Contacts of the helix formed by residues 10 - 38 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 4.0 3.9 + - - +
8B TYR 3.7 1.8 + - - -
9B HIS* 1.3 84.4 + - - +
11B ASP* 1.3 65.3 + - - +
13B GLU* 3.4 18.4 + - - +
14B ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B HIS* 2.8 23.6 + - + +
10B SER* 1.3 73.5 - - - +
12B CYS* 1.3 61.7 + - - +
14B ALA* 3.4 6.2 + - - +
15B ALA* 2.9 28.9 + - - +
18B ARG* 4.6 1.7 + - - -
116B LEU* 3.6 22.2 - - + +
120B LYS* 3.1 22.1 + - - +
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Residues in contact with CYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 4.1 10.1 - - + -
9B HIS* 3.1 24.4 + - + +
11B ASP* 1.3 79.8 - - - +
13B GLU* 1.3 57.6 + - - +
15B ALA* 3.1 3.8 + - - +
16B VAL* 2.9 35.9 + - - +
113B LEU* 4.3 0.8 - - - +
116B LEU* 4.0 25.4 - - - -
117B ALA* 4.3 8.1 - - - -
120B LYS* 4.1 15.3 - - - -
122B ASP* 5.0 5.4 - - - -
125B LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 2.7 34.2 + - - -
8B TYR* 3.7 21.2 + - + -
9B HIS 3.1 8.3 + - - +
10B SER* 3.5 17.3 + - - +
12B CYS* 1.3 80.0 - - - +
14B ALA* 1.3 63.4 + - - +
16B VAL 3.3 0.7 + - - -
17B ASN* 3.1 22.4 + - - +
69B GLN* 3.2 26.5 + - - +
74B GLY* 3.8 2.5 - - - -
75B ARG* 2.9 32.3 + - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER 3.1 17.1 + - - +
11B ASP* 3.7 7.4 - - - +
12B CYS 3.3 0.2 - - - -
13B GLU* 1.3 78.0 - - - +
15B ALA* 1.3 61.9 + - - +
17B ASN* 3.5 10.9 + - - +
18B ARG* 3.1 40.0 + - - +
79B GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP 2.9 17.5 + - - +
12B CYS 3.5 1.3 - - - +
14B ALA* 1.3 74.5 - - - +
16B VAL* 1.3 60.6 + - - +
18B ARG* 3.3 24.6 + - - +
19B MET* 2.9 29.1 + - - +
113B LEU* 3.5 27.5 - - + +
116B LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.6 15.3 - - - +
12B CYS 2.9 18.9 + - - +
13B GLU 3.6 5.2 - - - +
14B ALA 3.3 0.2 - - - -
15B ALA* 1.3 77.4 - - - +
17B ASN* 1.3 55.9 - - - +
19B MET* 3.2 7.4 + - - +
20B LEU* 2.9 29.7 + - + +
65B PHE* 3.9 34.3 - - + +
68B TYR* 4.6 4.9 - - + -
69B GLN* 3.5 21.1 - - + +
113B LEU* 4.3 13.0 - - + -
125B LEU* 4.3 22.7 - - + -
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Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 3.1 16.0 + - - +
14B ALA* 3.6 12.2 - - - +
15B ALA 3.3 0.2 - - - -
16B VAL* 1.3 76.5 - - - +
18B ARG* 1.3 61.6 + - - +
20B LEU* 3.5 17.0 - - - +
21B ASN* 3.4 20.3 + - - +
69B GLN* 3.4 12.2 + - - +
75B ARG 3.2 18.0 + - - -
76B VAL* 3.3 10.2 - - - -
77B VAL* 3.1 48.9 + - - +
79B GLN* 4.6 9.3 + - - +
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP 4.6 3.0 + - - -
