Contacts of the helix formed by residues 2 - 30 (chain A) in PDB entry 1CE0
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 LEU 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ARG* 1.3 78.0 - - - +
3A LEU* 1.3 57.3 + - + +
5A ARG* 3.8 11.3 - - - +
6A ILE* 3.0 28.8 + - - +
2B LEU* 3.8 17.0 - - + +
3B LEU* 3.2 59.5 - - + -
6B ILE* 4.4 15.9 - - + +
2C LEU* 3.6 34.1 - - + +
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Residues in contact with LEU 3 (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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1A ARG 2.9 3.2 + - - +
2A LEU* 1.3 74.9 - - + +
4A GLN* 1.3 61.5 + - - +
5A ARG 3.1 0.2 - - - -
6A ILE* 3.0 23.7 - - + +
7A LYS* 3.1 13.7 + - - +
2C LEU* 3.1 35.9 - - + -
5C ARG* 3.2 31.5 + - - +
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Residues in contact with GLN 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ARG* 2.7 36.6 + - - +
3A LEU* 1.3 75.7 - - - +
5A ARG* 1.3 63.2 + - + +
7A LYS* 4.1 6.7 - - - +
8A GLN* 3.3 25.5 + - - +
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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
----------------------------------------------------------
1A ARG* 2.7 79.6 + - + +
2A LEU* 3.8 6.7 - - - +
4A GLN* 1.3 84.6 - - + +
6A ILE* 1.3 59.0 + - - +
8A GLN* 3.9 15.1 - - - +
9A GLN* 3.1 26.7 + - - +
3B LEU* 3.6 12.7 + - - +
6B ILE* 3.8 16.3 - - + +
7B LYS* 3.7 28.7 - - - +
10B GLU* 2.8 46.2 + - - +
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Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 3.0 15.9 + - - +
3A LEU* 3.0 28.7 - - + +
5A ARG* 1.3 75.1 - - - +
7A LYS* 1.3 60.3 + - - +
9A GLN* 3.3 4.9 + - + +
10A GLU* 2.9 45.6 + - + +
6B ILE* 4.0 14.8 - - + +
2C LEU* 3.9 14.6 - - + +
5C ARG* 3.2 57.4 - - + +
6C ILE* 3.5 23.3 - - + +
9C GLN* 4.8 4.5 - - + -
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU 3.5 12.3 - - - +
4A GLN* 4.1 7.2 - - - +
5A ARG 3.3 0.2 - - - -
6A ILE* 1.3 82.4 - - - +
8A GLN* 1.3 56.3 + - - +
10A GLU* 3.1 15.1 + - - +
11A ASP* 2.9 54.0 + - - +
5C ARG* 3.8 11.4 - - - +
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Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.3 18.7 + - - +
5A ARG* 3.9 22.3 - - - +
7A LYS* 1.3 79.2 - - - +
9A GLN* 1.3 60.8 + - - +
11A ASP* 3.8 9.5 - - - +
12A LYS* 3.0 31.9 + - + +
10B GLU* 4.6 6.3 - - + +
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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 ARG 3.1 19.5 + - - +
6A ILE* 3.6 8.3 - - + +
7A LYS 3.2 0.2 - - - -
8A GLN* 1.3 76.4 - - - +
10A GLU* 1.3 60.2 + - - +
12A LYS* 3.4 7.2 + - - +
13A LEU* 2.8 29.1 + - - +
6B ILE* 5.8 4.3 - - + +
9B GLN* 2.7 49.3 + - + +
10B GLU* 3.5 22.9 - - + +
13B LEU* 3.3 27.8 - - - +
9C GLN* 3.1 22.5 + - + +
13C LEU* 4.7 2.0 - - - +
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 2.9 26.5 + - + +
7A LYS* 3.1 10.8 + - + +
9A GLN* 1.3 75.4 - - - +
11A ASP* 1.3 66.0 + - - +
13A LEU* 3.5 2.3 + - - +
14A GLU* 3.1 25.3 + - - +
5C ARG* 2.9 58.5 + - - +
8C GLN* 4.9 4.0 - - - +
9C GLN* 3.5 28.9 + - + +
12C LYS* 5.4 0.3 - - - -
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 2.9 54.8 + - - +
