Contacts of the helix formed by residues 2 - 39 (chain A) in PDB entry 2M0Q
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 2 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 1.3 70.0 - - - +
3A THR* 1.3 62.1 + - - +
4A LEU* 2.9 23.7 + - - +
5A SER* 2.9 34.4 + - - -
6A ASN* 3.8 6.6 + - - +
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Residues in contact with THR 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 11.9 + - + +
2A SER* 1.3 71.8 - - - +
4A LEU* 1.3 59.5 + - - +
5A SER 3.1 0.2 - - - -
6A ASN* 3.0 18.8 + - - +
7A PHE* 2.7 38.2 + - - +
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Residues in contact with LEU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.9 28.9 - - - +
3A THR* 1.3 85.8 + - - +
5A SER* 1.3 49.8 + - - +
7A PHE* 3.9 7.2 - - - +
8A THR* 2.3 40.2 + - - +
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Residues in contact with SER 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.9 18.0 + - - -
4A LEU* 1.3 75.1 - - - +
6A ASN* 1.3 78.3 + - - +
8A THR* 2.6 20.1 + - - -
9A GLN* 3.5 19.1 + - - +
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Residues in contact with ASN 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 3.8 5.6 + - - +
3A THR* 3.0 25.0 + - - +
5A SER* 1.3 90.6 + - - +
7A PHE* 1.3 63.3 + - - +
9A GLN* 3.6 24.5 + - - +
10A THR* 4.0 7.3 + - - -
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Residues in contact with PHE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 2.7 21.7 + - - +
4A LEU* 4.0 6.3 - - - +
6A ASN* 1.3 71.6 - - - +
8A THR* 1.3 62.0 + - + +
9A GLN 3.1 1.8 - - - -
10A THR* 2.8 38.6 + - + -
11A LEU* 3.0 34.6 + - + -
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU 2.3 33.6 + - - +
5A SER* 2.6 20.3 + - - -
7A PHE* 1.3 75.7 - - + +
9A GLN* 1.3 62.0 + - - +
11A LEU* 3.2 15.9 + - + +
12A GLU* 3.2 22.5 + - - +
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 3.5 18.0 + - - +
6A ASN* 3.6 14.6 - - - +
7A PHE 3.1 0.2 - - - -
8A THR* 1.3 77.8 - - - +
10A THR* 1.3 59.6 + - - +
12A GLU* 3.7 9.7 + - - +
13A ASP* 3.1 22.2 + - - +
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Residues in contact with THR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN 4.0 8.3 + - - -
7A PHE* 2.8 29.0 + - + -
9A GLN* 1.3 78.3 - - - +
11A LEU* 1.3 65.7 + - - +
12A GLU 3.1 0.2 - - - -
13A ASP* 2.9 19.5 + - + +
14A VAL* 3.1 22.5 + - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.0 31.1 + - + +
8A THR* 3.6 19.5 - - + +
10A THR* 1.3 76.8 - - - +
12A GLU* 1.3 56.8 + - - +
14A VAL* 3.1 7.7 + - - +
15A PHE* 2.7 75.6 + - + +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR 3.2 9.5 + - - +
9A GLN* 3.8 11.9 - - - +
10A THR 3.1 0.2 - - - -
11A LEU* 1.3 86.1 - - + +
13A ASP* 1.3 62.3 + - - +
15A PHE* 4.0 4.9 - - - +
16A ARG* 2.9 41.1 + - + +
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN 3.1 18.9 - - - +
10A THR* 2.9 13.9 + - + +
12A GLU* 1.3 82.9 - - - +
14A VAL* 1.3 63.1 + - + +
16A ARG* 3.4 10.9 - - - +
17A ARG* 3.3 19.1 + - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.5 23.1 - - + +
11A LEU* 3.1 8.8 + - - +
13A ASP* 1.3 76.3 - - + +
15A PHE* 1.3 60.9 + - + +
16A ARG 3.0 1.6 - - - -
17A ARG* 2.9 17.0 + - + +
18A ILE* 2.6 49.0 + - + +
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 2.7 56.7 + - + +
12A GLU* 4.0 6.1 - - - +
14A VAL* 1.3 80.2 - - + +
16A ARG* 1.3 53.4 + - - +
18A ILE* 3.3 16.5 - - + +
19A PHE* 2.5 40.9 + - + +
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 2.9 33.0 + - + +
13A ASP* 3.4 13.0 - - - +
14A VAL 3.0 0.2 - - - -
15A PHE* 1.3 78.4 - - - +
17A ARG* 1.3 56.4 + - - +
19A PHE* 3.8 3.9 - - - +
20A ILE* 3.0 54.2 + - + +
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 3.3 9.5 + - - +
14A VAL* 2.9 17.9 + - + +
16A ARG* 1.3 79.2 - - - +
18A ILE* 1.3 59.1 + - + +
20A ILE* 4.7 4.7 - - - -
21A THR* 2.2 53.1 + - - +
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 2.6 30.7 + - + +
15A PHE* 3.3 30.5 - - + +
17A ARG* 1.3 78.3 - - + +
19A PHE* 1.3 59.6 + - + +
21A THR* 4.1 5.6 - - + -
22A TYR* 2.3 47.6 + - + +
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 2.5 24.5 + - + +
16A ARG* 3.8 4.7 - - - +
18A ILE* 1.3 74.0 - - + +
20A ILE* 1.3 70.7 + - + +
22A TYR* 3.6 6.9 - + - +
23A MET* 2.7 66.0 + - + +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.0 41.7 + - + +
17A ARG* 4.2 4.3 - - - +
19A PHE* 1.3 86.4 - - + +
21A THR* 1.3 59.5 + - - +
23A MET* 3.6 4.9 + - - +
24A ASP* 3.0 26.4 + - + +
----------------------------------------------------------
