Contacts of the helix formed by residues 10 - 38 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ARG* 4.0 3.7 + - - +
8X TYR 3.7 1.6 + - - -
9X HIS* 1.3 81.9 + - - +
11X ASP* 1.3 66.2 + - - +
13X GLU* 3.4 19.2 + - - +
14X ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X HIS* 2.8 23.1 + - - +
10X SER* 1.3 74.7 - - - +
12X CYS* 1.3 62.9 + - - +
14X ALA* 3.4 7.1 + - - +
15X ALA* 2.9 28.9 + - - +
18X ARG* 4.6 2.1 + - - -
116X LEU* 3.6 21.6 - - + +
120X LYS* 3.1 22.1 + - - +
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Residues in contact with CYS 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X TYR* 4.1 10.3 - - + -
9X HIS* 3.1 25.2 + - + +
11X ASP* 1.3 79.7 - - - +
13X GLU* 1.3 57.9 + - - +
15X ALA* 3.1 3.5 + - - +
16X VAL* 2.9 34.9 + - - +
113X LEU* 4.3 1.0 - - - +
116X LEU* 4.0 25.1 - - - -
117X ALA* 4.3 8.1 - - - -
120X LYS* 4.1 15.7 - - - -
122X ASP* 5.0 4.9 - - - -
125X LEU* 4.0 25.6 - - + -
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Residues in contact with GLU 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X ARG* 2.7 34.7 + - - -
8X TYR* 3.7 19.9 + - + -
9X HIS 3.1 8.7 + - - +
10X SER* 3.5 17.7 + - - +
12X CYS* 1.3 80.7 - - - +
14X ALA* 1.3 62.7 + - - +
16X VAL 3.3 0.7 + - - -
17X ASN* 3.1 22.6 + - - +
69X GLN* 3.2 26.3 + - - +
74X GLY* 3.8 2.2 - - - -
75X ARG* 2.9 32.4 + - - +
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Residues in contact with ALA 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X SER 3.1 17.2 + - - +
11X ASP* 3.7 7.6 - - - +
12X CYS 3.3 0.2 - - - -
13X GLU* 1.3 78.1 - - - +
15X ALA* 1.3 60.8 - - - +
17X ASN* 3.5 10.4 + - - +
18X ARG* 3.1 39.2 + - - +
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Residues in contact with ALA 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X ASP 2.9 17.7 + - - +
12X CYS 3.5 1.3 - - - +
14X ALA* 1.3 76.4 - - - +
16X VAL* 1.3 60.3 + - - +
18X ARG* 3.3 25.4 + - - +
19X MET* 2.9 28.8 + - - +
113X LEU* 3.5 28.3 - - + +
116X LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X TYR* 3.6 14.6 - - - +
12X CYS 2.9 21.3 + - - +
13X GLU 3.6 4.7 - - - +
14X ALA 3.3 0.2 - - - -
15X ALA* 1.3 77.2 - - - +
17X ASN* 1.3 56.7 + - - +
19X MET* 3.2 7.6 + - - +
20X LEU* 2.9 29.4 + - + +
65X PHE* 3.9 32.8 - - + +
68X TYR* 4.6 5.2 - - + -
69X GLN* 3.5 22.0 - - + +
113X LEU* 4.3 11.7 - - + -
125X LEU* 4.3 23.8 - - + -
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Residues in contact with ASN 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X GLU* 3.1 17.2 + - - +
14X ALA* 3.6 12.4 - - - +
16X VAL* 1.3 76.5 - - - +
18X ARG* 1.3 62.4 + - - +
20X LEU* 3.5 16.8 - - - +
21X ASN* 3.4 20.1 + - - +
69X GLN* 3.4 12.6 + - - +
75X ARG 3.2 18.6 + - - -
76X VAL* 3.3 9.9 - - - -
77X VAL* 3.1 47.3 + - + +
79X GLN* 4.6 9.2 + - - +
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Residues in contact with ARG 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X ASP 4.6 2.6 + - - -
14X ALA* 3.1 21.9 + - - +
15X ALA* 3.4 34.1 - - - +
16X VAL 3.1 0.2 - - - -
