Contacts of the helix formed by residues 10 - 38 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S ARG* 4.0 3.5 + - - +
8S TYR 3.7 1.8 + - - -
9S HIS* 1.3 83.5 + - - +
11S ASP* 1.3 66.5 + - - +
13S GLU* 3.4 19.1 + - - +
14S ALA* 3.1 22.2 + - - +
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Residues in contact with ASP 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S HIS* 2.8 23.4 + - - +
10S SER* 1.3 72.7 - - - +
12S CYS* 1.3 62.7 + - - +
14S ALA* 3.4 6.5 + - - +
15S ALA* 2.9 29.1 + - - +
18S ARG* 4.6 2.1 + - - -
116S LEU* 3.6 22.2 - - + +
120S LYS* 3.1 23.2 + - + +
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Residues in contact with CYS 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8S TYR* 4.1 10.8 - - + -
9S HIS* 3.1 25.4 + - + +
11S ASP* 1.3 78.6 - - - +
13S GLU* 1.3 56.7 + - - +
15S ALA* 3.1 3.7 + - - +
16S VAL* 2.9 36.1 + - - +
113S LEU* 4.3 1.3 - - - +
116S LEU* 4.0 24.9 - - - -
117S ALA* 4.3 8.1 - - - -
120S LYS* 4.1 16.2 - - - -
122S ASP* 5.0 4.9 - - - -
125S LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S ARG* 2.7 34.2 + - - -
8S TYR* 3.7 21.0 + - + -
9S HIS 3.1 8.7 + - - +
10S SER* 3.5 18.0 + - - +
12S CYS* 1.3 78.9 - - - +
14S ALA* 1.3 62.5 + - - +
16S VAL 3.3 0.3 + - - -
17S ASN* 3.1 22.1 + - - +
69S GLN* 3.2 26.9 + - - +
74S GLY* 3.8 2.0 - - - -
75S ARG* 2.9 32.7 + - - +
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Residues in contact with ALA 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S SER 3.1 16.7 + - - +
11S ASP* 3.7 7.6 - - - +
12S CYS 3.3 0.2 - - - -
13S GLU* 1.3 78.7 - - - +
15S ALA* 1.3 62.0 + - - +
17S ASN* 3.5 10.0 + - - +
18S ARG* 3.1 38.7 + - - +
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Residues in contact with ALA 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S ASP 2.9 17.5 + - - +
12S CYS 3.1 1.8 + - - +
14S ALA* 1.3 74.3 - - - +
16S VAL* 1.3 60.7 + - - +
18S ARG* 3.3 23.4 + - - +
19S MET* 2.9 29.3 + - - +
113S LEU* 3.5 27.6 - - + +
116S LEU* 3.7 11.4 - - + -
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Residues in contact with VAL 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S TYR* 3.6 14.6 - - - +
12S CYS 2.9 20.2 + - - +
13S GLU 3.6 4.5 - - - +
15S ALA* 1.3 76.1 - - - +
17S ASN* 1.3 57.5 + - - +
19S MET* 3.2 7.9 + - - +
20S LEU* 2.9 29.6 + - + +
65S PHE* 3.9 33.6 - - + +
68S TYR* 4.6 5.4 - - + -
69S GLN* 3.5 22.0 - - + +
113S LEU* 4.3 12.3 - - + -
125S LEU* 4.3 23.3 - - + -
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Residues in contact with ASN 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S GLU* 3.1 16.0 + - - +
14S ALA* 3.6 12.0 - - - +
16S VAL* 1.3 76.6 - - - +
18S ARG* 1.3 61.7 + - - +
20S LEU* 3.5 16.2 - - - +
21S ASN* 3.4 20.3 + - - +
69S GLN* 3.4 13.0 + - - +
75S ARG 3.2 19.2 + - - -
76S VAL* 3.3 10.2 - - - -
77S VAL* 3.1 46.8 + - - +
79S GLN* 4.6 9.4 + - - +
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Residues in contact with ARG 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S ASP 4.6 2.8 + - - -
