Contacts of the helix formed by residues 10 - 38 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T ARG* 4.0 3.8 + - - +
8T TYR 3.7 1.6 + - - -
9T HIS* 1.3 82.5 + - - +
11T ASP* 1.3 65.1 + - - +
13T GLU* 3.4 18.9 + - - +
14T ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T HIS* 2.8 23.3 + - - +
10T SER* 1.3 73.9 - - - +
12T CYS* 1.3 62.5 + - - +
14T ALA* 3.4 6.1 + - - +
15T ALA* 2.9 28.9 + - - +
18T ARG* 4.6 2.4 + - - -
116T LEU* 3.6 22.0 - - + +
120T LYS* 3.1 21.8 + - - -
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Residues in contact with CYS 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T TYR* 4.1 10.1 - - + -
9T HIS* 3.1 26.8 + - + +
11T ASP* 1.3 79.1 - - - +
13T GLU* 1.3 56.5 + - - +
15T ALA* 3.1 2.9 + - - +
16T VAL* 2.9 35.8 + - - +
113T LEU* 4.3 1.2 - - - +
116T LEU* 4.0 25.8 - - - -
117T ALA* 4.3 7.6 - - - -
120T LYS* 4.1 15.5 - - - -
122T ASP* 5.0 4.7 - - - -
125T LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T ARG* 2.7 35.4 + - - -
8T TYR* 3.7 20.1 + - + -
9T HIS 3.1 8.1 + - - +
10T SER* 3.5 17.0 + - - +
12T CYS* 1.3 79.7 - - - +
14T ALA* 1.3 62.5 + - - +
16T VAL 3.3 0.7 + - - -
17T ASN* 3.1 22.8 + - - +
69T GLN* 3.2 27.0 + - - +
74T GLY* 3.8 2.0 - - - -
75T ARG* 2.9 33.2 + - - +
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Residues in contact with ALA 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T SER 3.1 17.4 + - - +
11T ASP* 3.7 7.6 - - - +
13T GLU* 1.3 78.3 - - - +
15T ALA* 1.3 61.5 + - - +
17T ASN* 3.5 10.2 + - - +
18T ARG* 3.1 39.2 + - - +
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Residues in contact with ALA 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T ASP 2.9 17.3 + - - +
12T CYS 3.1 1.3 + - - +
14T ALA* 1.3 75.3 - - - +
16T VAL* 1.3 61.8 + - - +
18T ARG* 3.3 23.0 + - - +
19T MET* 2.9 29.1 + - - +
113T LEU* 3.5 27.5 - - + +
116T LEU* 3.7 11.4 - - + -
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Residues in contact with VAL 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8T TYR* 3.6 14.6 - - - +
12T CYS 2.9 20.4 + - - +
13T GLU 3.6 5.6 - - - +
14T ALA 3.3 0.2 - - - -
15T ALA* 1.3 75.9 - - - +
17T ASN* 1.3 57.5 + - - +
19T MET* 3.2 7.7 + - - +
20T LEU* 2.9 29.7 + - + +
65T PHE* 3.9 33.7 - - + +
68T TYR* 4.6 5.4 - - + -
69T GLN* 3.5 22.0 - - + +
113T LEU* 4.3 11.7 - - + -
125T LEU* 4.3 23.1 - - + -
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Residues in contact with ASN 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T GLU* 3.1 15.7 + - - +
14T ALA* 3.6 12.2 - - - +
16T VAL* 1.3 76.2 - - - +
18T ARG* 1.3 62.0 + - - +
20T LEU* 3.5 17.6 - - - +
21T ASN* 3.4 19.4 + - - +
69T GLN* 3.4 13.1 + - - +
75T ARG 3.2 19.2 + - - -
76T VAL* 3.3 9.9 - - - -
77T VAL* 3.1 47.8 + - - +
79T GLN* 4.6 9.2 + - - +
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Residues in contact with ARG 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T ASP 4.6 3.0 + - - -
14T ALA* 3.1 21.9 + - - +
15T ALA* 3.4 34.3 - - - +
16T VAL 3.1 0.4 - - - -
