Contacts of the helix formed by residues 1 - 32 (chain B) in PDB entry 2G9J
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 MET 1 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.0 9.2 - - + -
0B GLY* 1.3 66.1 - - - -
2B ASP* 1.3 66.4 + - - +
3B ALA* 3.0 16.2 + - - -
4B ILE* 3.4 24.7 - - + +
5B LYS* 3.0 34.9 + - + +
270C ILE* 4.9 7.2 - - + -
273C GLU* 3.9 9.1 + - + +
274C LEU* 5.8 3.6 - - + -
277C ALA* 4.7 8.9 - - + +
278C LEU* 5.5 1.8 - - + -
274D LEU* 3.5 45.5 - - + +
275D ASP* 6.3 0.7 - - - -
278D LEU* 4.2 9.0 - - + -
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Residues in contact with ASP 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B GLY 2.9 11.8 + - - +
1B MET* 1.3 71.8 - - - +
3B ALA* 1.3 67.5 + - - +
5B LYS* 4.3 5.2 - - - -
6B LYS* 2.6 64.9 + - - +
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Residues in contact with ALA 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.0 11.8 + - - -
2B ASP* 1.3 80.5 - - - +
4B ILE* 1.3 59.4 + - - +
6B LYS* 4.2 1.2 - - - +
7B LYS* 2.9 39.4 + - - +
278D LEU* 3.5 30.7 - - + -
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Residues in contact with ILE 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.9 5.6 - - - -
4A ILE* 3.3 42.8 - - + -
1B MET* 3.4 28.3 - - + +
3B ALA* 1.3 73.2 - - - +
5B LYS* 1.3 63.8 + - + +
7B LYS* 4.1 6.5 - - - -
8B MET* 2.7 31.5 + - - +
278C LEU* 3.5 6.1 - - + -
281C MET* 3.3 33.2 - - + -
284C ILE* 4.3 2.9 - - + -
278D LEU* 3.4 24.7 - - + -
284D ILE* 4.2 7.2 - - + -
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Residues in contact with LYS 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B GLY* 4.8 5.8 - - - -
1B MET* 3.0 49.0 + - + +
2B ASP* 3.8 5.2 - - - +
4B ILE* 1.3 85.1 - - + +
6B LYS* 1.3 63.9 + - + +
8B MET* 3.7 9.6 - - - +
9B GLN* 3.3 17.7 + - - +
277C ALA* 3.0 37.2 + - + +
278C LEU* 5.5 0.2 - - - -
280C ASP* 5.4 2.4 - - - +
281C MET* 3.0 37.6 - - - +
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Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASP* 2.6 48.5 + - - +
3B ALA 4.2 1.1 - - - +
5B LYS* 1.3 79.5 - - + +
7B LYS* 1.3 60.2 + - - +
9B GLN* 3.3 17.7 + - - +
10B MET* 3.0 30.1 + - + +
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Residues in contact with LYS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 2.9 29.8 + - - +
4B ILE* 3.9 5.8 - - - +
6B LYS* 1.3 76.0 - - - +
8B MET* 1.3 53.9 + - - +
10B MET* 3.3 19.1 + - - +
11B LEU* 2.6 35.4 + - - +
278D LEU* 4.9 4.7 - - - -
281D MET* 4.4 8.3 - - + -
282D THR* 2.8 44.9 + - - +
283D SER* 4.1 0.9 - - - -
284D ILE* 3.3 38.6 - - + +
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Residues in contact with MET 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 2.7 23.3 + - + +
5B LYS* 3.7 9.9 - - - +
7B LYS* 1.3 69.7 - - - +
9B GLN* 1.3 65.4 + - + +
11B LEU* 3.1 19.1 - - + +
12B LYS* 2.9 61.0 + - - +
281C MET* 3.3 39.0 - - + +
284C ILE* 4.0 22.0 - - + -