14S ALA* 3.1 22.0 + - - +
15S ALA* 3.4 34.5 - - - +
16S VAL 3.1 0.2 - - - -
17S ASN* 1.3 78.8 - - - +
19S MET* 1.3 64.9 + - - +
21S ASN* 3.4 7.1 + - - +
22S LEU* 3.1 20.4 + - - +
79S GLN* 4.8 16.8 - - - +
116S LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S ALA 2.9 16.2 + - - +
16S VAL* 3.5 5.8 - - - +
18S ARG* 1.3 76.6 - - - +
20S LEU* 1.3 64.0 + - - +
22S LEU* 3.2 13.3 + - - +
23S GLU* 2.9 27.8 + - + +
65S PHE* 3.4 30.5 - - + -
106S VAL* 4.6 3.1 - - - +
109S ALA* 3.1 51.6 - - + +
110S LEU* 3.5 20.9 - - + +
113S LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S VAL* 2.9 15.3 + - + +
17S ASN* 3.5 20.2 - - - +
19S MET* 1.3 76.4 - - - +
21S ASN* 1.3 63.2 + - + +
23S GLU* 3.4 8.1 + - - +
24S LEU* 3.1 41.9 + - + +
62S ALA* 3.7 17.3 - - + +
65S PHE* 4.2 14.3 - - + +
66S MET* 3.8 36.1 - - + +
69S GLN* 5.8 0.4 - - - +
76S VAL* 4.0 19.1 - - + -
77S VAL 5.6 0.7 - - - +
78S LEU* 3.7 17.5 - - + -
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Residues in contact with ASN 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M TYR* 4.4 4.8 + - - +
17S ASN 3.4 7.0 + - - +
18S ARG 3.6 8.2 - - - +
20S LEU* 1.3 83.0 - - + +
22S LEU* 1.3 61.4 + - - +
24S LEU* 3.1 8.4 + - - +
25S TYR* 2.8 30.3 + - - +
79S GLN* 3.5 43.3 + - - +
80S ASP 3.2 27.1 + - - +
81S ILE* 4.3 7.2 - - - +
82S LYS 5.6 1.0 + - - -
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Residues in contact with LEU 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ARG 3.1 14.0 + - - +
19S MET* 3.2 15.7 + - - +
21S ASN* 1.3 78.2 + - - +
23S GLU* 1.3 58.0 + - + +
25S TYR* 3.2 23.7 + - + -
26S ALA* 2.9 27.1 + - - +
102S LEU* 5.4 1.3 - - + -
105S THR* 4.4 16.8 - - + +
106S VAL* 3.9 30.0 - - + +
109S ALA* 3.7 30.3 - - + -
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Residues in contact with GLU 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S MET* 2.9 19.8 + - + +
20S LEU 3.4 9.0 - - - +
22S LEU* 1.3 76.3 - - - +
24S LEU* 1.3 57.7 + - - +
26S ALA* 3.3 5.2 + - - +
27S SER* 2.9 28.2 + - - -
58S GLU* 2.7 20.9 - - - +
61S HIS* 3.4 18.2 - - + +
62S ALA* 3.8 14.6 - - + -
65S PHE* 4.1 19.3 - - + -
106S VAL* 4.0 14.9 - - - +
110S LEU* 4.9 2.3 - - - +
133S TYR* 3.7 14.7 - - - -
176S MG 2.4 30.7 - - - -
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Residues in contact with LEU 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M TYR* 3.6 39.3 - - + +
20S LEU* 3.1 30.4 + - + +
21S ASN* 3.5 9.4 - - - +
23S GLU* 1.3 75.9 - - - +
25S TYR* 1.3 57.4 + - - +
27S SER* 3.5 6.1 - - - +
28S TYR* 3.0 27.7 + - - +
59S ARG* 4.9 16.8 - - + -
62S ALA* 3.7 19.3 - - + -
63S GLU* 6.4 0.2 - - + -
66S MET* 5.1 6.1 - - + -
81S ILE* 3.7 24.8 - - + +
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Residues in contact with TYR 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S ASN* 2.8 17.8 + - - +
22S LEU* 3.4 26.7 - - + +
23S GLU 3.2 0.4 - - - -
24S LEU* 1.3 72.6 - - - +