17T ASN* 1.3 79.6 - - - +
19T MET* 1.3 65.0 + - - +
21T ASN* 3.4 7.8 + - + +
22T LEU* 3.1 20.8 + - - +
79T GLN* 4.8 16.6 - - - +
116T LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T ALA 2.9 16.0 + - - +
16T VAL* 3.5 5.8 - - - +
18T ARG* 1.3 76.2 - - - +
20T LEU* 1.3 64.7 + - - +
22T LEU* 3.2 13.1 + - - +
23T GLU* 2.9 27.3 + - + +
65T PHE* 3.4 30.1 - - + -
106T VAL* 4.6 3.8 - - - +
109T ALA* 3.1 50.9 - - + +
110T LEU* 3.5 22.0 - - + +
113T LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P TYR* 5.1 0.2 - - - +
16T VAL* 2.9 15.2 + - + +
17T ASN* 3.5 19.7 - - - +
19T MET* 1.3 77.6 - - - +
21T ASN* 1.3 63.7 + - + +
23T GLU* 3.3 9.1 + - - +
24T LEU* 3.1 42.0 + - + +
62T ALA* 3.7 17.2 - - + +
65T PHE* 4.2 14.1 - - + +
66T MET* 3.8 35.4 - - + +
69T GLN* 5.8 0.9 - - - +
76T VAL* 4.0 18.8 - - + -
77T VAL 5.6 0.7 - - - +
78T LEU* 3.7 17.3 - - + -
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Residues in contact with ASN 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P TYR* 4.4 5.2 + - - +
17T ASN 3.4 8.1 + - - +
18T ARG 3.6 9.1 - - - +
20T LEU* 1.3 82.1 - - + +
22T LEU* 1.3 61.1 + - - +
24T LEU* 3.1 8.7 + - - +
25T TYR* 2.8 30.3 + - - +
79T GLN* 3.5 43.8 + - - +
80T ASP 3.2 26.9 + - - +
81T ILE* 4.3 8.0 - - - +
82T LYS 5.6 0.5 + - - -
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Residues in contact with LEU 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ARG 3.1 13.5 + - - +
19T MET* 3.2 16.8 + - - +
21T ASN* 1.3 78.5 + - - +
23T GLU* 1.3 57.4 + - - +
25T TYR* 3.2 23.7 + - + -
26T ALA* 2.9 27.0 + - - +
102T LEU* 5.4 1.8 - - + -
105T THR* 4.4 16.4 - - + +
106T VAL* 3.9 31.1 - - + +
109T ALA* 3.7 29.8 - - + -
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Residues in contact with GLU 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T MET* 2.9 20.6 + - + +
20T LEU 3.4 9.2 - - - +
21T ASN 3.2 0.2 - - - -
22T LEU* 1.3 76.7 - - - +
24T LEU* 1.3 57.8 + - - +
26T ALA* 3.3 5.6 + - - +
27T SER* 2.9 28.2 + - - -
58T GLU* 2.7 20.8 - - - +
61T HIS* 3.4 18.4 - - + +
62T ALA* 3.8 13.9 - - + -
65T PHE* 4.1 18.3 - - + -
106T VAL* 4.0 15.0 - - - +
110T LEU* 4.9 2.6 - - - +
133T TYR* 3.7 15.2 - - - -
176T MG 2.4 30.9 - - - -
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Residues in contact with LEU 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P TYR* 3.6 39.3 - - + +
20T LEU* 3.1 31.2 + - + +
21T ASN* 3.1 8.9 + - - +
23T GLU* 1.3 75.8 - - - +
25T TYR* 1.3 55.7 + - - +
27T SER* 3.5 6.4 - - - -
28T TYR* 3.0 27.9 + - - +
59T ARG* 4.9 17.5 - - + -
62T ALA* 3.7 19.1 - - + -
63T GLU* 6.4 0.7 - - + -
66T MET* 5.1 5.8 - - + -
78T LEU* 4.8 0.2 - - + -
81T ILE* 3.7 24.0 - - + +
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Residues in contact with TYR 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T ASN* 2.8 18.2 + - - +
22T LEU* 3.4 27.4 - - + +
23T GLU 3.2 0.4 - - - -
24T LEU* 1.3 73.9 - - - +
26T ALA* 1.3 63.0 + - - +
28T TYR* 3.2 3.7 + - - +
29T THR* 2.9 47.8 + - + +