8A GLN* 3.8 7.9 - - - +
10A GLU* 1.3 75.5 - - - +
12A LYS* 1.3 67.5 + - - +
14A GLU* 3.0 8.6 + - - +
15A GLU* 3.0 35.6 + - - +
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Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 3.0 21.3 + - + +
9A GLN* 3.5 9.6 - - - +
10A GLU 3.3 0.2 - - - -
11A ASP* 1.3 79.4 - - - +
13A LEU* 1.3 56.9 + - - +
15A GLU* 3.2 16.6 + - + +
16A THR* 2.9 30.8 + - - -
10B GLU 5.9 0.2 - - - -
13B LEU* 3.5 28.7 - - + -
14B GLU* 3.0 30.9 + - - -
17B LEU* 3.6 18.4 - - + +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN 2.8 18.4 + - - +
10A GLU 3.9 0.9 - - - +
11A ASP 3.2 0.2 - - - -
12A LYS* 1.3 73.2 - - - +
14A GLU* 1.3 61.7 + - - +
16A THR* 4.1 10.8 - - + -
17A LEU* 3.0 27.6 + - + +
13B LEU* 3.9 15.4 - - + +
9C GLN* 3.2 35.9 - - - +
12C LYS* 3.4 37.0 - - + -
13C LEU* 3.8 28.7 - - + +
16C THR* 3.9 18.8 - - + +
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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
----------------------------------------------------------
10A GLU 3.1 13.4 + - - +
11A ASP* 3.0 12.9 + - - +
13A LEU* 1.3 74.1 - - - +
15A GLU* 1.3 64.6 + - + +
17A LEU* 3.5 14.0 + - - +
18A SER* 3.2 20.4 + - - -
12C LYS* 2.5 34.6 + - - -
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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* 3.0 28.2 + - - +
12A LYS* 3.4 14.8 + - - +
14A GLU* 1.3 74.6 - - + +
16A THR* 1.3 64.2 + - - +
18A SER* 3.3 9.9 + - - -
19A LYS* 3.2 29.6 + - - +
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Residues in contact with THR 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 LYS 2.9 18.2 + - - -
13A LEU* 3.6 14.1 - - + -
15A GLU* 1.3 75.9 - - - +
17A LEU* 1.3 64.0 + - - +
19A LYS* 2.9 12.8 + - - +
20A ILE* 2.9 20.5 + - + +
13B LEU* 3.7 10.3 - - + +
16B THR* 4.4 7.0 - - + -
17B LEU* 3.4 22.4 - - + +
20B ILE* 3.4 29.4 - - + -
16C THR* 4.2 19.1 - - + -
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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 LEU* 3.0 19.7 + - + +
14A GLU* 3.7 16.2 - - - +
15A GLU 3.3 0.2 - - - -
16A THR* 1.3 76.8 - - - +
18A SER* 1.3 56.8 + - - +
20A ILE* 3.3 7.8 + - + +
21A TYR* 2.9 28.1 + - - +
12C LYS* 3.8 39.3 - - + +
16C THR* 3.4 31.6 - - + +
19C LYS* 4.7 20.9 - - + -
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 3.2 13.8 + - - -
15A GLU* 3.4 13.6 + - - -
16A THR 3.1 0.4 - - - -
17A LEU* 1.3 73.4 - - - +
19A LYS* 1.3 66.1 + - - +
21A TYR* 3.3 10.0 + - - +
22A HIS* 3.0 46.8 + - - -
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.6 16.8 - - - +
16A THR 2.9 9.5 + - - +
18A SER* 1.3 81.3 - - - +
20A ILE* 1.3 57.4 + - - +
22A HIS* 3.3 9.9 + - + +
23A LEU* 2.9 30.5 + - - +
17B LEU* 4.6 15.5 - - + -
20B ILE* 4.0 23.6 - - + -
21B TYR* 4.4 19.1 - - + -
24B GLU* 3.8 25.2 + - - +
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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 THR 2.9 20.2 + - - +
17A LEU* 3.4 12.3 - - + +
18A SER 3.3 0.2 - - - -
19A LYS* 1.3 76.4 - - - +
21A TYR* 1.3 57.6 + - - +
23A LEU* 3.1 8.5 + - + +
24A GLU* 2.8 48.3 + - - +
20B ILE* 3.3 34.8 - - + -
16C THR* 4.3 12.8 - - + -
