Contacts of the helix formed by residues 4 - 40 (chain A) in PDB entry 1NF6
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 ASN 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLY* 1.3 74.4 - - - -
5A ARG* 1.3 69.5 + - + +
6A GLU* 3.6 10.8 + - - +
7A ASP* 2.8 58.3 + - - +
8A ARG* 2.8 12.8 + - - +
6O GLU* 4.0 7.3 + - - +
7O ASP* 4.6 10.4 + - - +
10O ALA* 3.2 33.3 - - - +
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Residues in contact with ARG 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASN* 1.3 75.2 - - + +
6A GLU* 1.3 66.3 + - - +
7A ASP 2.9 1.2 + - - -
8A ARG* 3.0 43.5 + - - +
9A LYS* 3.1 47.9 + - - +
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASN* 3.4 9.6 + - - +
5A ARG* 1.3 79.9 - - - +
7A ASP* 1.3 55.6 + - - +
9A LYS* 3.6 8.9 + - - +
10A ALA* 3.0 30.1 + - - +
6O GLU* 3.8 27.7 - - + +
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Residues in contact with ASP 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLY* 3.9 9.5 - - - -
4A ASN* 2.8 39.0 + - - +
6A GLU* 1.3 74.7 - - - +
8A ARG* 1.3 61.7 + - - +
10A ALA* 3.4 2.3 + - - +
11A LYS* 3.0 53.3 + - - +
116A GLN* 4.7 0.4 - - - +
5O ARG 5.8 1.0 + - - -
6O GLU* 3.9 11.3 + - - +
7O ASP* 3.4 34.3 + - - +
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLY* 4.3 18.6 + - - +
4A ASN 2.8 19.1 + - - +
5A ARG* 3.0 39.4 + - - +
7A ASP* 1.3 73.9 - - + +
9A LYS* 1.3 64.6 + - + +
11A LYS* 3.5 2.3 + - - +
12A VAL* 3.2 29.1 + - - +
116A GLN* 2.8 45.5 + - - +
117A GLY* 3.5 24.0 + - - -
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 3.1 51.3 + - - +
6A GLU* 3.8 7.6 - - - +
8A ARG* 1.3 76.7 - - + +
10A ALA* 1.3 60.7 + - - +
12A VAL* 3.3 4.1 + - - +
13A ILE* 2.8 36.7 + - + +
69A GLU 5.1 2.7 - - - -
70A LEU* 3.4 56.0 - - + +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLU 3.0 19.7 + - - +
7A ASP* 3.4 5.4 + - - +
9A LYS* 1.3 75.8 - - - +
11A LYS* 1.3 58.8 - - + +
13A ILE* 3.4 12.7 + - - +
14A GLU* 3.1 27.2 + - - +
6O GLU* 4.1 23.1 - - + +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLY* 5.4 6.1 - - - -
7A ASP* 3.0 37.7 + - - +
8A ARG 3.8 4.7 - - - +
9A LYS 3.2 0.2 - - - -
10A ALA* 1.3 77.8 - - + +
12A VAL* 1.3 61.2 + - - +
14A GLU* 3.3 25.3 - - - +
15A VAL* 3.4 14.7 + - - +
112A VAL* 4.2 7.2 - - + +
116A GLN* 3.3 40.3 + - + +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG 3.2 17.5 - - - +
9A LYS* 3.3 4.6 + - - +
11A LYS* 1.3 73.9 - - - +
13A ILE* 1.3 66.6 + - - +
14A GLU 3.1 1.8 - - - -
15A VAL* 3.2 8.1 + - - +
16A LEU* 3.0 27.3 + - + +
70A LEU* 3.8 4.0 - - + -
112A VAL* 4.8 1.3 - - + -
113A CYS* 3.8 14.8 - - - -
