Contacts of the helix formed by residues 3 - 36 (chain A) in PDB entry 1I5Y
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 ILE 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 1.3 68.8 + - - +
5A GLN* 3.4 5.5 - - - +
6A GLN* 3.1 16.9 + - - +
7A GLN* 2.9 32.1 + - + +
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Residues in contact with VAL 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 1.3 79.4 - - - +
5A GLN* 1.3 60.7 + - - +
7A GLN* 3.1 15.5 + - - +
8A ASN* 3.1 29.3 + - - -
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Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE 3.4 2.6 - - - +
4A VAL* 1.3 74.2 - - - +
6A GLN* 1.3 62.7 + - - +
8A ASN* 3.1 9.8 + - - +
9A ASN* 3.0 37.3 + - - +
12A ARG* 3.2 12.9 - - - +
201A SO4 2.6 49.9 + - - -
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Residues in contact with GLN 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.1 22.2 + - - +
5A GLN* 1.3 80.2 - - - +
7A GLN* 1.3 61.8 + - + +
9A ASN* 3.2 13.5 + - - +
10A LEU* 3.0 32.1 + - + +
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 2.9 21.1 + - + +
4A VAL* 3.1 13.9 + - - +
6A GLN* 1.3 73.7 - - + +
8A ASN* 1.3 68.4 + - - +
10A LEU* 3.4 16.6 + - + +
11A LEU* 3.0 23.7 + - - +
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Residues in contact with ASN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL 3.1 18.9 + - - +
5A GLN* 3.1 15.6 + - - +
7A GLN* 1.3 80.7 - - - +
9A ASN* 1.3 61.4 + - - +
11A LEU* 3.3 12.4 + - - +
12A ARG* 3.1 32.4 + - - +
201A SO4 2.9 32.5 + - - +
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Residues in contact with ASN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.0 27.7 + - - +
6A GLN* 3.5 13.5 - - - +
8A ASN* 1.3 72.9 - - - +
10A LEU* 1.3 68.2 + - + +
12A ARG* 2.5 39.4 + - - +
13A ALA* 2.9 22.8 + - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.0 23.9 + - + +
7A GLN* 3.6 18.8 - - + +
8A ASN 3.4 0.2 - - - -
9A ASN* 1.3 76.0 - - + +
11A LEU* 1.3 63.5 + - - +
13A ALA* 3.3 9.1 + - + +
14A ILE* 3.0 35.0 + - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN 3.0 14.2 + - - +
8A ASN* 3.4 14.4 - - - +
9A ASN 3.1 0.2 - - - -
10A LEU* 1.3 76.1 - - - +
12A ARG* 1.3 58.6 + - + +
14A ILE* 3.1 17.5 + - + +
15A GLU* 2.8 50.1 + - + +
59A ILE* 4.6 13.2 - - + -
62A SER* 3.9 34.3 - - - +
63A GLN* 3.6 31.6 - - + +
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.2 12.7 - - - +
8A ASN* 3.1 14.8 + - - +
9A ASN* 2.5 45.0 + - - +
11A LEU* 1.3 75.5 - - + +
13A ALA* 1.3 63.7 + - - +
15A GLU* 3.3 17.8 + - - +
16A ALA* 2.9 24.8 + - - +
201A SO4 2.7 39.2 + - - -
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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 ASN 2.9 12.7 + - - +
10A LEU* 3.4 14.8 - - + +
12A ARG* 1.3 76.6 - - - +
14A ILE* 1.3 58.8 + - + +
16A ALA* 3.4 6.2 + - - +
17A GLN* 3.0 41.3 + - + +
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.0 23.1 + - + +
