Contacts of the helix formed by residues 11 - 40 (chain A) in PDB entry 3SN6
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 ASP 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 1.3 84.4 - - + +
12A GLN* 1.3 60.0 + - + +
13A ARG 3.1 2.5 - - - -
14A ASN* 2.8 32.6 + - + +
15A GLU* 2.9 22.8 + - + +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR 3.0 18.3 + - - +
10A GLU* 3.2 23.5 - - - +
11A ASP* 1.3 79.0 - - + +
13A ARG* 1.3 62.8 + - - +
15A GLU* 3.0 17.5 + - - +
16A GLU* 2.9 39.3 + - + +
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 2.9 57.5 + - - +
10A GLU 3.9 6.0 - - - +
11A ASP 3.1 0.2 - - - -
12A GLN* 1.3 76.2 - - - +
14A ASN* 1.3 66.1 + - - +
16A GLU* 3.8 9.4 + - - +
17A LYS* 3.5 17.5 + - - +
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Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 4.4 9.8 + - - -
11A ASP* 2.8 18.4 + - + +
13A ARG* 1.3 82.5 - - - +
15A GLU* 1.3 59.8 + - + +
17A LYS* 3.1 14.6 + - - +
18A ALA* 2.9 25.5 + - - +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 2.9 23.2 + - + +
12A GLN* 3.0 18.9 + - - +
14A ASN* 1.3 73.4 - - + +
16A GLU* 1.3 69.0 + - - +
18A ALA* 2.9 19.8 + - + +
19A GLN* 2.9 15.9 + - - +
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 2.9 31.4 + - + +
13A ARG* 3.8 8.7 - - - +
15A GLU* 1.3 75.5 - - - +
17A LYS* 1.3 57.4 - - - +
19A GLN* 3.6 8.4 + - - +
20A ARG* 3.0 28.8 + - - +
68B ARG* 5.9 0.5 + - - -
86B THR* 4.3 18.5 - - - +
88B ASN* 5.2 2.8 + - - -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG 3.5 10.4 + - - +
14A ASN* 3.1 16.7 + - - +
16A GLU* 1.3 75.9 - - - +
18A ALA* 1.3 61.0 + - - +
20A ARG* 3.1 8.6 - - + +
21A GLU* 2.9 54.8 + - + +
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 2.9 11.9 + - - +
15A GLU* 2.9 15.2 + - - +
17A LYS* 1.3 73.1 - - - +
19A GLN* 1.3 66.0 + - - +
21A GLU* 2.9 9.1 + - - +
22A ALA* 2.9 23.7 + - - +
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU 2.9 13.4 + - - +
16A GLU* 4.1 7.7 - - - +
18A ALA* 1.3 75.8 - - - +
20A ARG* 1.3 62.0 + - - +
22A ALA* 4.0 6.6 - - + +
23A ASN* 2.9 27.3 + - - +
68B ARG* 4.9 0.9 + - - -
69B LEU* 5.3 0.4 - - - +
83B ASP* 3.2 21.5 + - - +
86B THR* 3.0 27.3 + - - +
88B ASN* 3.2 25.5 + - + +
89B LYS 5.2 4.3 - - - +
90B VAL* 3.7 23.6 - - + +
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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
----------------------------------------------------------
16A GLU 3.0 16.8 + - - +
17A LYS* 3.1 17.5 - - + +
19A GLN* 1.3 77.9 - - - +
21A GLU* 1.3 64.3 + - - +
23A ASN* 3.5 12.4 + - - +
24A LYS* 2.9 31.0 + - + +
88B ASN* 4.5 11.2 - - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 2.9 47.5 + - + +
18A ALA* 2.9 6.9 + - - +
20A ARG* 1.3 79.5 - - - +
22A ALA* 1.3 61.1 + - - +
24A LYS* 2.8 26.5 + - - +
