Contacts of the helix formed by residues 2 - 35 (chain A) in PDB entry 6LVN
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 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 1.3 69.3 + - - +
4A GLY 3.2 5.4 - - - +
5A ILE* 3.1 38.4 + - + +
6A ASN* 3.0 45.5 + - - +
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Residues in contact with SER 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 1.3 85.2 - - - +
4A GLY* 1.3 55.4 + - - +
6A ASN* 3.4 13.5 + - - +
7A ALA* 2.9 29.1 + - - +
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Residues in contact with GLY 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE 3.2 3.4 - - - +
3A SER* 1.3 78.1 - - - +
5A ILE* 1.3 57.2 + - - +
7A ALA* 3.5 6.3 + - - +
8A SER* 2.9 32.7 + - - -
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Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 3.1 37.5 + - + +
4A GLY* 1.3 74.8 - - - +
6A ASN* 1.3 64.8 + - - +
8A SER* 3.2 7.4 + - - -
9A VAL* 2.9 34.1 + - + +
33C LEU* 3.5 45.1 - - + +
34C GLN* 5.6 0.2 - - - -
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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 ILE* 3.0 31.3 + - - +
3A SER* 3.8 15.8 + - - +
5A ILE* 1.3 78.8 - - - +
7A ALA* 1.3 62.0 + - - +
9A VAL* 3.2 11.0 + - - +
10A VAL* 3.0 27.3 + - + +
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Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER 2.9 19.3 + - - +
4A GLY* 3.8 7.0 - - - +
6A ASN* 1.3 75.6 - - - +
8A SER* 1.3 57.4 + - - +
10A VAL* 3.3 6.4 + - - +
11A ASN* 2.8 45.5 + - - +
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Residues in contact with SER 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLY 2.9 19.7 + - - -
5A ILE* 3.5 8.5 - - - -
7A ALA* 1.3 76.3 - - - +
9A VAL* 1.3 57.8 + - - +
11A ASN* 4.1 6.2 - - - +
12A ILE* 2.9 48.0 + - - +
33C LEU* 4.6 9.9 - - - -
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 2.9 23.9 + - + +
6A ASN* 3.2 10.9 + - - +
8A SER* 1.3 76.6 - - - +
10A VAL* 1.3 66.9 + - + +
13A GLN* 3.0 24.1 + - + +
30C LEU* 3.7 24.3 - - + +
33C LEU* 3.9 26.7 - - + -
34C GLN* 4.0 34.8 - - + +
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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
----------------------------------------------------------
6A ASN* 3.0 16.5 + - + +
7A ALA* 3.7 9.6 - - - +
9A VAL* 1.3 79.4 - - + +
11A ASN* 1.3 72.3 + - - +
13A GLN* 3.3 7.2 + - - +
14A LYS* 3.0 32.7 + - + +
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 2.8 30.5 + - - +
8A SER* 4.1 5.3 - - - +
10A VAL* 1.3 84.8 - - - +
12A ILE* 1.3 64.4 + - + +
14A LYS* 3.1 24.9 + - - +
15A GLU* 3.0 29.6 + - + +
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 2.9 28.2 + - - +
11A ASN* 1.3 77.2 - - + +
13A GLN* 1.3 57.7 + - - +
15A GLU* 3.2 9.2 + - + +
16A ILE* 2.9 36.1 + - + +
26C LEU* 4.3 26.7 - - + +
29C SER* 6.0 4.5 - - - -
30C LEU* 3.7 22.7 - - + +
33C LEU* 4.2 23.6 - - + -
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.0 19.1 + - + +
10A VAL* 3.5 7.2 - - - +
12A ILE* 1.3 77.0 - - - +
14A LYS* 1.3 62.9 + - - +
16A ILE* 3.2 13.5 + - - +
17A ASP* 3.0 50.5 + - - +
27C ASN* 3.8 14.0 + - - +