26S ALA* 1.3 64.6 + - - +
28S TYR* 3.2 3.8 + - - +
29S THR* 2.9 47.9 + - + +
81S ILE* 4.0 9.8 - - + +
82S LYS* 3.4 38.6 - - + +
83S LYS 3.8 11.8 + - - -
84S PRO* 4.1 1.6 - - + -
85S GLU* 3.8 25.3 + - - +
102S LEU* 4.1 17.3 - - + -
105S THR* 6.5 0.7 - - + -
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Residues in contact with ALA 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S LEU 2.9 13.4 + - - +
23S GLU* 3.5 10.1 - - - +
25S TYR* 1.3 77.3 - - - +
27S SER* 1.3 61.8 + - - +
29S THR* 3.3 3.3 + - - -
30S TYR* 3.1 31.3 + - + -
58S GLU* 4.2 16.2 - - + -
102S LEU* 4.0 26.2 - - + -
103S GLU* 6.5 0.4 - - - -
106S VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S GLU 2.9 17.3 + - - -
24S LEU* 3.5 11.6 - - - +
26S ALA* 1.3 76.1 - - - +
28S TYR* 1.3 61.6 + - - +
30S TYR 3.1 2.6 + - - -
31S SER* 3.0 18.9 + - - -
55S SER* 2.9 40.0 + - - +
58S GLU* 3.8 12.5 - - - +
59S ARG* 3.6 16.9 - - - +
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Residues in contact with TYR 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASN* 4.4 2.9 + - - +
24M LEU* 3.6 27.8 - - + +
66M MET* 5.6 0.2 - - + -
78M LEU* 3.4 37.0 - - + +
79M GLN 2.9 30.1 + - - -
81M ILE* 3.7 22.9 - - + +
24S LEU 3.0 18.4 + - - +
25S TYR* 3.5 5.8 - - - +
27S SER* 1.3 77.6 + - - +
29S THR* 1.3 60.0 + - - +
31S SER* 3.2 16.3 - - - -
32S SER* 3.2 18.9 + - - -
81S ILE* 4.0 12.8 - - + -
82S LYS 3.6 17.7 - - - -
83S LYS* 4.0 3.8 - - - -
84S PRO* 3.7 17.8 - - + +
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Residues in contact with THR 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S TYR* 2.9 31.3 + - + +
26S ALA 3.6 8.3 - - - -
27S SER 3.2 0.4 - - - -
28S TYR* 1.3 75.7 - - - +
30S TYR* 1.3 61.3 + - - +
32S SER* 3.2 6.4 + - - -
33S MET* 3.2 39.0 + - + +
84S PRO* 3.4 20.6 - - + +
85S GLU* 5.0 0.4 + - - +
89S TRP* 4.0 15.7 - - + -
102S LEU* 3.7 25.8 - - + -
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Residues in contact with TYR 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S ALA* 3.1 23.4 + - + -
27S SER 3.1 6.5 + - - +
29S THR* 1.3 73.7 - - - +
31S SER* 1.3 59.6 + - - +
33S MET* 3.2 12.0 + - + +
34S TYR* 2.8 28.9 + - - +
50S PHE* 5.9 0.4 - + - -
51S PHE* 3.6 47.9 - + - +
54S HIS* 3.9 28.5 + + + -
55S SER* 3.7 6.5 - - - -
58S GLU* 4.0 13.7 - - + -
99S ALA* 3.9 25.3 + - + +
102S LEU* 3.9 17.9 - - + +
103S GLU* 2.8 40.0 + - - +
144S ILE* 4.3 3.0 - - + +
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Residues in contact with SER 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M LEU* 6.1 0.7 - - - +
63M GLU* 4.9 6.1 + - - +
66M MET* 3.3 29.3 - - - +
78M LEU* 4.8 2.2 - - - -
27S SER 3.0 12.0 + - - -
28S TYR* 3.2 24.8 - - - -
30S TYR* 1.3 74.6 - - - +
32S SER* 1.3 61.7 + - - +
34S TYR* 3.4 12.5 + - - +
35S ALA* 3.1 23.2 + - - +
55S SER* 3.8 12.9 + - - -
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Residues in contact with SER 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M LEU* 3.4 16.9 - - - +