25A LYS* 2.9 18.6 + - + +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 2.9 14.5 + - - +
19A GLN* 4.0 7.9 - - + +
21A GLU* 1.3 74.3 - - - +
23A ASN* 1.3 63.2 + - - +
25A LYS* 3.2 11.4 + - - +
26A ILE* 3.0 31.8 + - + +
89B LYS 4.9 5.8 - - - +
90B VAL* 5.7 2.9 - - - +
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Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN 2.9 19.9 + - - +
20A ARG* 3.5 11.2 + - - +
22A ALA* 1.3 76.5 - - - +
24A LYS* 1.3 60.7 + - - +
26A ILE* 3.4 4.8 + - - +
27A GLU* 2.9 54.5 + - - +
87B THR 4.7 1.0 - - - +
88B ASN* 3.5 19.0 + - - +
89B LYS* 2.8 50.9 + - - +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 2.9 19.8 + - - +
21A GLU* 2.8 28.3 + - - +
23A ASN* 1.3 73.9 - - - +
25A LYS* 1.3 62.8 + - + +
27A GLU* 3.1 10.0 + - - +
28A LYS* 2.9 20.7 + - - +
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 2.9 16.7 + - + +
22A ALA* 3.2 9.4 + - - +
24A LYS* 1.3 75.9 - - + +
26A ILE* 1.3 64.8 + - + +
28A LYS* 2.8 25.6 + - + +
29A GLN* 3.0 14.7 + - - +
112A ASN* 3.8 39.4 + - - +
113A LEU* 6.2 0.6 - - - +
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.0 21.0 + - + +
23A ASN* 3.6 6.7 - - - +
25A LYS* 1.3 76.0 - - + +
27A GLU* 1.3 63.2 + - - +
29A GLN* 3.4 5.5 + - - +
30A LEU* 2.9 36.8 + - + +
89B LYS* 3.2 46.9 - - + +
90B VAL 4.1 13.7 - - - +
91B HIS* 4.1 9.9 - - - +
92B ALA* 3.7 27.1 - - + +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 2.9 41.4 + - - +
24A LYS* 3.2 11.4 - - - +
26A ILE* 1.3 75.6 - - - +
28A LYS* 1.3 58.0 + - - +
30A LEU* 3.4 9.9 + - - +
31A GLN* 2.9 28.8 + - - +
52B ARG 4.9 3.3 - - - +
89B LYS* 3.3 27.4 + - + +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS 2.9 10.8 + - - +
25A LYS* 2.8 20.3 + - + +
27A GLU* 1.3 73.9 - - - +
29A GLN* 1.3 66.8 + - - +
31A GLN* 2.7 21.2 + - + +
32A LYS* 3.0 46.2 + - + +
112A ASN* 6.2 0.2 - - - +
135A MET* 6.0 4.4 - - - +
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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
----------------------------------------------------------
25A LYS 3.0 7.8 + - - +
26A ILE* 4.0 7.4 - - - +
28A LYS* 1.3 82.7 - - + +
30A LEU* 1.3 53.6 + - - +
32A LYS* 3.0 17.9 + - + +
33A ASP* 2.5 46.1 + - - +
170A GLN* 4.0 31.2 + - - +
78B LYS* 4.6 11.8 - - - +
94B PRO* 6.1 0.4 - - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 2.9 31.1 + - + +
27A GLU* 3.5 9.6 - - - +
29A GLN* 1.3 74.1 - - - +
31A GLN* 1.3 61.1 + - - +
33A ASP* 2.9 10.2 + - + +
34A LYS* 2.9 30.5 + - - +
53B GLY* 3.6 26.9 - - - +
55B LEU* 4.4 14.2 - - + +
78B LYS* 4.2 32.1 - - + +
80B ILE* 4.3 6.7 - - + -
89B LYS* 4.0 25.8 - - - +
92B ALA* 5.1 4.5 - - + -
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 2.9 13.2 + - - +
28A LYS* 2.7 19.6 + - - +
30A LEU* 1.3 71.7 - - - +
32A LYS* 1.3 60.8 + - + +
33A ASP 3.5 0.3 + - - -
34A LYS* 3.7 34.0 + - - +
35A GLN* 3.8 12.5 + - - +