30C LEU* 3.4 22.5 - - + +
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Residues in contact with LYS 14 (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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10A VAL* 3.0 28.2 + - + +
11A ASN* 3.1 24.5 + - - +
13A GLN* 1.3 75.4 - - - +
15A GLU* 1.3 70.3 + - - +
17A ASP* 3.3 12.7 + - - +
18A ARG* 3.0 29.1 + - + +
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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 ASN* 3.0 18.3 + - + +
12A ILE* 3.2 9.4 + - + +
14A LYS* 1.3 87.1 + - - +
16A ILE* 1.3 60.3 + - - +
18A ARG* 3.2 26.4 + - - +
19A LEU* 2.9 38.1 + - + +
26C LEU* 5.5 5.2 - - + -
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 2.9 20.9 + - + +
13A GLN* 3.2 24.2 + - - +
15A GLU* 1.3 76.4 - - - +
17A ASP* 1.3 62.0 + - - +
19A LEU* 3.2 9.6 + - - +
20A ASN* 3.0 36.2 + - - +
23C ALA* 4.2 11.0 - - + +
26C LEU* 3.7 40.2 - - + +
27C ASN* 3.6 41.1 - - - +
30C LEU* 4.1 7.6 - - + -
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 40.3 + - - +
14A LYS* 3.5 12.1 - - - +
16A ILE* 1.3 75.5 - - - +
18A ARG* 1.3 62.3 + - - +
20A ASN* 3.2 14.4 + - - +
21A GLU* 3.0 22.3 + - - +
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Residues in contact with ARG 18 (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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14A LYS 3.0 16.9 + - - +
15A GLU* 3.2 29.8 + - - +
17A ASP* 1.3 75.6 - - + +
19A LEU* 1.3 60.0 + - + +
21A GLU* 3.2 23.5 + - - +
22A VAL* 2.9 39.4 + - + +
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Residues in contact with LEU 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 21.2 + - + +
16A ILE* 3.2 9.4 + - - +
18A ARG* 1.3 77.5 - - + +
20A ASN* 1.3 63.9 + - - +
22A VAL* 3.2 12.5 + - + +
23A ALA* 3.0 21.7 + - - +
19C LEU* 4.1 29.8 - - + +
22C VAL* 3.7 30.5 - - + -
23C ALA* 4.7 11.7 - - + +
26C LEU* 3.8 18.8 - - + -
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.0 33.7 + - - +
17A ASP* 3.2 14.0 + - - +
19A LEU* 1.3 74.3 - - - +
21A GLU* 1.3 62.9 + - - +
23A ALA* 3.2 9.5 + - - +
24A LYS* 3.0 43.7 + - - +
20C ASN* 4.9 7.8 - - - +
23C ALA* 3.8 18.1 - - - +
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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 ASP 3.0 13.1 + - - +
18A ARG* 3.5 24.4 + - - +
20A ASN* 1.3 77.6 - - - +
22A VAL* 1.3 62.3 + - + +
24A LYS* 3.2 13.8 + - + +
25A ASN* 3.0 41.5 + - - +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 2.9 27.9 + - + +
19A LEU* 3.2 15.2 + - + +
21A GLU* 1.3 77.2 - - + +
23A ALA* 1.3 57.8 + - - +
25A ASN* 3.2 8.3 + - - +
26A LEU* 2.9 40.3 + - + +
19C LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 23 (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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19A LEU 3.0 13.3 + - - +
20A ASN* 3.2 12.5 + - - +
22A VAL* 1.3 76.8 - - - +
24A LYS* 1.3 64.0 + - + +
26A LEU* 3.3 5.3 + - - +
27A ASN* 3.0 22.9 + - - +
16C ILE* 4.1 18.9 - - + +
19C LEU* 4.3 19.7 - - + +
20C ASN* 4.3 17.0 - - - +
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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 ASN* 3.0 35.6 + - - +