81T ILE* 4.0 9.4 - - + +
82T LYS* 3.4 38.6 - - + +
83T LYS 3.8 11.8 + - - -
84T PRO* 4.1 1.3 - - + -
85T GLU* 3.8 24.9 + - - +
102T LEU* 4.1 16.8 - - + -
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Residues in contact with ALA 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T LEU 2.9 14.0 + - - +
23T GLU* 3.3 10.7 + - - +
25T TYR* 1.3 77.4 - - - +
27T SER* 1.3 61.3 + - - +
29T THR* 3.3 2.9 + - - -
30T TYR* 3.1 32.2 + - + -
58T GLU* 4.2 15.3 - - + -
102T LEU* 3.9 26.9 - - + +
103T GLU* 6.2 0.4 - - - +
106T VAL* 4.2 18.4 - - + -
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Residues in contact with SER 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T GLU 2.9 16.8 + - - -
24T LEU* 3.5 12.0 - - - +
26T ALA* 1.3 76.5 - - - +
28T TYR* 1.3 62.4 + - - +
30T TYR 3.1 2.9 + - - -
31T SER* 3.0 19.5 + - - -
55T SER* 2.9 40.1 + - - +
58T GLU* 3.8 12.3 - - - +
59T ARG* 3.6 16.7 - - - +
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Residues in contact with TYR 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P LEU* 5.1 0.2 - - - +
21P ASN* 4.4 3.1 + - - +
24P LEU* 3.6 28.0 - - + +
66P MET* 5.5 0.4 - - + -
78P LEU* 3.4 37.0 - - + +
79P GLN 3.0 30.8 + - - -
81P ILE* 3.7 21.7 - - + +
24T LEU 3.0 19.2 + - - +
25T TYR* 3.2 5.8 + - - +
27T SER* 1.3 77.8 - - - +
29T THR* 1.3 60.3 + - - +
31T SER* 3.2 16.7 - - - -
32T SER* 3.2 18.7 + - - -
81T ILE* 4.0 13.5 - - + -
82T LYS 3.6 18.4 - - - +
83T LYS* 4.0 2.9 - - - -
84T PRO* 3.7 17.8 - - + +
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Residues in contact with THR 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T TYR* 2.9 30.4 + - - +
26T ALA 3.6 8.3 - - - -
27T SER 3.2 0.4 - - - -
28T TYR* 1.3 75.9 - - - +
30T TYR* 1.3 62.1 + - - +
32T SER* 3.2 6.4 + - - -
33T MET* 3.2 39.2 + - + +
84T PRO* 3.4 21.9 - - + +
85T GLU* 5.0 0.4 + - - +
89T TRP* 4.0 15.0 - - + -
102T LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T ALA* 3.1 24.1 + - + -
27T SER 3.1 6.7 + - - +
29T THR* 1.3 74.3 - - - +
31T SER* 1.3 61.1 + - - +
33T MET* 3.2 12.8 + - + +
34T TYR* 2.8 28.6 + - - +
50T PHE* 5.9 0.2 - + - -
51T PHE* 3.6 47.0 - + - +
54T HIS* 3.9 28.3 - + + -
55T SER* 3.7 7.9 - - - -
58T GLU* 4.0 13.0 - - + -
99T ALA* 3.9 24.6 + - + +
102T LEU* 3.9 18.2 - - + +
103T GLU* 2.8 40.8 + - - +
144T ILE* 4.3 3.4 - - + +
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Residues in contact with SER 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P LEU* 6.1 0.5 - - - +
63P GLU* 4.9 6.1 + - - +
66P MET* 3.3 31.2 - - - +
78P LEU* 4.8 1.3 - - - -
27T SER 3.0 12.0 + - - -
28T TYR* 3.2 24.6 - - - -
30T TYR* 1.3 75.1 - - - +
32T SER* 1.3 61.4 + - - +
34T TYR* 3.4 11.4 + - - +
35T ALA* 3.1 22.5 + - - +
55T SER* 3.8 13.1 + - - -
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Residues in contact with SER 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P VAL* 6.4 0.2 - - - -
78P LEU* 3.3 17.6 - - - +
28T TYR 3.2 5.1 + - - -
29T THR 3.2 11.6 + - - -
30T TYR 3.2 0.4 - - - -