17X ASN* 1.3 79.7 - - - +
19X MET* 1.3 63.7 + - - +
21X ASN* 3.4 7.5 + - + +
22X LEU* 3.1 20.6 + - - +
79X GLN* 4.8 16.8 - - - +
116X LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X ALA 2.9 16.9 + - - +
16X VAL* 3.2 6.3 + - - +
18X ARG* 1.3 76.2 - - - +
20X LEU* 1.3 64.4 + - - +
22X LEU* 3.2 13.1 + - - +
23X GLU* 2.9 28.1 + - + +
65X PHE* 3.4 30.1 - - + -
106X VAL* 4.6 3.6 - - - +
109X ALA* 3.1 50.0 - - + +
110X LEU* 3.5 21.5 - - + +
113X LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X VAL* 2.9 16.8 + - + +
17X ASN* 3.5 20.0 - - - +
19X MET* 1.3 76.4 - - - +
21X ASN* 1.3 62.9 + - + +
23X GLU* 3.4 8.1 + - - +
24X LEU* 3.1 42.5 + - + +
62X ALA* 3.7 16.3 - - - +
65X PHE* 4.2 13.6 - - + +
66X MET* 3.8 36.1 - - + +
69X GLN* 5.8 0.2 - - - +
76X VAL* 4.0 19.3 - - + -
77X VAL 5.6 0.4 - - - +
78X LEU* 3.7 17.5 - - + -
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Residues in contact with ASN 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 4.4 5.0 + - - +
17X ASN 3.4 8.3 + - - +
18X ARG* 3.6 8.9 - - + +
19X MET 3.2 0.4 - - - -
20X LEU* 1.3 81.5 - - + +
22X LEU* 1.3 60.9 + - - +
24X LEU* 3.1 8.5 + - - +
25X TYR* 2.8 29.6 + - - +
79X GLN* 3.5 43.6 + - - +
80X ASP 3.2 26.9 + - - +
81X ILE* 4.3 7.7 - - - +
82X LYS 5.6 0.9 + - - -
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Residues in contact with LEU 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X ARG 3.1 14.5 + - - +
19X MET* 3.2 15.7 + - - +
21X ASN* 1.3 77.7 + - - +
23X GLU* 1.3 58.0 + - - +
25X TYR* 3.2 23.5 + - + -
26X ALA* 2.9 26.3 + - - +
102X LEU* 5.4 1.8 - - + -
105X THR* 4.4 17.3 - - + +
106X VAL* 3.9 32.3 - - + +
109X ALA* 3.7 30.7 - - + -
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Residues in contact with GLU 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X MET* 2.9 19.1 + - + +
20X LEU 3.4 9.4 - - - +
22X LEU* 1.3 77.3 - - - +
24X LEU* 1.3 59.5 + - - +
26X ALA* 3.3 5.6 + - - +
27X SER* 2.9 28.2 + - - -
58X GLU* 2.7 20.8 - - - +
61X HIS* 3.4 18.9 - - + +
62X ALA* 3.8 13.9 - - + -
65X PHE* 4.1 19.4 - - + -
106X VAL* 4.0 14.9 - - - +
110X LEU* 4.9 2.4 - - - +
133X TYR* 3.7 14.9 - - - -
176X MG 2.4 29.8 - - - -
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Residues in contact with LEU 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR* 3.7 37.9 - - + +
20X LEU* 3.1 32.6 + - + +
21X ASN* 3.1 9.4 + - - +
23X GLU* 1.3 75.5 - - - +
25X TYR* 1.3 57.9 + - - +
27X SER* 3.5 6.3 - - - -
28X TYR* 3.0 27.9 + - - +
59X ARG* 4.9 17.9 - - + +
62X ALA* 3.7 18.2 - - + -
63X GLU* 6.4 0.4 - - + -
66X MET* 5.1 6.5 - - + -
81X ILE* 3.7 24.4 - - + +
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Residues in contact with TYR 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ASN* 2.8 18.0 + - - +
22X LEU* 3.4 26.9 - - + +
23X GLU 3.2 0.4 - - - -
24X LEU* 1.3 73.1 - - - +
26X ALA* 1.3 64.0 + - - +
28X TYR* 3.2 3.8 + - - +
29X THR* 2.9 48.9 + - - +
81X ILE* 4.0 10.5 - - + +
82X LYS* 3.4 38.4 - - + +
83X LYS 3.8 11.6 + - - -