116A GLN* 3.7 24.0 - - + -
118A ASP* 3.5 32.1 - - + +
121A THR* 3.7 26.5 - - + +
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 2.8 27.9 + - + +
10A ALA* 3.6 10.5 - - - +
12A VAL* 1.3 75.8 - - - +
14A GLU* 1.3 57.6 + - - +
16A LEU* 3.4 9.8 + - - +
17A ASN* 2.8 45.4 + - - +
67A ILE* 4.3 8.9 - - + +
70A LEU* 3.7 40.2 - - + +
71A GLY 4.4 1.1 - - - +
72A GLY* 3.8 28.7 - - - -
73A GLU 4.9 1.1 - - - +
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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
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10A ALA 3.1 13.4 + - - +
11A LYS* 3.3 19.2 - - - +
13A ILE* 1.3 79.0 - - - +
15A VAL* 1.3 66.5 + - + +
17A ASN* 3.3 6.5 + - - +
18A LYS* 3.1 48.7 + - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS 3.4 9.2 + - - +
12A VAL* 3.2 22.2 + - - +
14A GLU* 1.3 82.3 - - + +
16A LEU* 1.3 57.8 + - - +
18A LYS* 3.3 10.3 + - + +
19A ALA* 2.8 30.0 + - - +
109A PHE* 3.4 51.1 - - + +
112A VAL* 4.0 24.0 - - + -
113A CYS* 4.4 3.6 - - - -
125A PHE* 4.3 9.2 - - + -
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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
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12A VAL* 3.0 26.6 + - + +
13A ILE* 3.5 5.2 - - - +
15A VAL* 1.3 79.6 - - - +
17A ASN* 1.3 58.1 + - - +
19A ALA* 3.8 5.1 - - - +
20A ARG* 2.8 29.8 + - - +
63A PHE* 3.6 34.1 - - + +
66A ARG* 4.0 13.9 - - + -
67A ILE* 3.6 24.8 - - + +
70A LEU* 3.6 29.4 - - + -
121A THR* 3.6 24.2 - - + -
124A LEU* 4.5 1.3 - - + -
125A PHE* 4.0 7.9 - - + -
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 2.8 32.0 + - - +
14A GLU* 3.3 6.2 + - - +
15A VAL 3.2 0.2 - - - -
16A LEU* 1.3 75.3 - - - +
18A LYS* 1.3 60.5 + - - +
21A ALA* 2.8 30.0 + - - +
67A ILE* 3.3 14.1 - - - +
73A GLU 3.0 21.0 + - - -
75A THR* 2.6 46.4 + - + +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.1 42.5 + - - +
15A VAL* 3.5 12.5 - - + +
17A ASN* 1.3 75.8 - - - +
19A ALA* 1.3 65.9 + - - +
21A ALA* 3.2 6.6 + - - +
22A MET* 3.0 27.8 + - - +
79A GLU* 4.9 0.7 - - - +
109A PHE* 3.6 27.7 - - + -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL 2.8 17.6 + - - +
16A LEU* 3.8 4.0 - - - +
18A LYS* 1.3 76.0 - - - +
20A ARG* 1.3 63.1 + - - +
22A MET* 3.1 3.6 + - - +
23A GLU* 3.0 18.4 + - - +
63A PHE* 3.9 10.5 - - + -
106A TYR* 3.2 35.6 + - + -
109A PHE* 3.5 15.2 - - + -
125A PHE* 3.7 15.3 - - + -
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU 2.8 19.7 + - - +
17A ASN* 3.8 6.3 - - - +
19A ALA* 1.3 77.4 - - - +
21A ALA* 1.3 63.1 + - - +
23A GLU* 3.0 5.2 + - - +
24A LEU* 2.9 28.8 + - + +