14B ALA* 3.1 20.1 + - - +
15B ALA* 3.4 33.2 - - - +
17B ASN* 1.3 79.9 - - - +
19B MET* 1.3 64.9 + - - +
21B ASN* 3.4 7.2 + - - +
22B LEU* 3.1 19.8 + - - +
79B GLN* 4.8 16.6 - - - +
116B LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 2.9 17.7 + - - +
16B VAL* 3.2 6.0 + - - +
18B ARG* 1.3 76.3 - - - +
20B LEU* 1.3 63.7 + - - +
22B LEU* 3.2 13.1 + - - +
23B GLU* 2.9 27.3 + - - +
65B PHE* 3.4 30.3 - - + -
106B VAL* 4.6 3.1 - - - +
109B ALA* 3.1 50.7 - - + +
110B LEU* 3.5 21.3 - - + +
113B LEU* 3.7 18.8 - - + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 2.9 15.6 + - + +
17B ASN* 3.5 19.3 - - - +
19B MET* 1.3 78.6 - - - +
21B ASN* 1.3 62.9 + - + +
23B GLU* 3.3 9.2 + - - +
24B LEU* 3.1 41.4 + - + +
62B ALA* 3.7 16.8 - - - +
65B PHE* 4.2 14.3 - - + +
66B MET* 3.8 35.7 - - + +
69B GLN* 5.8 0.7 - - - +
76B VAL* 4.0 19.1 - - + -
77B VAL 5.6 0.7 - - - +
78B LEU* 3.7 16.6 - - + -
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASN 3.4 7.2 + - - +
18B ARG 3.6 8.9 - - - +
19B MET 3.2 0.4 - - - -
20B LEU* 1.3 82.6 - - + +
22B LEU* 1.3 61.4 + - - +
24B LEU* 3.1 8.4 + - - +
25B TYR* 2.8 30.7 + - - +
79B GLN* 3.5 44.3 + - - +
80B ASP 3.2 27.9 + - - +
81B ILE* 4.3 7.4 - - - +
82B LYS 5.6 0.9 + - - -
28F TYR* 4.4 5.0 + - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 3.1 13.7 + - - +
19B MET* 3.2 16.1 + - - +
21B ASN* 1.3 78.3 + - - +
23B GLU* 1.3 57.2 + - - +
25B TYR* 3.2 23.5 + - + -
26B ALA* 2.9 27.4 + - - +
102B LEU* 5.4 1.1 - - + -
105B THR* 4.4 16.8 - - + +
106B VAL* 3.9 31.4 - - + +
109B ALA* 3.7 30.5 - - + -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 2.9 19.7 + - + +
20B LEU 3.4 9.2 - - - +
22B LEU* 1.3 76.8 - - - +
24B LEU* 1.3 57.8 + - - +
26B ALA* 3.3 5.0 + - - +
27B SER* 2.9 28.2 + - - -
58B GLU* 2.7 21.3 - - - +
61B HIS* 3.4 17.8 - - + +
62B ALA* 3.8 13.9 - - + +
65B PHE* 4.1 18.3 - - + -
106B VAL* 4.0 14.7 - - + +
110B LEU* 4.9 2.8 - - - +
133B TYR* 3.7 15.6 - - - -
176B MG 2.4 29.8 - - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.1 31.2 + - + +
21B ASN* 3.1 9.4 + - - +
23B GLU* 1.3 75.8 - - - +
25B TYR* 1.3 57.7 + - - +
27B SER* 3.5 5.9 - - - -
28B TYR* 3.0 27.2 + - - +
59B ARG* 4.9 18.2 - - + +
62B ALA* 3.7 18.2 - - + -
63B GLU* 6.4 0.2 - - + -
66B MET* 5.1 7.0 - - + -
81B ILE* 3.7 24.9 - - + +
28F TYR* 3.6 39.3 - - + +
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASN* 2.8 18.0 + - - +
22B LEU* 3.4 26.2 - - + +
23B GLU 3.2 0.2 - - - -
24B LEU* 1.3 72.6 - - - +
26B ALA* 1.3 63.1 + - - +
28B TYR* 3.2 3.5 + - - +
29B THR* 2.9 49.2 + - - -
81B ILE* 4.0 10.0 - - + +