84X PRO* 4.1 1.3 - - + -
85X GLU* 3.8 25.3 + - - +
102X LEU* 4.1 17.0 - - + -
105X THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X LEU 2.9 13.6 + - - +
23X GLU* 3.3 9.8 + - - +
25X TYR* 1.3 77.5 - - - +
27X SER* 1.3 62.9 + - - +
29X THR* 3.3 2.6 + - - -
30X TYR* 3.1 31.3 + - + -
58X GLU* 4.2 15.7 - - + -
102X LEU* 3.9 25.5 - - + +
103X GLU* 6.2 0.4 - - - +
106X VAL* 4.2 19.3 - - + -
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Residues in contact with SER 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X GLU 2.9 16.6 + - - -
24X LEU* 3.5 11.7 - - - +
26X ALA* 1.3 75.9 - - - +
28X TYR* 1.3 62.6 + - - +
30X TYR 3.1 2.6 + - - -
31X SER* 3.0 19.0 + - - -
55X SER* 2.9 39.3 + - - +
58X GLU* 3.8 13.6 - - - +
59X ARG* 3.6 17.2 - - - +
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Residues in contact with TYR 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LEU* 5.1 0.2 - - - +
21J ASN* 4.4 2.8 + - - +
24J LEU* 3.5 27.6 - - + +
66J MET* 5.5 0.7 - - + -
78J LEU* 3.4 37.6 - - + +
79J GLN 3.0 30.7 + - - -
81J ILE* 3.7 22.6 - - + +
24X LEU 3.0 18.2 + - - +
25X TYR* 3.2 5.6 + - - +
27X SER* 1.3 78.1 + - - +
29X THR* 1.3 60.9 + - - +
31X SER* 3.2 16.2 - - - -
32X SER* 3.2 18.5 + - - -
81X ILE* 4.0 13.0 - - + -
82X LYS 3.6 18.6 - - - +
83X LYS* 4.0 3.1 - - - -
84X PRO* 3.7 18.7 - - + +
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Residues in contact with THR 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X TYR* 2.9 30.5 + - + +
26X ALA 3.6 8.5 - - - -
27X SER 3.2 0.2 - - - -
28X TYR* 1.3 76.1 - - - +
30X TYR* 1.3 62.4 + - - +
32X SER* 3.2 6.4 + - - -
33X MET* 3.2 38.4 + - + +
84X PRO* 3.4 20.5 - - + +
85X GLU* 5.8 0.4 - - - +
89X TRP* 4.0 15.0 - - + -
102X LEU* 3.7 26.0 - - + -
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Residues in contact with TYR 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26X ALA* 3.1 22.8 + - + -
27X SER 3.1 6.5 + - - +
29X THR* 1.3 74.7 - - - +
31X SER* 1.3 60.5 + - - +
33X MET* 3.2 11.5 + - + +
34X TYR* 2.8 29.6 + - - +
50X PHE* 5.9 0.2 - + - -
51X PHE* 3.6 45.9 - + - +
54X HIS* 3.9 29.3 + + + -
55X SER* 3.7 7.2 - - - -
58X GLU* 4.0 13.7 - - + -
99X ALA* 3.9 24.8 + - + +
102X LEU* 3.9 17.5 - - + +
103X GLU* 2.8 41.5 + - - +
144X ILE* 4.3 2.9 - - + +
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Residues in contact with SER 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J LEU* 6.1 0.2 - - - +
63J GLU* 4.8 6.4 + - - +
66J MET* 3.3 30.6 - - - +
78J LEU* 4.9 1.1 - - - -
27X SER 3.0 13.1 + - - -
28X TYR* 3.2 23.6 - - - -
30X TYR* 1.3 75.8 - - - +
32X SER* 1.3 60.9 + - - +
34X TYR* 3.4 13.3 + - - +
35X ALA* 3.1 22.5 + - - +
55X SER* 3.8 12.7 + - - -
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Residues in contact with SER 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J LEU* 3.4 17.1 - - - +
28X TYR 3.2 5.3 + - - -
29X THR 3.2 12.0 + - - -
30X TYR 3.2 0.4 - - - -
31X SER* 1.3 73.5 - - - +
33X MET* 1.3 60.0 - - - +
35X ALA* 3.2 7.2 + - - +
36X PHE* 2.9 28.1 + - - +
