Contacts of the helix formed by residues 6 - 35 (chain A) in PDB entry 1FX8
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 THR 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 1.3 66.7 + - - +
8A LYS* 3.6 12.7 + - + +
9A GLY* 3.0 33.5 + - - +
10A GLN* 3.0 22.6 + - - +
85A LYS* 5.3 0.2 - - - -
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 1.3 74.4 + - - +
8A LYS* 1.3 62.5 + - - +
10A GLN* 3.1 9.5 + - - +
11A CYS* 2.9 34.2 + - - -
84A ARG* 4.7 4.5 - - + +
85A LYS* 3.2 51.1 - - + +
88A PRO* 4.3 19.7 - - + -
89A PHE* 4.1 10.5 - - + -
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.2 11.5 + - + +
7A LEU* 1.3 79.2 - - - +
9A GLY* 1.3 61.8 + - - +
11A CYS* 3.5 6.9 + - - +
12A ILE* 3.2 44.6 + - + +
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Residues in contact with GLY 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.0 22.0 + - - +
8A LYS* 1.3 81.5 - - - +
10A GLN* 1.3 57.6 + - - +
12A ILE* 3.5 11.6 + - - +
13A ALA* 3.2 16.8 + - - +
62A VAL* 3.6 17.1 - - - +
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Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR 3.0 17.0 + - - +
7A LEU* 3.1 7.5 + - - +
9A GLY* 1.3 75.8 - - - +
11A CYS* 1.3 60.6 + - - +
13A ALA 3.4 0.3 + - - -
14A GLU* 3.0 33.6 + - - +
62A VAL* 3.2 30.0 + - + +
63A SER* 3.5 21.4 + - - +
81A PHE* 6.3 0.2 - - - -
85A LYS* 2.7 42.7 + - - +
89A PHE* 3.7 16.4 - - + -
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Residues in contact with CYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 2.9 29.8 + - - +
8A LYS* 3.8 7.0 - - - +
10A GLN* 1.3 74.3 - - - +
12A ILE* 1.3 62.3 + - + +
14A GLU* 4.4 2.5 - - - -
15A PHE* 3.0 24.8 + - - +
88A PRO* 3.6 42.2 - - - -
89A PHE* 4.4 3.1 - - - -
92A SER* 3.1 24.9 + - - +
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.2 38.8 + - + +
9A GLY* 3.7 9.2 - - - +
10A GLN 3.2 0.2 - - - -
11A CYS* 1.3 78.3 - - + +
13A ALA* 1.3 57.6 + - - +
15A PHE* 3.2 8.7 + - + +
16A LEU* 2.9 47.0 + - + +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.2 14.5 + - - +
10A GLN 3.7 5.2 - - - +
11A CYS 3.3 0.2 - - - -
12A ILE* 1.3 79.2 - - - +
14A GLU* 1.3 60.1 + - - +
16A LEU* 4.5 6.5 - - - -
17A GLY* 2.8 27.0 + - - -
59A THR* 3.1 25.0 - - + +
62A VAL* 3.9 21.5 - - + -
63A SER* 3.8 13.0 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN 3.0 21.4 + - - +
11A CYS 3.8 4.3 - - - +
13A ALA* 1.3 75.7 - - - +
15A PHE* 1.3 61.6 + - - +
18A THR* 2.6 32.4 + - - -
63A SER* 2.7 22.9 + - - +
65A ALA* 3.5 2.4 - - - -
66A HIS* 3.0 21.3 + - - +
67A LEU* 2.7 22.1 + - - +
89A PHE* 3.8 29.4 - - + +
92A SER* 4.1 14.4 - - - -
93A GLN* 2.7 32.3 + - + -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS 3.0 14.6 + - - +
12A ILE* 3.3 13.5 - - + +
13A ALA 3.2 0.2 - - - -
14A GLU* 1.3 77.1 - - - +
16A LEU* 1.3 76.3 + - + +
19A GLY* 3.0 23.7 + - - -
92A SER* 3.5 17.7 + - - +
95A ALA* 3.5 18.8 - - + -
96A GLY* 3.3 42.5 - - - -
99A CYS* 3.7 25.8 - - + -
475A BOG 6.5 1.1 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 2.9 37.0 + - + +
13A ALA* 3.8 6.7 - - - +
15A PHE* 1.3 92.0 - - + +
