - +
75m GLU 4.2 3.8 - - - +
76m ASN* 1.3 78.5 - - - +
78m VAL* 1.3 63.5 + - - +
79m SER 5.0 0.9 - - - +
61n ARG* 4.0 15.2 - - + +
64n ASN* 5.3 2.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 78 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20m ILE* 2.9 24.6 + - + +
21m LEU 4.5 9.4 - - - +
22m GLN* 4.9 4.3 - - + +
76m ASN 3.9 0.6 + - - -
77m LEU* 1.3 76.0 - - - +
79m SER* 1.3 63.5 + - - +
60n ILE* 3.8 2.4 - - - +
61n ARG* 3.1 29.6 + - - +
64n ASN* 4.7 16.3 - - + +
----------------------------------------------------------
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Residues in contact with SER 79 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18m ARG 3.9 0.4 - - - +
19m CYS* 3.4 4.2 - - - +
20m ILE* 2.8 39.8 + - - +
77m LEU* 4.9 1.8 - - - +
78m VAL* 1.3 85.2 - - - +
80m MET* 1.3 62.1 + - - +
58n LEU* 6.0 3.4 - - - -
59n SER 3.1 16.8 - - - -
60n ILE* 4.5 4.7 - - - -
61n ARG 4.9 0.2 - - - +
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Residues in contact with MET 80 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17m MET* 5.4 7.0 - - + -
18m ARG 3.2 9.6 - - - +
19m CYS* 4.9 6.3 - - + -
79m SER* 1.3 76.5 - - - +
81m THR* 1.3 59.6 + - - +
57n THR 4.8 0.2 - - - -
58n LEU* 3.6 3.2 - - - -
59n SER* 2.9 43.3 + - - +
----------------------------------------------------------
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Residues in contact with THR 81 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17m MET* 3.6 5.3 - - - +
18m ARG* 2.8 40.6 + - - +
80m MET* 1.3 73.3 - - - +
82m VAL* 1.3 65.1 + - - +
55n LEU* 4.8 10.1 - - - -
57n THR* 3.2 23.6 - - - -
58n LEU* 4.7 3.1 - - - -
----------------------------------------------------------
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Residues in contact with VAL 82 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12m HIS* 6.3 3.8 - - + -
15m TYR* 5.7 5.4 - - + -
16m ARG 4.0 6.7 - - - +
17m MET* 4.8 1.3 - - - +
18m ARG* 5.4 0.4 - - - +
81m THR* 1.3 76.5 - - - +
83m GLU* 1.3 62.4 + - - +
84m GLY 5.0 3.8 - - - +
57n THR* 4.4 12.7 + - - -
----------------------------------------------------------
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Residues in contact with GLU 83 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W LEU* 5.7 2.9 - - - +
43W GLN* 4.6 11.0 - - - +
16m ARG* 2.9 20.4 + - + +
17m MET 4.0 2.2 - - - +
18m ARG* 3.9 26.5 - - + +
28m ILE* 5.5 6.1 - - + -
81m THR 3.5 1.0 + - - -
82m VAL* 1.3 74.9 - - - +
84m GLY* 1.3 58.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 84 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43W GLN* 5.1 7.2 - - - -
15m TYR* 4.0 4.9 - - - +
16m ARG* 3.1 28.3 + - - +
82m VAL* 3.8 3.5 - - - +
83m GLU* 1.3 81.5 - - - +
85m PRO* 1.3 77.8 - - - +
----------------------------------------------------------
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Residues in contact with PRO 85 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W LEU* 6.5 1.1 - - + -
43W GLN* 5.6 5.4 - - + -
15m TYR* 5.2 0.9 - - + -
16m ARG* 4.0 7.1 + - - +
84m GLY* 1.3 90.4 - - - +
86m PRO* 1.4 81.3 - - + +
87m PRO* 3.5 6.2 - - - +
----------------------------------------------------------
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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