Contacts of the helix formed by residues 6 - 36 (chain A) in PDB entry 1IHQ
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 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 1.3 72.4 - - - +
7A LEU* 1.3 54.9 + - - +
8A GLU* 2.8 13.0 - - - +
9A ALA* 2.5 43.4 + - - +
10A VAL* 2.7 15.5 + - - +
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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
----------------------------------------------------------
2A ALA 6.6 0.2 - - - -
4A SER* 5.0 7.6 - - - +
5A SER 2.9 12.0 - - - +
6A SER* 1.3 77.8 - - - +
8A GLU* 1.3 49.8 + - - +
10A VAL* 3.4 10.8 - - + +
11A ARG* 2.5 45.6 + - + +
4B SER* 4.0 14.6 - - - +
5B SER* 3.3 56.3 - - - +
6B SER 4.3 4.0 - - - +
7B LEU* 4.2 20.0 - - + +
10B VAL* 5.3 0.2 - - + -
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 2.7 8.2 + - - +
7A LEU* 1.3 78.5 - - - +
9A ALA* 1.3 67.0 + - + +
11A ARG* 3.7 9.6 - - - +
12A ARG* 2.8 31.9 + - - +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 2.5 32.9 + - - +
8A GLU* 1.3 80.9 - - + +
10A VAL* 1.3 56.3 + - - +
12A ARG* 3.4 6.6 + - - +
13A LYS* 2.9 35.9 + - + +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER 5.4 0.2 - - - +
6A SER* 2.7 14.7 + - - +
7A LEU* 3.4 22.7 - - + +
9A ALA* 1.3 71.9 - - - +
11A ARG* 1.3 59.3 + - + +
12A ARG 3.1 0.4 - - - -
13A LYS* 3.6 5.0 - - - +
14A ILE* 2.7 37.1 + - - +
7B LEU* 4.3 17.0 - - + +
10B VAL* 3.4 25.7 - - + +
11B ARG* 4.8 12.1 - - - +
14B ILE* 3.9 29.3 - - + +
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 2.5 34.1 + - + +
8A GLU* 3.7 7.6 - - - +
9A ALA 3.3 0.2 - - - -
10A VAL* 1.3 75.6 - - + +
12A ARG* 1.3 58.9 + - - +
14A ILE* 3.0 12.8 - - + +
15A ARG* 3.0 47.1 + - + +
5B SER* 3.9 24.5 + - - +
10B VAL* 4.3 2.2 - - + -
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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
----------------------------------------------------------
8A GLU 2.8 18.5 + - - +
9A ALA* 3.7 6.1 - - - +
10A VAL 3.1 0.2 - - - -
11A ARG* 1.3 76.2 - - - +
13A LYS* 1.3 74.0 + - - +
14A ILE 3.2 0.2 - - - -
15A ARG* 4.4 5.6 - - + +
16A SER* 2.8 55.2 + - - +
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 2.9 23.3 + - + +
10A VAL* 3.6 3.8 - - - +
12A ARG* 1.3 97.0 + - - +
14A ILE* 1.3 58.5 + - - +
16A SER* 4.4 5.5 + - - -
17A LEU* 2.8 44.3 + - + +
14B ILE* 3.5 28.3 - - + -
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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 VAL 2.7 14.9 + - - +
11A ARG* 3.0 20.9 - - + +
13A LYS* 1.3 76.4 - - - +
15A ARG* 1.3 69.6 + - + +
18A GLN* 2.8 43.8 + - + +
10B VAL* 3.5 28.5 - - + +
13B LYS* 3.5 33.7 - - + -
14B ILE* 3.8 12.8 - - + +
17B LEU* 3.3 19.5 - - + +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 3.0 34.8 + - + +
12A ARG* 4.1 5.4 - - - +
14A ILE* 1.3 83.6 - - + +
16A SER* 1.3 58.6 + - - +
18A GLN* 3.4 19.0 + - - +
19A GLU* 3.0 71.1 + - - +
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.8 46.2 + - - +