82B LYS* 3.4 37.5 - - + +
83B LYS 3.8 12.5 + - - -
84B PRO* 4.1 1.5 - - + -
85B GLU* 3.8 25.6 + - - +
102B LEU* 4.1 17.7 - - + -
105B THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 2.9 13.6 + - - +
23B GLU* 3.5 9.9 - - - +
25B TYR* 1.3 76.9 - - - +
27B SER* 1.3 61.9 + - - +
29B THR* 3.3 3.3 + - - -
30B TYR* 3.1 31.6 + - + -
58B GLU* 4.2 15.9 - - + -
102B LEU* 3.9 25.7 - - + +
103B GLU* 6.2 0.7 - - - +
106B VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU 2.9 16.6 + - - -
24B LEU* 3.5 11.1 - - - +
26B ALA* 1.3 76.5 - - - +
28B TYR* 1.3 62.9 + - - -
30B TYR 3.1 2.3 + - - -
31B SER* 3.0 19.5 + - - -
55B SER* 2.9 39.1 + - - +
58B GLU* 3.8 12.9 - - - +
59B ARG* 3.6 17.2 - - - +
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Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 3.0 18.1 + - - +
25B TYR* 3.5 6.1 - - - +
27B SER* 1.3 77.4 + - - +
29B THR* 1.3 60.4 + - - +
31B SER* 3.2 15.6 - - - -
32B SER* 3.2 19.1 + - - -
81B ILE* 4.0 13.2 - - + -
82B LYS 3.6 17.9 - - - +
83B LYS* 4.0 3.1 - - - -
84B PRO* 3.7 16.9 - - + +
21F ASN* 4.4 2.9 + - - +
24F LEU* 3.6 28.6 - - + +
66F MET* 5.5 0.2 - - + -
78F LEU* 3.4 37.7 - - + +
79F GLN 2.9 31.8 + - - -
81F ILE* 3.7 23.9 - - + +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 2.9 31.2 + - + +
26B ALA 3.6 8.3 - - - -
27B SER 3.2 0.4 - - - -
28B TYR* 1.3 75.9 - - - +
30B TYR* 1.3 61.2 + - - +
32B SER* 3.2 6.6 + - - -
33B MET* 3.2 39.0 + - + +
84B PRO* 3.4 20.7 - - - +
85B GLU 5.8 0.2 - - - +
89B TRP* 4.0 15.5 - - + -
102B LEU* 3.7 25.4 - - + -
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Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.1 23.4 + - + -
27B SER 3.1 6.7 + - - +
29B THR* 1.3 73.0 - - - +
31B SER* 1.3 60.2 + - - +
33B MET* 3.2 12.2 + - + +
34B TYR* 2.8 29.5 + - - +
50B PHE* 5.9 0.2 - + - -
51B PHE* 3.6 46.6 - + - +
54B HIS* 3.9 27.3 + - + -
55B SER* 3.7 7.2 - - - -
58B GLU* 4.0 12.8 - - + -
99B ALA* 3.9 24.9 + - + +
102B LEU* 3.9 17.7 - - + +
103B GLU* 2.8 41.5 + - - +
144B ILE* 4.3 4.0 - - + +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER 3.0 12.2 + - - -
28B TYR* 3.2 23.9 - - - -
30B TYR* 1.3 75.8 - - - +
32B SER* 1.3 62.4 + - - +
34B TYR* 3.4 12.7 + - - +
35B ALA* 3.1 23.2 + - - +
55B SER* 3.8 12.4 + - - -
24F LEU* 6.1 0.5 - - - +
63F GLU* 4.9 6.2 + - - +
66F MET* 3.3 32.2 - - - +
78F LEU* 4.8 1.3 - - - -
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR 3.2 5.7 + - - -
29B THR 3.2 11.3 + - - -
30B TYR 3.2 0.2 - - - -
31B SER* 1.3 72.9 - - - +
33B MET* 1.3 60.1 - - - +
35B ALA* 3.2 6.9 + - - +