19C LYS* 4.0 21.8 - - + -
20C ILE* 3.4 22.0 - - + -
23C LEU* 4.1 15.3 - - + -
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 2.9 13.5 + - - +
18A SER* 3.3 12.8 - - - +
19A LYS 3.2 0.2 - - - -
20A ILE* 1.3 77.3 - - - +
22A HIS* 1.3 87.4 + + - +
24A GLU* 3.2 17.9 + - - +
25A ASN* 3.0 56.5 + - - -
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.0 35.2 + - - -
19A LYS* 3.7 10.5 - - + +
21A TYR* 1.3 96.2 - + - +
23A LEU* 1.3 60.6 + - - +
25A ASN* 3.4 9.1 + - - +
26A GLU* 2.9 35.8 + - + +
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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 LYS 2.9 12.6 + - - +
20A ILE* 3.3 16.4 - - + +
22A HIS* 1.3 74.7 - - - +
24A GLU* 1.3 66.1 + - - +
26A GLU* 3.1 5.8 + - + +
27A ILE* 3.0 40.5 + - + +
20B ILE* 4.2 14.8 - - + +
23B LEU* 4.0 30.1 - - + -
24B GLU* 3.9 39.9 - - + +
27B ILE* 4.1 21.5 - - + -
23C LEU* 4.1 10.5 - - + -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 2.8 31.7 + - - +
21A TYR* 3.5 19.6 - - - +
23A LEU* 1.3 76.2 - - - +
25A ASN* 1.3 59.3 + - - +
27A ILE* 3.9 1.4 - - - +
28A ALA* 3.0 29.5 + - - +
19C LYS* 4.0 22.8 - - - +
22C HIS* 6.0 2.1 - - + -
23C LEU* 3.6 30.3 - - + +
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Residues in contact with ASN 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 TYR* 3.0 61.0 + - - +
22A HIS* 3.5 11.9 + - - +
23A LEU 3.1 0.2 - - - -
24A GLU* 1.3 78.2 - - - +
26A GLU* 1.3 60.4 + - + +
28A ALA* 3.3 7.3 + - - +
29A ARG* 3.1 28.6 + - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 2.9 24.0 + - + +
23A LEU* 3.1 8.5 + - + +
25A ASN* 1.3 78.9 - - + +
27A ILE* 1.3 57.4 + - - +
29A ARG* 3.3 18.6 + - - +
30A VAL* 2.9 33.6 + - - +
27B ILE* 4.2 22.0 - - + -
31B LYS* 2.7 38.9 + - - +
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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
----------------------------------------------------------
23A LEU* 3.0 24.6 + - + +
24A GLU* 4.1 3.4 - - - +
26A GLU* 1.3 76.3 - - - +
28A ALA* 1.3 57.5 + - - +
30A VAL* 4.5 2.5 - - + -
31A LYS* 3.1 37.5 + - + +
27B ILE* 3.4 25.1 - - + -
23C LEU* 3.5 30.7 - - + +
26C GLU* 4.1 27.6 - - + +
27C ILE* 3.6 32.1 - - + +
30C VAL* 4.8 4.9 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 3.0 20.1 + - - +
25A ASN* 3.6 8.5 - - - +
26A GLU 3.2 0.2 - - - -
27A ILE* 1.3 76.3 - - - +
29A ARG* 1.3 55.3 + - - +
31A LYS* 2.7 29.4 - - - +
32A LYS* 4.1 8.7 - - - +
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN 3.1 15.1 + - - +
26A GLU* 3.7 18.5 + - - +
28A ALA* 1.3 77.7 - - - +
30A VAL* 1.3 71.3 + - - +
31A LYS 3.1 3.3 - - - +
32A LYS 4.0 1.3 - - - +
33A LEU* 2.8 41.4 - - + +
31B LYS* 3.2 40.6 - - - +
36B GLU* 2.5 32.5 + - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU 2.9 18.8 + - - +
27A ILE* 4.4 4.5 - - - +
29A ARG* 1.3 85.9 - - - +
31A LYS* 1.3 60.7 + - + +
33A LEU* 3.2 29.7 - - - +
34A LEU* 3.5 10.7 - - + +
27B ILE* 4.6 7.6 - - + -
30B VAL* 3.5 27.1 - - + -
31B LYS* 3.4 34.8 - - + -
34B LEU* 3.7 15.3 - - + -
30C VAL* 4.0 15.3 - - + -
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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