13A LYS* 4.1 8.5 + - - -
15A ARG* 1.3 74.9 - - - +
17A LEU* 1.3 67.5 + - - +
18A GLN 3.0 1.6 - - - -
19A GLU* 2.9 9.5 + - - +
20A GLN* 2.9 22.6 + - - +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 2.8 34.8 + - + +
14A ILE 4.0 0.9 - - - +
16A SER* 1.3 77.7 - - - +
18A GLN* 1.3 52.9 + - - +
20A GLN* 3.2 3.4 + - - +
21A ASN* 2.7 40.0 + - - -
14B ILE* 3.2 44.2 - - + +
17B LEU* 3.6 10.5 - - + -
18B GLN* 3.7 14.8 - - + +
21B ASN* 3.0 46.2 + - + +
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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* 2.8 25.8 + - + +
15A ARG* 3.4 23.7 + - - +
17A LEU* 1.3 77.3 - - - +
19A GLU* 1.3 84.2 + - - +
21A ASN* 3.0 17.0 + - + +
22A TYR* 3.0 21.8 + - + +
17B LEU* 3.7 18.5 - - + +
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.0 49.6 + - - +
16A SER* 2.9 10.8 + - - +
18A GLN* 1.3 92.1 - - - +
20A GLN* 1.3 52.9 + - - +
22A TYR* 3.4 6.1 + - - +
23A HIS* 2.8 57.4 + - + +
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER 2.9 12.4 + - - +
17A LEU* 3.5 5.3 - - - +
19A GLU* 1.3 75.0 - - - +
21A ASN* 1.3 57.3 + - - +
23A HIS* 3.9 7.4 - - - -
24A LEU* 2.7 62.8 + - + +
21B ASN* 2.6 46.4 + - - +
22B TYR* 6.3 0.2 - - - -
25B GLU* 4.6 10.1 + - - +
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Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 2.7 7.1 + - - +
18A GLN* 3.0 11.4 + - + +
20A GLN* 1.3 78.0 - - - +
22A TYR* 1.3 51.9 + - + +
25A GLU* 2.7 40.1 + - - +
17B LEU* 2.7 32.1 + - + +
20B GLN* 2.6 46.6 + - - +
21B ASN* 2.6 38.6 - - - +
24B LEU* 3.4 6.6 - - - +
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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
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18A GLN* 3.0 21.4 + - + +
19A GLU* 3.8 7.2 - - - +
21A ASN* 1.3 75.2 - - + +
23A HIS* 1.3 61.8 + - + +
25A GLU* 3.8 24.7 - - - -
26A ASN* 2.6 65.2 + - - +
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Residues in contact with HIS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 2.8 44.8 + - + +
20A GLN* 3.7 8.5 - - - +
22A TYR* 1.3 79.7 + - - +
24A LEU* 1.3 60.5 + - + +
26A ASN* 4.3 3.0 + - - +
27A GLU* 2.7 38.5 + - - +
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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
----------------------------------------------------------
20A GLN* 2.7 58.4 + - + +
23A HIS* 1.3 82.6 - - + +
25A GLU* 1.3 58.6 + - - +
27A GLU* 3.7 9.0 - - + +
28A VAL* 2.7 26.9 + - - +
21B ASN* 3.7 15.0 - - - +
24B LEU* 2.9 35.7 - - + +
25B GLU* 3.8 17.5 - - + +
28B VAL* 5.1 8.7 - - + -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN 2.7 23.3 + - - +
22A TYR* 3.8 30.6 - - - -
24A LEU* 1.3 79.0 - - - +
26A ASN* 1.3 64.9 + - - +
28A VAL* 3.6 2.0 - - - +
29A ALA* 2.8 32.9 + - + +
20B GLN* 4.4 10.4 + - - +
24B LEU* 3.4 15.7 - - + +
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 2.6 56.8 + - - +
23A HIS* 4.3 2.4 + - - +