60A ALA* 3.0 40.0 + - + +
63A PHE* 4.0 14.0 - - + -
64A ALA* 3.7 14.9 - - - +
67A ILE* 4.2 5.6 - - - -
74A PRO* 3.7 13.4 + - - +
75A THR* 2.7 44.7 + - + +
76A THR* 4.6 4.9 - - - +
1005A FEC 2.8 43.0 + - - -
32B ASN* 6.3 0.2 - - - +
35B TYR* 4.3 6.7 - - - -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN 2.8 22.6 + - - +
18A LYS* 3.2 7.2 + - - +
20A ARG* 1.3 73.1 - - - +
22A MET* 1.3 61.4 + - - +
24A LEU* 3.3 2.1 + - - +
25A HIS 3.2 12.8 + - - -
75A THR* 4.0 5.6 - - + +
77A GLN 3.1 24.9 - - - +
78A LYS* 3.3 3.4 - - - +
79A GLU* 2.8 36.3 + - + +
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Residues in contact with MET 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.0 18.6 + - - +
19A ALA 3.3 7.4 - - - +
20A ARG 3.1 0.2 - - - -
21A ALA* 1.3 76.1 - - - +
23A GLU* 1.3 62.7 + - - +
25A HIS* 3.4 7.3 + - - +
26A ALA* 3.2 21.8 + - - +
79A GLU* 4.2 20.0 - - + +
98A GLN* 4.6 2.4 + - - -
101A ALA* 4.5 2.9 - - + +
102A THR* 3.5 44.2 - - + +
105A ALA* 3.7 23.6 - - + -
106A TYR* 4.1 14.8 - - - +
109A PHE* 4.2 10.1 - - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 3.0 10.7 + - - +
20A ARG 3.0 7.5 + - - +
22A MET* 1.3 75.0 - - - +
24A LEU* 1.3 66.1 + - - +
26A ALA* 3.4 4.9 + - - +
27A ILE* 3.0 29.1 + - - +
56A GLU* 3.3 37.4 - - - +
59A HIS* 2.9 34.1 + - + +
60A ALA* 4.0 10.3 - - + +
63A PHE* 3.8 15.9 - - + -
102A THR* 5.5 0.4 - - - -
106A TYR* 2.6 37.1 + - - +
132A GLU* 3.8 5.7 - - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 2.9 22.1 + - + +
21A ALA* 3.3 8.3 + - - +
23A GLU* 1.3 76.9 - - - +
25A HIS* 1.3 59.2 + - - +
27A ILE* 3.4 8.4 + - + +
28A HIS* 2.6 37.7 + - + -
60A ALA* 4.4 4.9 - - + -
75A THR* 3.9 9.4 - - + +
76A THR* 3.6 38.4 - - - +
77A GLN 3.9 10.8 - - - +
78A LYS* 3.7 10.5 - - + +
1005A FEC 4.0 40.4 - - + +
28B HIS* 4.2 13.7 - - + +
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Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 3.2 10.0 + - - +
22A MET* 3.5 9.4 + - - +
23A GLU 3.2 0.2 - - - -
24A LEU* 1.3 76.1 - - - +
26A ALA* 1.3 49.8 + - - +
28A HIS* 3.1 4.5 + - - +
29A GLN* 2.7 51.0 + - + +
78A LYS* 3.4 14.2 - - + +
79A GLU 3.3 28.2 + - - +
80A GLY* 3.7 13.8 - - - -
81A LYS 2.9 32.2 + - - -
82A VAL* 3.9 7.3 + - + -
98A GLN* 3.2 33.5 + - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A MET 3.2 11.2 + - - +
23A GLU* 3.7 9.2 - - - +
25A HIS* 1.3 75.8 + - - +
27A ILE* 1.3 61.1 + - - +
29A GLN* 4.2 2.9 - - - -
30A TYR* 2.8 55.0 + - + -
56A GLU* 4.2 11.4 - - + +
98A GLN* 3.4 24.9 - - - +
99A GLU* 5.2 0.7 - - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU 3.0 24.2 + - - +