11A LEU* 3.4 15.9 - - + +
13A ALA* 1.3 76.5 - - + +
15A GLU* 1.3 63.9 + - - +
17A GLN* 3.4 14.2 + - - +
18A GLN* 3.0 22.6 + - + +
55A ILE* 5.3 7.6 - - + -
59A ILE* 4.9 16.2 - - + -
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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 LEU* 2.8 29.5 + - + +
12A ARG* 3.3 22.3 + - - +
14A ILE* 1.3 75.9 - - - +
16A ALA* 1.3 62.2 + - - +
18A GLN* 3.3 8.8 + - - +
19A HIS* 3.2 31.8 + - + +
59A ILE* 3.4 30.8 - - + +
63A GLN* 2.9 36.3 + - - +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 2.9 16.6 + - - +
13A ALA* 3.7 6.1 - - - +
15A GLU* 1.3 74.8 - - - +
17A GLN* 1.3 64.7 + - + +
19A HIS* 3.1 15.1 + - - +
20A LEU* 3.1 24.1 + - + +
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.0 30.3 + - + +
14A ILE* 3.8 15.8 - - - +
15A GLU 3.3 0.2 - - - -
16A ALA* 1.3 75.1 - - + +
18A GLN* 1.3 60.8 + - - +
20A LEU* 3.1 16.3 + - + +
21A LEU* 2.8 34.9 + - + +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.0 14.2 + - - +
15A GLU* 3.5 12.1 - - - +
16A ALA 3.2 0.2 - - - -
17A GLN* 1.3 76.1 - - - +
19A HIS* 1.3 57.6 + - + +
21A LEU* 3.3 23.7 + - - +
22A GLN* 2.9 58.0 + - + +
52A THR* 4.0 14.0 + - - +
55A ILE* 3.5 38.3 - - + +
56A HIS* 4.6 9.8 + - + +
59A ILE* 4.6 11.7 - - + -
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.2 26.2 + - + +
16A ALA* 3.1 14.2 + - - +
18A GLN* 1.3 78.8 - - + +
20A LEU* 1.3 62.4 + - + +
22A GLN* 3.3 7.1 + - - +
23A LEU* 3.1 30.6 + - + +
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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 ALA 3.1 14.8 + - - +
17A GLN* 3.1 20.1 + - + +
19A HIS* 1.3 77.4 - - + +
21A LEU* 1.3 62.0 + - - +
23A LEU* 3.0 28.8 + - + +
24A THR* 3.1 22.0 + - + +
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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 GLN* 2.8 17.8 + - + +
18A GLN* 3.4 34.3 - - - +
20A LEU* 1.3 76.9 - - - +
22A GLN* 1.3 60.7 + - - +
24A THR* 2.7 27.3 + - - +
25A VAL* 3.0 23.3 + - + +
55A ILE* 5.1 6.1 - - + -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 2.9 39.3 + - + +
19A HIS* 3.8 6.1 - - - +
20A LEU 3.3 0.2 - - - -
21A LEU* 1.3 81.9 - - - +
23A LEU* 1.3 59.6 + - + +
25A VAL* 3.4 20.9 + - - +
26A TRP* 3.0 27.9 + - - +
48A ILE* 4.9 4.2 - - - +
52A THR* 3.0 34.1 + - + +
56A HIS* 5.7 2.7 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 3.1 20.1 + - + +
20A LEU* 3.0 25.4 + - + +
22A GLN* 1.3 76.8 - - + +
24A THR* 1.3 64.7 + - + +
26A TRP* 3.4 13.9 + - + +
27A ALA* 3.1 23.2 + - - +
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Residues in contact with THR 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 15.6 + - + +
21A LEU* 2.7 29.3 + - - +
23A LEU* 1.3 75.1 - - + +
25A VAL* 1.3 61.7 + - - +
27A ALA* 3.4 6.5 + - - +
28A ILE* 2.9 44.5 + - - +
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.0 26.5 + - + +
22A GLN* 3.6 20.4 - - - +
24A THR* 1.3 80.6 + - - +
26A TRP* 1.3 64.6 + - - +