28S TYR 3.2 5.8 + - - -
29S THR 3.2 10.9 + - - -
30S TYR 3.2 0.4 - - - -
31S SER* 1.3 73.5 - - - +
33S MET* 1.3 61.2 + - - +
35S ALA* 3.2 7.4 + - - +
36S PHE* 2.9 28.9 + - - +
84S PRO* 3.2 29.2 - - - +
86S ARG 4.0 6.2 + - - -
87S ASP* 5.1 7.9 + - - +
89S TRP* 3.4 17.4 + - - -
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Residues in contact with MET 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S THR* 3.2 34.0 + - + +
30S TYR* 3.2 15.7 + - + +
32S SER* 1.3 76.5 - - - +
34S TYR* 1.3 65.3 + - - +
36S PHE* 3.3 0.6 + - - -
37S PHE* 3.0 33.6 + - + -
51S PHE* 3.8 42.2 - - + -
89S TRP* 3.7 43.5 - - + -
95S ALA* 3.8 22.4 - - + +
98S ALA* 4.0 7.6 - - + -
99S ALA* 4.2 9.9 - - - +
102S LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M GLU* 5.1 12.7 + - + +
66M MET* 4.5 22.9 - - + -
67M LYS* 3.3 37.4 - - + +
70M ASN* 6.3 0.2 - - - -
30S TYR 2.8 13.8 + - - +
31S SER* 3.4 15.0 - - - +
33S MET* 1.3 76.5 - - - +
35S ALA* 1.3 72.3 + - - +
36S PHE 3.3 0.2 + - - -
37S PHE 3.4 0.3 + - - -
38S ASP* 3.2 30.1 + - + +
48S ALA* 3.2 38.9 - - + +
49S GLU* 3.6 19.7 + - - -
51S PHE* 4.0 2.6 - - - +
52S LYS* 3.7 41.7 + - + +
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Residues in contact with ALA 35 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M MET* 4.3 15.0 - - + -
70M ASN* 3.1 27.3 + - - +
76M VAL* 4.2 31.6 - - + -
31S SER 3.1 9.2 + - - +
32S SER* 3.2 9.6 + - - +
34S TYR* 1.3 86.9 - - - +
36S PHE* 1.3 61.7 + - - +
38S ASP* 3.9 1.1 - - - -
39S ARG* 3.5 11.0 + - - +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32S SER 2.9 16.7 + - - +
33S MET 3.5 5.6 - - - +
34S TYR 3.1 0.4 - - - -
35S ALA* 1.3 77.9 - - - +
37S PHE* 1.3 84.3 + + - +
39S ARG* 3.3 52.5 - - - +
42S VAL* 3.3 37.1 - - + +
87S ASP 4.5 3.8 - - - +
88S GLU* 3.8 11.4 - - + -
89S TRP* 3.6 33.0 - - + -
90S GLY* 3.5 42.0 - - - -
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Residues in contact with PHE 37 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S MET* 3.0 26.1 + - + -
36S PHE* 1.3 90.9 - + - +
38S ASP* 1.3 60.6 + - - +
39S ARG 3.2 0.4 - - - -
42S VAL* 3.5 23.3 - - + -
43S ALA* 3.5 8.1 + - - -
44S LEU* 3.2 49.0 + - + +
45S HIS* 4.3 0.7 + - - -
47S VAL* 3.9 11.7 - - + -
48S ALA* 3.7 15.4 - - + +
51S PHE* 3.7 19.3 - + - -
89S TRP* 4.8 0.4 - - + -
91S ASN* 3.5 24.5 - - - -
92S THR* 3.6 27.6 - - - -
95S ALA* 3.7 22.7 - - + -
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Residues in contact with ASP 38 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M LYS* 3.2 44.4 + - - +
70M ASN* 3.1 31.9 + - - +
34S TYR* 3.2 29.8 + - + +
35S ALA* 4.4 1.1 - - - -
36S PHE 3.2 0.4 - - - -
37S PHE* 1.3 74.4 - - - +
39S ARG* 1.3 61.8 + - - +
45S HIS* 3.4 24.1 + - - -
48S ALA* 4.1 2.5 - - + +
142T LYS* 2.9 31.1 + - - -
----------------------------------------------------------
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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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