24A LEU* 3.7 15.0 - - + +
25A HIS 3.2 0.2 - - - -
26A ALA* 1.3 76.6 - - - +
28A HIS* 1.3 59.5 + - - +
30A TYR* 4.2 0.5 - - - +
31A MET* 3.0 30.5 + - - +
53A ALA* 3.9 6.7 - - - +
56A GLU* 3.9 9.0 - - + +
57A MET* 3.7 53.2 - - + +
60A ALA* 4.4 1.8 - - + -
1005A FEC 3.9 59.0 - - + -
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Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.6 27.5 + - + -
25A HIS 3.1 6.1 + - - +
27A ILE* 1.3 75.2 - - + +
29A GLN* 1.3 65.3 + - - +
31A MET* 4.2 0.3 - - - +
32A ASN* 3.0 25.1 + - - +
78A LYS* 3.9 16.6 + - + +
82A VAL* 3.6 17.1 - - + +
1005A FEC 3.9 37.3 - - + +
24B LEU* 4.1 14.5 - - + +
28B HIS* 3.8 35.1 - + - -
76B THR* 3.7 30.6 + - - +
78B LYS* 5.8 0.4 - - - -
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 2.7 37.7 + - + +
26A ALA* 4.0 5.8 - - - +
28A HIS* 1.3 77.0 - - - +
30A TYR* 1.3 67.3 + - + +
32A ASN* 3.3 2.3 + - - +
33A GLN* 3.3 28.3 + - - +
81A LYS 4.0 0.9 - - - +
82A VAL* 3.5 14.6 - - + +
83A VAL* 2.8 51.6 + - - +
86A GLN* 3.6 15.3 + - - -
95A ASP* 4.5 2.2 - - - +
98A GLN* 4.0 16.6 - - - +
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 2.8 38.0 + - + +
29A GLN* 1.3 75.8 - - + +
31A MET* 1.3 62.7 + - - +
33A GLN* 3.2 19.0 + - - +
34A HIS 3.0 17.5 + - - -
49A MET* 3.3 20.3 - - - +
52A ILE* 4.2 7.0 - - + -
53A ALA* 4.0 14.8 - - + -
56A GLU* 3.4 35.2 - - + -
95A ASP* 3.4 25.8 + - + -
98A GLN* 3.8 27.9 + - - +
99A GLU* 2.3 31.2 + - - +
139A TYR* 3.8 19.4 - + - -
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE 3.0 22.4 + - - +
28A HIS 4.2 0.2 - - - +
30A TYR* 1.3 77.8 - - - +
32A ASN* 1.3 63.0 + - - +
34A HIS* 3.1 27.1 + - + +
35A TYR* 2.9 50.5 + - + +
50A LYS* 3.8 32.8 - - + +
53A ALA* 3.9 19.1 - - + -
57A MET* 4.6 8.7 - - + -
1005A FEC 3.5 49.1 - - + +
61B GLU* 4.3 2.2 - - - +
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS 3.0 18.3 + - - +
29A GLN* 3.5 6.6 - - - +
30A TYR 3.2 0.2 - - - -
31A MET* 1.3 77.6 - - - +
33A GLN* 1.3 64.1 + - - +
35A TYR* 3.4 14.1 + - - +
36A SER* 3.2 23.3 + - - -
82A VAL* 4.4 9.0 - - + -
83A VAL 3.9 5.1 + - - -
84A THR* 3.5 30.8 - - - +
85A GLY 4.3 2.6 - - - +
86A GLN 5.7 0.4 - - - +
1005A FEC 5.3 0.6 + - - -
68B LYS* 5.2 0.2 - - - -
73B GLU* 2.9 28.0 + - - +
74B PRO* 3.9 19.8 - - - +
76B THR* 4.4 5.0 - - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.3 19.9 + - - +
30A TYR* 3.2 21.2 + - - +
32A ASN* 1.3 76.9 - - - +
34A HIS* 1.3 54.9 + - - +
36A SER* 3.2 9.4 + - - -
37A LEU* 2.7 41.2 + - - +
49A MET* 3.5 10.4 - - + +
86A GLN* 2.5 32.1 + - - +
91A ILE* 3.7 28.2 - - + +
95A ASP* 2.5 43.4 + - - +