31T SER* 1.3 74.1 - - - +
33T MET* 1.3 59.5 + - - +
35T ALA* 3.2 6.5 + - - +
36T PHE* 2.9 28.1 + - - +
84T PRO* 3.2 29.6 - - - +
86T ARG 4.0 6.2 + - - -
87T ASP* 5.1 7.4 + - - +
89T TRP* 3.4 17.0 + - - -
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Residues in contact with MET 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T THR* 3.2 34.0 + - + +
30T TYR* 3.2 15.5 + - + +
32T SER* 1.3 76.5 - - - +
34T TYR* 1.3 65.4 + - - +
36T PHE* 3.3 0.5 + - - +
37T PHE* 3.0 33.4 + - + -
51T PHE* 3.8 43.1 - - + -
89T TRP* 3.7 43.3 - - + -
95T ALA* 3.8 23.6 - - + +
98T ALA* 4.0 7.6 - - + +
99T ALA* 4.2 9.4 - - - +
102T LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P GLU* 5.1 12.1 + - + -
66P MET* 4.5 23.3 - - + -
67P LYS* 3.3 36.4 - - + +
30T TYR 2.8 13.3 + - - +
31T SER* 3.4 14.6 - - - +
32T SER 3.2 0.2 - - - -
33T MET* 1.3 77.9 - - - +
35T ALA* 1.3 72.2 + - - +
37T PHE 3.4 0.3 + - - -
38T ASP* 3.2 30.1 + - + +
48T ALA* 3.2 38.0 - - + +
49T GLU* 3.6 19.3 + - - -
51T PHE* 4.0 3.0 - - - +
52T LYS* 3.7 42.6 + - + +
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Residues in contact with ALA 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P MET* 4.3 15.0 - - + -
70P ASN* 3.0 28.8 + - - +
76P VAL* 4.2 31.9 - - + -
31T SER 3.1 10.4 + - - +
32T SER* 3.2 9.2 + - - +
34T TYR* 1.3 85.6 - - - +
36T PHE* 1.3 62.2 + - - +
38T ASP* 4.4 0.9 - - - -
39T ARG* 3.5 10.0 + - - +
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Residues in contact with PHE 36 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T SER 2.9 16.1 + - - +
33T MET 3.5 5.2 - - - +
34T TYR 3.1 0.4 - - - -
35T ALA* 1.3 78.3 - - - +
37T PHE* 1.3 85.4 + + - +
39T ARG* 3.3 52.6 - - - +
42T VAL* 3.3 35.2 - - + +
87T ASP 4.5 4.3 - - - +
88T GLU* 3.8 11.2 - - + -
89T TRP* 3.6 33.0 - - + -
90T GLY* 3.5 42.8 - - - -
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Residues in contact with PHE 37 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T MET* 3.0 26.6 + - + -
34T TYR 3.4 0.2 + - - -
36T PHE* 1.3 90.1 - + - +
38T ASP* 1.3 60.9 + - - +
39T ARG 3.2 0.4 - - - -
42T VAL* 3.5 23.3 - - + -
43T ALA* 3.5 7.2 + - - -
44T LEU* 3.2 48.8 + - + +
45T HIS* 4.3 0.9 + - - -
47T VAL* 3.9 11.2 - - + -
48T ALA* 3.7 15.0 - - + -
51T PHE* 3.7 19.7 - + - -
89T TRP* 4.8 0.7 - - + -
91T ASN* 3.5 24.0 - - - -
92T THR* 3.6 27.8 - - - -
95T ALA* 3.7 22.2 - - + -
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Residues in contact with ASP 38 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P LYS* 3.1 44.8 + - - +
70P ASN* 3.2 31.1 + - - +
34T TYR* 3.2 28.6 + - + +
35T ALA* 4.4 1.1 - - - -
36T PHE 3.2 0.4 - - - -
37T PHE* 1.3 75.4 - - - +
39T ARG* 1.3 61.5 + - - +
45T HIS* 3.4 22.6 + - - -
48T ALA* 4.5 1.7 - - + +
142U LYS* 2.9 31.3 + - - -
----------------------------------------------------------
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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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