25A GLU* 1.3 84.2 - - - +
27A GLU* 1.3 61.0 + - - +
29A ALA* 3.9 4.1 - - - +
30A ARG* 3.0 30.7 + - - +
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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 HIS 2.7 25.4 + - - +
24A LEU* 3.9 8.6 - - + +
25A GLU 3.3 0.2 - - - -
26A ASN* 1.3 75.9 - - - +
28A VAL* 1.3 55.9 + - - +
30A ARG* 3.3 10.1 + - - +
31A LEU* 2.7 40.3 + - + +
28B VAL* 4.3 13.2 - - + -
32B LYS* 5.5 6.5 - - - -
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 2.7 18.6 + - - +
25A GLU* 3.6 5.8 - - + +
27A GLU* 1.3 73.2 - - - +
29A ALA* 1.3 67.3 + - + +
31A LEU* 2.6 22.0 + - - +
32A LYS* 2.7 40.9 + - - +
24B LEU* 3.1 26.0 - - + -
27B GLU* 4.1 3.1 - - + -
28B VAL* 3.0 46.9 - - + +
31B LEU* 3.4 13.7 - - + -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 2.8 22.1 + - + +
26A ASN* 3.9 5.6 - - - +
28A VAL* 1.3 86.2 - - + +
30A ARG* 1.3 64.5 - - - +
31A LEU 2.9 0.2 + - - -
32A LYS* 3.1 9.9 + - - +
33A LYS* 3.0 20.3 + - - +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN 3.0 18.7 + - - +
27A GLU* 3.8 9.4 - - - +
29A ALA* 1.3 79.5 - - - +
31A LEU* 1.3 51.9 + - - +
33A LYS* 3.5 8.5 + - + +
34A LEU* 2.7 59.4 + - + +
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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 GLU* 2.7 17.7 + - + +
28A VAL 2.6 19.9 + - - +
30A ARG* 1.3 69.7 - - - +
32A LYS* 1.3 52.3 + - - +
33A LYS 2.9 0.7 - - - -
34A LEU* 2.5 23.0 + - + -
35A VAL* 2.4 60.8 + - + +
28B VAL* 3.6 14.1 - - + -
31B LEU* 3.4 12.8 - - + -
32B LYS* 3.4 47.8 - - + +
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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 VAL* 2.7 60.1 + - + +
29A ALA* 3.7 7.9 - - - +
31A LEU* 1.3 72.0 - - - +
33A LYS* 1.3 61.4 + - - +
35A VAL* 3.1 11.2 - - + +
36A GLY* 3.1 24.3 + - - -
27B GLU* 4.1 24.6 + - - -
31B LEU* 3.4 22.6 - - + +
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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 ALA 3.0 14.4 + - - +
30A ARG* 3.7 10.1 - - + +
31A LEU 2.9 0.8 - - - -
32A LYS* 1.3 82.5 + - - +
34A LEU* 1.3 62.7 + - - +
36A GLY* 4.2 7.4 + - - -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 2.7 43.7 + - + +
31A LEU* 2.5 28.4 + - + +
33A LYS* 1.3 73.2 - - - +
35A VAL* 1.3 72.6 + - + +
36A GLY* 3.5 0.5 + - - -
37B GLU* 5.5 4.5 - - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.4 60.0 + - + +
32A LYS* 3.1 19.3 - - - +
34A LEU* 1.3 74.0 - - + +
36A GLY* 1.3 66.6 + - - +
37A GLU* 2.5 24.0 + - + +
31B LEU* 4.1 4.7 - - + -
32B LYS* 5.4 2.2 - - - -
35B VAL* 3.1 49.4 - - + -
37B GLU* 4.5 14.8 - - + +
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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 LYS 3.1 13.2 + - - -
33A LYS* 4.5 6.5 - - - -
34A LEU 3.3 2.8 - - - -
35A VAL* 1.3 83.0 - - - +
37A GLU* 1.3 66.5 + - - +
38A ARG 4.1 3.3 - - - +
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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