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 2.2 41.4 + - + +
18A ILE* 3.9 6.5 - - + -
20A ILE* 1.3 78.5 - - - +
22A TYR* 1.3 59.1 + - - +
24A ASP* 3.0 6.9 + - + +
25A ASN* 2.8 48.8 + - - +
----------------------------------------------------------
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 2.3 46.7 + - + +
19A PHE* 3.6 8.5 - + - +
21A THR* 1.3 71.0 - - - +
23A MET* 1.3 80.0 + - + +
25A ASN* 3.5 6.7 + - - +
26A TRP* 2.9 64.6 + + - +
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Residues in contact with MET 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.7 52.2 + - + +
20A ILE* 3.9 5.8 - - - +
22A TYR* 1.3 89.7 - - + +
24A ASP* 1.3 59.9 + - - +
26A TRP* 3.8 8.7 - - - +
27A ARG* 3.4 25.4 + - - +
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Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.0 20.1 + - + +
21A THR* 3.0 10.9 + - - +
23A MET* 1.3 76.4 - - - +
25A ASN* 1.3 72.6 + - - +
27A ARG* 3.0 30.6 + - - +
28A GLN* 3.6 6.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 2.8 39.7 + - - +
22A TYR* 3.9 6.6 - - - +
24A ASP* 1.3 80.9 + - - +
26A TRP* 1.3 58.5 + - + +
28A GLN* 2.9 31.5 + - - +
29A ASN* 3.3 6.9 + - - +
----------------------------------------------------------
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Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 2.9 59.2 + + + +
23A MET* 3.8 12.8 - - - +
25A ASN* 1.3 80.7 - - + +
27A ARG* 1.3 53.3 + - + +
29A ASN* 3.4 8.7 + - + +
30A THR* 2.3 62.9 + - + -
----------------------------------------------------------
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 3.4 18.5 + - - +
24A ASP* 3.0 19.3 + - - +
26A TRP* 1.3 77.3 - - + +
28A GLN* 1.3 59.8 + - + +
30A THR* 3.8 12.2 - - - +
31A THR* 3.3 21.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.6 6.9 + - - +
25A ASN* 2.9 15.4 + - - +
27A ARG* 1.3 78.5 - - + +
29A ASN* 1.3 59.8 + - - +
30A THR 3.2 0.2 - - - -
31A THR* 2.8 32.0 + - - +
----------------------------------------------------------
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Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN 3.3 7.3 + - - +
26A TRP* 3.4 11.2 + - + +
28A GLN* 1.3 76.9 - - - +
30A THR* 1.3 64.4 + - - +
31A THR* 3.2 1.3 - - - -
32A ALA* 3.3 22.7 + - - +
33A GLU* 4.0 3.8 + - - +
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 2.3 48.4 + - + -
27A ARG* 3.8 15.4 - - - +
28A GLN 3.2 0.2 - - - -
29A ASN* 1.3 77.0 - - - +
31A THR* 1.3 65.6 + - - +
33A GLU* 2.9 22.2 + - + +
34A GLN* 3.1 18.2 + - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG 3.3 14.8 - - - +
28A GLN* 2.8 30.9 + - - +
30A THR* 1.3 76.6 - - - +
32A ALA* 1.3 61.2 + - - +
34A GLN* 2.7 15.5 + - - +
35A GLU* 2.6 36.2 + - - +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 3.3 20.3 + - - +
30A THR 3.2 0.6 - - - -
31A THR* 1.3 84.3 + - - +
33A GLU* 1.3 62.7 + - + +
35A GLU* 3.5 9.5 + - - +
36A ALA* 3.4 20.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN 4.0 3.6 + - - +
30A THR* 2.9 19.5 + - + +
32A ALA* 1.3 80.4 - - + +
34A GLN* 1.3 62.0 + - - +
36A ALA* 3.6 5.1 + - - +
37A LEU* 3.2 39.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 3.1 18.3 + - + +
31A THR* 2.7 19.4 + - - +
33A GLU* 1.3 71.3 - - - +
35A GLU* 1.3 55.6 + - - +
37A LEU* 3.0 8.7 + - + -
38A GLN* 2.6 46.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR 2.6 18.3 + - - +
32A ALA* 3.7 11.3 - - - +
34A GLN* 1.3 73.2 - - - +
36A ALA* 1.3 66.5 + - - +
38A GLN* 3.2 39.9 + - - +
39A ALA* 3.5 8.5 + - - +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA 3.4 10.3 + - - +
33A GLU* 3.9 10.3 - - - +
34A GLN 3.1 0.4 - - - -
35A GLU* 1.3 84.8 + - - +
37A LEU* 1.3 72.2 + - + +
39A ALA* 3.2 18.8 - - - +
40A LYS* 4.0 7.4 + - - +
----------------------------------------------------------
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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 GLU* 3.2 32.0 + - + +
34A GLN* 3.0 9.3 + - + +
36A ALA* 1.3 80.1 - - + +
38A GLN* 1.3 54.6 + - - +
39A ALA 2.9 5.4 - - - -
40A LYS* 2.6 37.4 + - + +
41A VAL* 3.1 8.0 + - - -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 2.6 23.8 + - + +
35A GLU* 3.2 42.2 + - - +
37A LEU* 1.3 72.0 - - - +
39A ALA* 1.3 66.6 + - - +
41A VAL* 3.2 23.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.5 10.1 + - - +
36A ALA* 3.2 17.2 + - - +
37A LEU 2.8 0.4 + - - -
38A GLN* 1.3 83.9 - - + +
40A LYS* 1.3 60.8 + - + +
41A VAL* 4.8 2.8 - - - +
----------------------------------------------------------
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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