84X PRO* 3.2 29.2 - - - +
86X ARG 4.0 6.4 + - - -
87X ASP* 5.1 7.6 + - - +
89X TRP* 3.4 17.2 + - - -
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Residues in contact with MET 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29X THR* 3.2 33.3 + - + +
30X TYR* 3.2 16.1 + - + +
32X SER* 1.3 76.4 - - - +
34X TYR* 1.3 65.8 + - - +
36X PHE* 3.3 0.7 + - - +
37X PHE* 3.0 33.2 + - + -
51X PHE* 3.8 41.3 - - + -
89X TRP* 3.7 44.2 - - + +
95X ALA* 3.8 23.1 - - - +
98X ALA* 4.0 7.9 - - + -
99X ALA* 4.2 9.6 - - - +
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Residues in contact with TYR 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J GLU* 5.1 11.4 - - + -
66J MET* 4.6 22.7 - - + -
67J LYS* 3.3 37.3 - - + +
70J ASN* 6.3 0.2 - - - -
30X TYR 2.8 14.1 + - - +
31X SER* 3.4 14.8 - - - +
33X MET* 1.3 77.9 - - - +
35X ALA* 1.3 73.1 + - - +
36X PHE 3.3 0.2 + - - -
37X PHE 3.4 0.3 + - - -
38X ASP* 3.2 29.2 + - + +
48X ALA* 3.2 38.8 - - + +
49X GLU* 3.6 19.7 + - - -
51X PHE* 4.0 2.4 - - - +
52X LYS* 3.7 41.8 + - + +
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Residues in contact with ALA 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J MET* 4.3 14.8 - - + -
70J ASN* 3.0 29.2 + - - +
76J VAL* 4.2 31.6 - - + -
78J LEU* 6.4 0.2 - - + -
31X SER 3.1 10.8 + - - +
32X SER* 3.2 9.2 + - - +
34X TYR* 1.3 84.6 - - + +
36X PHE* 1.3 63.0 + - - +
38X ASP* 4.4 0.7 - - - -
39X ARG* 3.5 9.9 + - - +
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Residues in contact with PHE 36 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32X SER 2.9 16.6 + - - +
33X MET 3.5 4.5 - - - +
34X TYR 3.1 0.4 - - - -
35X ALA* 1.3 77.7 - - - +
37X PHE* 1.3 84.6 + + - +
39X ARG* 3.3 52.9 - - - +
42X VAL* 3.3 35.9 - - + +
87X ASP 4.5 4.0 - - - +
88X GLU* 3.8 11.9 - - + -
89X TRP* 3.6 33.2 - - + -
90X GLY* 3.5 40.6 - - - -
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Residues in contact with PHE 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33X MET* 3.0 27.0 + - + +
34X TYR 3.4 0.6 + - - -
36X PHE* 1.3 90.5 - + - +
38X ASP* 1.3 60.6 + - - +
39X ARG 3.2 0.4 - - - -
42X VAL* 3.5 22.4 - - + -
43X ALA* 3.5 7.3 + - - -
44X LEU* 3.2 49.2 + - + +
45X HIS* 4.3 0.5 + - - -
47X VAL* 3.9 11.9 - - + -
48X ALA* 3.7 15.0 - - + +
51X PHE* 3.7 20.0 - + - -
89X TRP* 4.8 0.4 - - + -
91X ASN* 3.5 24.7 - - - -
92X THR* 3.6 27.8 - - - -
95X ALA* 3.7 22.2 - - + -
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Residues in contact with ASP 38 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LYS* 3.2 44.5 + - - +
70J ASN* 3.2 32.0 + - - +
142Q LYS* 2.9 31.4 + - - -
34X TYR* 3.2 29.3 + - + +
35X ALA* 4.3 1.3 - - - -
36X PHE 3.2 0.4 - - - -
37X PHE* 1.3 75.7 - - - +
39X ARG* 1.3 61.9 + - - +
45X HIS* 3.4 23.1 + - - -
48X ALA* 4.1 3.0 - - + +
----------------------------------------------------------
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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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