147R LYS* 6.0 3.6 - - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 3.0 50.0 + - + +
29A GLN* 3.0 19.3 + - + +
31A GLN* 1.3 81.4 - - + +
33A ASP* 1.3 59.1 + - - +
35A GLN* 3.8 6.1 + - - +
36A VAL* 3.4 19.5 + - - +
104A GLU* 5.9 1.4 + - - -
135A MET* 5.5 8.7 - - - +
136A ASN* 5.7 7.9 - - - -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 2.5 45.5 + - - +
30A LEU* 2.9 12.9 + - + +
32A LYS* 1.3 77.0 - - - +
34A LYS* 1.3 64.4 + - - +
35A GLN 3.2 0.4 - - - -
36A VAL* 3.0 11.9 - - - +
37A TYR* 2.9 26.2 + - - +
55B LEU* 3.9 14.4 - - + -
78B LYS* 3.6 28.2 + - - -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 2.9 11.3 + - - +
31A GLN* 4.1 29.6 + - - +
32A LYS 3.5 0.2 - - - -
33A ASP* 1.3 75.6 - - - +
35A GLN* 1.3 58.7 + - - +
37A TYR* 4.4 0.2 - - - -
38A ARG* 2.9 58.8 + - + +
55B LEU* 3.5 36.1 - - + +
67R VAL* 5.9 3.8 - - - +
147R LYS* 4.7 22.8 - - - +
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 3.8 10.1 + - - +
32A LYS* 3.9 10.3 - - - +
33A ASP 3.2 0.6 - - - -
34A LYS* 1.3 83.0 - - - +
36A VAL* 1.3 57.2 + - - +
38A ARG* 3.8 2.7 - - - +
39A ALA* 2.9 30.4 + - - +
142R GLN 5.4 0.9 - - - +
143R SER* 5.2 7.8 - - - +
146R THR* 6.0 6.3 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS 3.4 13.4 + - - +
33A ASP* 3.0 28.7 - - + +
35A GLN* 1.3 77.0 - - - +
37A TYR* 1.3 56.0 + - - +
39A ALA* 3.1 8.3 + - - +
40A THR* 2.6 39.8 + - - +
218A ASN* 4.3 14.3 + - - +
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP 2.9 19.3 + - - +
34A LYS 3.8 1.8 - - - +
36A VAL* 1.3 78.6 - - + +
38A ARG* 1.3 71.2 + - + +
40A THR* 2.9 34.1 + - - +
42A ARG* 2.9 45.2 + - + +
240A ASP* 5.2 1.6 - - - +
55B LEU* 3.9 41.7 - - + -
56B ALA* 3.2 18.7 - - + +
75B GLN 4.9 0.2 - - - -
76B ASP* 4.2 21.5 - - + -
98B SER* 6.4 0.9 - - - -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 2.9 48.2 + - + +
35A GLN* 4.0 3.1 - - - +
37A TYR* 1.3 85.8 - - + +
39A ALA* 1.3 58.7 + - - +
40A THR 3.2 6.0 + - - +
41A HIS* 5.0 2.8 - - - -
55B LEU 5.8 3.0 + - - -
67R VAL* 5.0 16.4 - - - +
142R GLN* 3.8 39.4 + - + +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN 2.9 18.9 + - - +
36A VAL* 3.4 10.5 - - - +
37A TYR 3.1 0.4 - - - -
38A ARG* 1.3 76.4 - - - +
40A THR* 1.3 61.2 + - - +
41A HIS* 3.5 15.2 + - - -
217A VAL* 4.8 2.3 - - - +
218A ASN* 4.0 19.4 + - - +
139R PHE 5.2 2.4 - - - +
142R GLN* 5.3 0.2 - - - -
143R SER* 3.6 37.1 - - - +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 2.6 28.1 + - - +
37A TYR* 2.9 20.8 + - - +
38A ARG 3.7 5.7 - - - +
39A ALA* 1.3 81.8 - - - +
41A HIS* 1.3 74.6 + - - +
42A ARG* 4.1 7.8 + - + +
211A LYS* 5.7 2.5 - - + -
218A ASN* 3.6 21.1 - - + +
219A PHE 3.9 3.8 - - - +
220A HIS* 3.7 34.8 - - + +
242A THR* 5.2 1.2 - - - +
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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