17A GLY* 1.3 59.1 + - - +
19A GLY* 3.3 1.4 + - - -
20A LEU* 2.8 32.0 + - - +
58A LEU* 4.6 17.9 - - + +
475A BOG 6.4 2.2 - - + -
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Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 2.8 20.5 + - - -
16A LEU* 1.3 73.4 - - - +
18A THR* 1.3 61.5 + - - +
20A LEU* 3.3 2.7 + - - -
21A LEU* 3.0 25.3 + - - +
55A ALA* 3.3 16.1 - - - +
58A LEU* 4.7 1.3 - - - -
59A THR* 3.8 12.7 - - - +
67A LEU* 3.6 16.4 - - - -
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 2.6 23.5 + - - -
15A PHE 4.1 1.6 - - - -
17A GLY* 1.3 75.8 - - - +
19A GLY* 1.3 63.0 + - - +
21A LEU* 3.3 10.5 - - + +
22A ILE* 3.2 36.5 + - + +
67A LEU* 3.4 32.2 - - - +
93A GLN* 3.2 36.5 - - + +
97A ALA* 4.0 13.5 - - + -
203A ASN* 5.2 0.7 - - - +
205A ALA* 4.4 5.6 - - + -
206A ARG 5.1 1.8 - - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.0 16.3 + - - -
16A LEU* 3.7 1.8 - - - -
18A THR* 1.3 78.3 - - - +
20A LEU* 1.3 55.7 + - - +
22A ILE 3.3 0.3 + - - -
23A PHE* 2.9 27.1 + - - +
96A GLY* 3.3 25.1 - - - -
100A ALA* 3.0 15.5 - - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 2.8 17.9 + - - +
17A GLY* 3.5 9.0 - - - +
18A THR 3.3 0.2 - - - -
19A GLY* 1.3 76.3 - - - +
21A LEU* 1.3 62.3 + - - +
23A PHE* 3.2 15.0 + - + +
24A PHE* 3.1 60.3 + - + -
54A MET* 4.2 7.0 - - + +
55A ALA* 3.8 26.9 - - + +
58A LEU* 4.7 13.9 - - + -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY 3.0 28.6 + - - +
18A THR* 3.3 18.4 - - + -
20A LEU* 1.3 80.4 - - - +
22A ILE* 1.3 90.7 + - + +
24A PHE* 4.1 1.6 - - - +
25A GLY* 2.9 22.3 + - - -
48A TRP* 3.4 22.2 - - + +
51A GLY* 4.1 9.1 - - - +
52A VAL* 3.9 38.1 - - + +
55A ALA* 4.2 2.4 - - + +
67A LEU* 4.1 23.8 - - + +
203A ASN* 5.3 4.0 - - - +
206A ARG* 4.8 7.6 - - + -
662A GOL 5.8 0.7 - - - +
663A GOL 4.8 6.1 - - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.2 21.3 + - + +
19A GLY 3.7 2.2 - - - +
20A LEU 3.2 0.2 - - - -
21A LEU* 1.3 108.0 - - + +
23A PHE* 1.3 59.3 + - - +
25A GLY 4.4 0.2 - - - +
26A VAL* 2.6 49.5 + - + +
48A TRP* 4.4 4.3 - - + -
97A ALA* 3.7 22.4 - - + +
100A ALA* 3.3 24.0 - - + -
101A ALA* 3.6 15.3 - - + +
206A ARG* 3.9 29.6 - - + +
210A PRO* 4.3 10.8 - - + -
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 2.9 13.9 + - - +
20A LEU* 3.3 18.4 - - + +
22A ILE* 1.3 78.6 - - - +
24A PHE* 1.3 80.1 + + - +
27A GLY* 2.9 27.9 + - - -
100A ALA* 4.4 4.5 - - + -
103A LEU* 3.8 32.5 - - + -
104A VAL* 3.6 24.9 - - + +
107A LEU* 3.8 26.2 - - + -
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.1 48.3 + - + +
21A LEU 4.1 2.7 - - - +
23A PHE* 1.3 98.7 - + - +
25A GLY* 1.3 63.7 + - - +
27A GLY* 3.8 0.4 - - - -
28A CYS* 3.0 26.2 + - - +
47A ILE* 4.2 12.7 - - + +
48A TRP* 6.1 0.2 - - - -
51A GLY* 3.6 31.0 - - - -
54A MET* 4.3 16.6 - - + -
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 2.9 16.9 + - - -
24A PHE* 1.3 75.3 - - - +
26A VAL* 1.3 64.2 + - - +
28A CYS* 3.2 23.2 - - - -
29A VAL* 3.3 10.2 + - - +
48A TRP* 3.3 38.7 + - - +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 2.6 43.2 + - + +
25A GLY* 1.3 73.0 - - - -
27A GLY* 1.3 59.7 + - - +