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Residues in contact with HIS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR 3.0 13.5 + - - +
31A MET* 3.3 33.6 - - + +
33A GLN* 1.3 74.4 - - - +
35A TYR* 1.3 73.7 + + - +
37A LEU* 3.9 5.5 - - - +
38A ASP* 2.8 49.2 + - - +
46A ALA* 2.6 38.5 + - + +
47A ALA* 4.7 2.0 - - - -
49A MET* 3.9 14.1 - - + +
50A LYS* 3.6 28.8 - - + +
162A SER* 5.3 4.3 - - - -
1001A SO4 5.3 3.8 - - - -
61B GLU* 4.3 5.9 + - - -
65B GLU* 5.0 3.4 + - - -
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 2.9 41.4 + - + +
32A ASN* 3.6 11.9 - - - +
34A HIS* 1.3 95.1 - + - +
36A SER* 1.3 56.4 + - - +
38A ASP* 3.7 5.4 - - + +
39A ASP* 2.9 30.3 + - - +
1005A FEC 2.4 35.0 + - - +
20B ARG* 3.8 6.2 + - - -
61B GLU* 3.5 29.4 - - + -
64B ALA* 3.5 29.8 - - + -
65B GLU* 4.5 11.9 - - + -
68B LYS* 3.7 24.3 - - + +
74B PRO* 4.3 10.5 - - + -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.2 16.7 + - - -
33A GLN* 3.2 12.4 + - - -
35A TYR* 1.3 78.3 - - - +
37A LEU* 1.3 57.2 + - - +
39A ASP* 2.9 6.8 + - - +
40A MET* 2.9 45.2 + - - +
85A GLY* 5.3 6.9 + - - -
86A GLN 5.1 6.6 + - - -
91A ILE* 4.8 5.8 - - - -
68B LYS* 3.4 24.0 + - - +
73B GLU* 4.9 1.4 + - - -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 2.7 24.1 + - - +
34A HIS 3.9 2.9 - - - +
36A SER* 1.3 72.8 - - - +
38A ASP* 1.3 60.8 + - - +
40A MET* 3.3 23.3 + - + +
41A ASP 3.1 4.0 + - - -
42A TYR* 3.0 32.1 + - + +
45A LEU* 3.6 29.8 - - + +
46A ALA* 3.9 13.7 - - + +
49A MET* 3.8 24.7 - - + -
88A VAL* 4.2 10.5 - - + -
91A ILE* 4.1 13.9 - - + -
92A TYR* 3.4 28.9 - - + +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 2.8 32.8 + - + +
35A TYR* 3.7 6.9 - - + +
37A LEU* 1.3 75.5 - - - +
39A ASP* 1.3 63.2 + - - +
41A ASP* 3.3 17.1 + - - +
42A TYR 5.0 0.2 - - - +
43A GLY* 5.1 1.2 - - - -
46A ALA* 3.6 13.1 - - + +
162A SER* 3.6 27.4 + - - -
65B GLU* 3.8 18.5 - - - +
141N ASN* 5.5 1.7 + - - +
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR 2.9 19.3 + - - +
36A SER* 2.9 8.4 + - - +
38A ASP* 1.3 78.6 - - - +
40A MET* 1.3 61.1 + - - +
41A ASP 3.1 0.9 + - - -
68B LYS* 3.9 45.8 + - + +
69B GLU* 5.2 1.9 - - - +
141N ASN* 3.9 13.2 - - - +
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 2.9 36.8 + - - +
37A LEU* 3.3 25.1 + - + +
38A ASP 3.3 0.2 - - - -
39A ASP* 1.3 78.4 - - + +
41A ASP* 1.3 68.9 + - - +
42A TYR* 3.4 23.4 - - + -
86A GLN 5.5 2.2 - - - +
87A ALA* 6.2 0.2 - - - -
88A VAL* 3.5 35.2 - - + +
91A ILE* 4.5 5.2 - - + -
141N ASN* 5.0 0.4 - - - -
144N SER* 5.2 7.7 + - - -
145N HIS* 3.2 17.0 + - - -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il