36B PHE* 2.9 28.2 + - - +
84B PRO* 3.2 29.4 - - - +
86B ARG 4.0 6.4 + - - -
87B ASP* 5.1 7.0 + - - +
89B TRP* 3.4 17.7 + - - -
76F VAL* 6.3 0.2 - - - -
78F LEU* 3.3 17.8 - - - +
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Residues in contact with MET 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.2 33.8 + - + +
30B TYR* 3.2 16.4 + - + +
32B SER* 1.3 77.1 - - - +
34B TYR* 1.3 64.9 + - - +
36B PHE* 3.3 1.1 + - - +
37B PHE* 3.0 33.4 + - + -
51B PHE* 3.8 41.7 - - + -
89B TRP* 3.7 43.1 - - + +
95B ALA* 3.8 23.3 - - + +
98B ALA* 4.0 7.6 - - + -
99B ALA* 4.2 9.6 - - - +
102B LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR 2.8 14.0 + - - +
31B SER* 3.4 15.3 - - - +
33B MET* 1.3 77.6 - - - +
35B ALA* 1.3 72.2 + - - +
36B PHE 3.3 0.2 + - - -
37B PHE 3.4 0.5 + - - -
38B ASP* 3.2 29.8 + - + +
48B ALA* 3.2 37.9 - - + +
49B GLU* 3.6 20.3 + - - -
51B PHE* 4.0 2.2 - - - +
52B LYS* 3.7 42.0 + - + +
63F GLU* 5.1 12.7 + - + -
66F MET* 4.5 23.3 - - + -
67F LYS* 3.3 36.9 - - + +
70F ASN* 6.3 0.2 - - - -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER 3.1 10.4 + - - +
32B SER* 3.2 9.8 + - - +
34B TYR* 1.3 84.5 - - - +
36B PHE* 1.3 63.4 + - - +
38B ASP* 4.4 1.1 - - - -
39B ARG* 3.5 9.4 + - - +
66F MET* 4.3 15.3 - - + -
70F ASN* 3.0 28.5 + - - +
76F VAL* 4.1 32.5 - - + +
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER 2.9 16.4 + - - +
33B MET 3.5 4.7 - - - +
34B TYR 3.1 0.4 - - - -
35B ALA* 1.3 77.4 - - - +
37B PHE* 1.3 85.4 + + - +
39B ARG* 3.3 51.6 - - - +
42B VAL* 3.3 36.3 - - + +
87B ASP 4.5 3.6 - - - +
88B GLU* 3.8 12.6 - - + -
89B TRP* 3.6 32.8 - - + -
90B GLY* 3.5 41.1 - - - -
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B MET* 3.0 27.1 + - + +
34B TYR 3.4 0.2 + - - -
36B PHE* 1.3 90.7 - + - +
38B ASP* 1.3 61.5 + - - +
39B ARG 3.2 0.4 - - - -
42B VAL* 3.5 22.0 - - + -
43B ALA* 3.5 7.1 + - - -
44B LEU* 3.2 51.0 + - + +
45B HIS* 4.3 0.7 + - - -
47B VAL* 3.9 11.2 - - + -
48B ALA* 3.7 14.8 - - + +
51B PHE* 3.7 20.4 - + - -
89B TRP* 4.8 0.4 - - + -
91B ASN* 3.5 23.8 - - - -
92B THR* 3.6 27.6 - - - -
95B ALA* 3.7 21.1 - - + -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.2 28.8 + - + +
35B ALA* 4.3 1.1 - - - -
36B PHE 3.2 0.6 - - - -
37B PHE* 1.3 74.8 - - - +
39B ARG* 1.3 60.2 + - - +
45B HIS* 3.4 22.2 + - - -
48B ALA* 4.1 2.6 - - + +
67F LYS* 3.1 44.7 + - - +
70F ASN* 3.1 31.7 + - - +
142G LYS* 2.9 31.6 + - - -
----------------------------------------------------------
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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