29A VAL* 3.3 0.7 + - - -
30A ALA* 2.9 23.0 + - - +
48A TRP* 4.4 10.3 - - + -
101A ALA* 5.0 1.6 - - - -
104A VAL* 3.8 19.1 - - + -
134A THR* 3.4 31.9 - - + +
135A PHE* 3.8 39.3 - - + +
210A PRO* 5.0 2.2 - - + -
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE 2.9 22.2 + - - -
24A PHE* 3.8 0.9 - - - -
25A GLY 3.1 0.2 - - - -
26A VAL* 1.3 78.1 - - - +
28A CYS* 1.3 60.6 + - - +
30A ALA* 3.2 2.9 + - - +
31A ALA 3.1 17.5 + - - -
104A VAL* 3.8 15.4 - - - +
108A TYR* 3.4 18.5 + - - -
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Residues in contact with CYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE 3.0 12.8 + - - +
25A GLY 3.2 17.9 - - - -
27A GLY* 1.3 72.8 - - - +
29A VAL* 1.3 67.7 + - - +
31A ALA* 3.3 9.7 + - - +
32A LEU* 3.1 17.7 + - - +
39A PHE* 3.5 15.6 - - + -
44A ILE* 3.9 18.3 - - - +
47A ILE* 3.8 42.4 - - + -
48A TRP* 4.3 11.2 - - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 3.3 15.1 + - - +
26A VAL* 3.3 6.0 + - - +
27A GLY 3.3 0.6 - - - -
28A CYS* 1.3 77.9 - - - +
30A ALA* 1.3 61.6 + - - +
32A LEU* 3.3 11.2 + - + +
33A LYS* 2.9 46.1 + - + +
44A ILE* 4.5 12.6 - - + -
48A TRP* 3.8 18.8 - - + +
133A GLY 3.8 6.3 - - - +
134A THR* 3.6 30.1 - - - +
206A ARG* 6.0 0.7 - - - +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 2.9 18.1 + - - +
27A GLY 3.2 5.8 + - - +
29A VAL* 1.3 75.2 - - - +
31A ALA* 1.3 58.4 + - - +
33A LYS* 4.7 0.2 - - - -
34A VAL* 2.8 43.6 + - + +
104A VAL* 4.4 4.5 - - + -
108A TYR* 4.0 28.0 - - + -
112A PHE* 4.5 4.5 - - + -
134A THR* 3.7 22.6 - - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.1 8.1 + - - +
28A CYS* 3.4 11.4 - - - +
30A ALA* 1.3 77.8 - - - +
32A LEU* 1.3 58.4 + - - +
35A ALA* 3.0 33.1 + - + +
36A GLY 3.1 0.2 + - - -
37A ALA* 3.1 24.8 + - + -
39A PHE* 3.9 15.5 - - + -
108A TYR* 3.4 19.0 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS 3.1 13.2 + - - +
29A VAL* 3.5 13.7 - - + +
31A ALA* 1.3 80.0 - - - +
33A LYS* 1.3 77.1 + - + +
36A GLY* 3.9 11.4 + - - -
37A ALA* 3.7 21.1 - - - +
39A PHE* 3.8 32.1 - - + +
44A ILE* 4.4 19.3 - - + -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 2.9 33.9 + - + +
30A ALA 4.2 0.7 - - - +
32A LEU* 1.3 90.7 - - + +
34A VAL* 1.3 60.7 + - + +
36A GLY 4.8 0.7 + - - -
115A PHE* 3.2 27.4 - - - -
130A ASP* 3.2 48.8 + - - +
131A LEU* 4.0 12.1 - - + +
133A GLY* 4.0 9.6 - - - -
134A THR* 3.4 26.0 - - - +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 2.8 30.9 + - - +
33A LYS* 1.3 78.7 - - + +
35A ALA* 1.3 57.1 + - - +
36A GLY 3.5 1.6 - - - -
108A TYR* 4.0 11.0 - - + -
111A LEU* 3.7 43.7 - - + +
112A PHE* 4.1 26.5 - - + -
115A PHE* 4.0 25.7 - - + +
131A LEU* 3.6 24.7 - - + -
134A THR* 5.3 0.2 - - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.5 1.0 + - - -
31A ALA* 3.0 26.6 + - + +
34A VAL* 1.3 78.9 - - - +
36A GLY* 1.3 64.9 + - - +
37A ALA* 3.2 4.3 + - + +
108A TYR* 4.1 8.3 - - + -
111A LEU* 3.6 20.9 - - + -
----------------------------------------------------------
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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