21A GLU* 3.2 14.8 + - + +
23A ALA* 1.3 77.0 - - + +
25A ASN* 1.3 65.8 + - - +
27A ASN* 3.2 10.0 + - - +
28A GLU* 3.0 24.0 + - - +
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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
----------------------------------------------------------
21A GLU* 3.0 37.4 + - - +
22A VAL* 3.8 6.7 - - + +
24A LYS* 1.3 79.9 - - - +
26A LEU* 1.3 59.9 + - + +
28A GLU* 3.2 9.3 + - - +
29A SER* 3.0 31.2 + - - -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 2.9 25.7 + - + +
23A ALA 3.8 4.0 - - - +
24A LYS 3.3 0.2 - - - -
25A ASN* 1.3 77.0 - - + +
27A ASN* 1.3 57.2 + - - +
29A SER* 3.3 11.1 + - - +
30A LEU* 2.9 30.0 + - - +
12C ILE* 4.3 18.3 - - + +
15C GLU* 5.5 5.2 - - + -
16C ILE* 3.8 23.6 - - + +
19C LEU* 3.8 29.4 - - + -
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.0 14.4 + - - +
24A LYS* 3.2 12.1 + - - +
26A LEU* 1.3 76.2 - - - +
28A GLU* 1.3 62.1 + - - +
30A LEU* 3.2 12.1 + - - +
31A ILE* 3.0 47.5 + - - +
13C GLN* 5.3 2.3 - - - +
16C ILE* 3.6 13.6 - - + +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS 3.0 14.1 + - - +
25A ASN* 3.2 11.9 + - - +
27A ASN* 1.3 83.1 + - - +
29A SER* 1.3 56.8 + - - +
31A ILE* 3.2 16.3 + - + +
32A ASP* 3.0 41.3 + - - +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN 3.0 14.4 + - - -
26A LEU* 3.3 15.2 + - - +
28A GLU* 1.3 76.9 - - - +
30A LEU* 1.3 56.9 + - - +
32A ASP* 3.3 9.8 + - - +
33A LEU* 2.9 38.6 + - - +
12C ILE* 6.0 4.0 - - - -
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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 LEU 2.9 9.8 + - - +
27A ASN* 3.2 14.8 + - - +
29A SER* 1.3 74.1 - - - +
31A ILE* 1.3 65.7 + - + +
33A LEU* 3.1 4.3 + - + +
34A GLN* 3.0 39.8 + - - +
9C VAL* 3.5 44.0 - - + +
12C ILE* 3.8 26.8 - - + +
13C GLN* 3.5 35.9 - - + +
16C ILE* 4.1 14.6 - - + -
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.0 38.5 + - - +
28A GLU* 3.2 16.8 + - + +
30A LEU* 1.3 76.6 - - + +
32A ASP* 1.3 67.4 + - - +
34A GLN* 3.5 18.6 + - - +
35A GLU* 3.2 35.8 - - - +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.0 28.1 + - - +
29A SER* 3.7 10.4 - - - +
30A LEU 3.2 0.2 - - - -
31A ILE* 1.3 84.3 - - - +
33A LEU* 1.3 61.7 + - + +
35A GLU* 3.4 27.7 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 2.9 24.1 + - - +
30A LEU* 3.1 6.9 + - + +
32A ASP* 1.3 79.6 - - + +
34A GLN* 1.3 61.6 + - - +
35A GLU 3.3 6.6 + - - +
5C ILE* 3.4 39.5 - - + +
8C SER* 4.7 9.9 - - - -
9C VAL* 4.1 17.7 - - + -
12C ILE* 3.8 28.9 - - + -
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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 LEU* 3.0 30.6 + - - +
31A ILE* 3.5 17.9 + - - +
32A ASP 3.3 0.6 - - - -
33A LEU* 1.3 77.5 - - - +
35A GLU* 1.3 62.5 + - + +
5C ILE* 5.4 0.2 - - - -
9C VAL* 4.3 26.2 - - + +
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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 ILE* 3.2 36.7 + - - +
32A ASP* 3.4 22.5 + - - +
33A LEU 3.2 7.8 - - - +
34A GLN* 1.3 84.9 - - + +
5C ILE* 5.9 1.7 - - - +
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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