28A ILE* 3.3 9.5 + - + +
29A LYS* 3.0 46.9 + - + +
44A TRP* 4.4 10.0 - - + -
48A ILE* 4.1 38.4 - - + -
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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 GLN 3.0 17.3 + - - +
23A LEU* 3.6 14.1 - - + +
24A THR 3.3 0.2 - - - -
25A VAL* 1.3 79.4 - - - +
27A ALA* 1.3 71.7 + - + +
29A LYS* 3.4 11.8 + - + +
30A GLN* 3.1 64.6 + - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.1 17.0 + - - +
24A THR* 3.7 7.2 - - - +
25A VAL 3.3 0.2 - - - -
26A TRP* 1.3 86.3 - - + +
28A ILE* 1.3 67.6 + - + +
30A GLN* 3.0 8.0 + - - +
31A LEU* 2.9 30.7 + - + +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 2.9 33.9 + - - +
25A VAL* 3.5 9.0 - - + +
27A ALA* 1.3 77.0 - - + +
29A LYS* 1.3 57.8 + - - +
31A LEU* 3.1 16.0 + - + +
32A GLN* 2.9 48.6 + - + +
44A TRP* 3.8 29.6 - - + -
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Residues in contact with LYS 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 VAL* 3.0 36.1 + - + +
26A TRP* 3.6 13.0 - - + +
27A ALA 3.2 0.4 - - - -
28A ILE* 1.3 75.4 - - - +
30A GLN* 1.3 60.6 + - + +
32A GLN* 3.2 11.2 + - - +
33A ALA* 2.8 32.4 + - - +
38A ARG* 3.7 26.0 - - - +
44A TRP* 4.2 7.2 - - + -
45A ASP* 3.4 30.8 + - - +
48A ILE* 5.5 3.0 - - - +
49A ASN* 4.8 13.1 + - - +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 3.1 60.7 + - + +
27A ALA* 3.0 8.0 + - - +
29A LYS* 1.3 77.2 - - - +
31A LEU* 1.3 63.8 + - + +
33A ALA* 3.3 10.0 + - - +
34A ARG* 3.3 18.7 + - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 2.9 20.1 + - + +
28A ILE* 3.4 17.0 - - + +
30A GLN* 1.3 78.0 - - + +
32A GLN* 1.3 62.4 + - + +
34A ARG* 3.1 22.6 - - + +
35A SER* 4.1 1.9 + - - -
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 2.9 35.0 + - + +
29A LYS* 3.4 11.9 - - - +
31A LEU* 1.3 72.1 - - + +
33A ALA* 1.3 58.9 + - - +
34A ARG 2.8 11.4 + - - -
35A SER* 2.9 26.0 + - - -
36A GLY 3.7 3.4 + - - +
37A GLY 5.4 0.5 - - - +
38A ARG* 2.7 42.0 + - - +
41A TRP* 3.2 55.8 + - + +
44A TRP* 4.1 10.0 - - - -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS 2.8 19.1 + - - +
30A GLN* 3.3 11.0 + - - +
32A GLN* 1.3 72.9 - - - +
34A ARG* 1.3 62.8 + - - +
35A SER 3.4 0.2 - - - -
36A GLY* 3.2 24.1 + - - +
38A ARG* 4.0 13.8 - - + +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLN 3.3 8.9 + - - +
31A LEU* 3.1 19.4 + - + +
32A GLN 2.8 2.0 + - - -
33A ALA* 1.3 79.2 - - - +
35A SER* 1.3 62.4 + - - +
36A GLY* 3.3 1.2 + - - -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 4.1 1.5 + - - -
32A GLN* 2.9 20.3 + - - -
34A ARG* 1.3 79.9 - - - +
36A GLY* 1.3 58.4 + - - +
37A GLY 5.3 1.7 + - - -
41A TRP* 5.7 2.1 + - - -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN 3.7 1.2 + - - +
33A ALA* 3.2 26.7 - - - +
34A ARG 3.2 4.1 - - - -
35A SER* 1.3 84.1 + - - +
37A GLY* 1.3 67.4 + - - +
38A ARG* 3.7 0.9 + - - +
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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