284D ILE* 4.4 2.8 - - - +
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS 3.3 10.3 + - - +
6B LYS* 3.4 20.2 - - - +
8B MET* 1.3 84.2 - - + +
10B MET* 1.3 57.4 + - - +
12B LYS* 3.8 2.5 - - - +
13B LEU* 2.9 55.4 + - + +
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Residues in contact with MET 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 3.0 16.5 + - + +
7B LYS* 3.5 21.1 - - + +
9B GLN* 1.3 75.5 - - - +
11B LEU* 1.3 62.8 + - - +
13B LEU* 3.5 10.7 + - - +
14B ASP* 3.1 24.3 + - + +
284D ILE 6.1 0.2 - - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.4 40.6 - - + -
15A ASN* 3.9 8.1 - - - +
7B LYS 2.6 21.4 + - - +
8B MET* 3.1 27.6 - - + +
10B MET* 1.3 76.5 - - - +
12B LYS* 1.3 67.7 + - + +
14B ASP* 3.1 3.5 + - - +
15B ASN* 2.8 52.2 + - - +
284C ILE* 4.2 5.8 - - + -
284D ILE* 3.3 37.9 + - + +
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.8 3.1 - - + -
8B MET* 2.9 54.5 + - - +
9B GLN* 4.3 2.5 - - - +
11B LEU* 1.3 82.2 - - + +
13B LEU* 1.3 57.3 + - - +
15B ASN* 4.2 7.9 - - + +
16B TYR* 2.7 63.8 + - + +
283C SER* 3.1 31.7 + - - +
284C ILE* 3.9 4.6 - - - +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 2.9 49.9 + - + +
10B MET* 3.7 8.1 - - - +
12B LYS* 1.3 78.0 - - - +
14B ASP* 1.3 60.9 + - - +
16B TYR* 3.9 5.8 - - + +
17B HIS* 3.2 24.6 + - - +
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MET* 3.1 15.2 + - + +
11B LEU* 3.5 8.5 - - - +
13B LEU* 1.3 75.5 - - - +
15B ASN* 1.3 74.1 + - - +
17B HIS* 2.7 48.2 + - - -
18B LEU* 3.0 18.7 + - - +
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Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.2 36.6 + - - +
18A LEU* 4.4 11.7 - - + +
11B LEU* 2.8 50.9 + - - +
12B LYS* 4.2 9.6 - - + +
14B ASP* 1.3 85.9 + - - +
16B TYR* 1.3 52.8 + - + +
18B LEU* 3.2 17.5 + - - +
19B GLU* 2.7 39.1 + - - +
284D ILE* 5.1 0.6 + - - -
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Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 2.7 58.7 + - + +
13B LEU* 3.9 7.0 - - + +
15B ASN* 1.3 73.4 - - + +
17B HIS* 1.3 59.2 + - - +
19B GLU* 3.1 29.3 - - - +
20B ASN* 2.8 48.3 + - - +
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 3.2 10.6 + - - +
14B ASP* 2.7 54.0 + - - -
16B TYR* 1.3 78.6 - - - +
18B LEU* 1.3 66.7 + - + +
20B ASN* 3.8 6.8 - - - +
21B GLU* 3.0 31.4 + - - +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 29.8 - - + +
19A GLU* 4.1 23.1 - - + -
22A VAL* 3.9 26.1 - - + +
14B ASP* 3.0 22.6 + - - +
15B ASN* 3.3 20.2 - - - +
16B TYR 3.1 0.2 - - - -
17B HIS* 1.3 85.8 + - + +
19B GLU* 1.3 64.1 + - - +
21B GLU* 3.2 9.5 + - - +
22B VAL* 2.8 33.0 + - + +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.9 17.6 - - + +
15B ASN* 2.7 19.1 + - - +
16B TYR* 3.1 54.4 + - - +
18B LEU* 1.3 72.6 - - - +
20B ASN* 1.3 63.4 + - - +
22B VAL* 3.2 13.4 - - + +
23B ALA* 2.9 32.1 + - - +
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 2.8 45.1 + - - +
17B HIS* 3.8 7.6 - - - +
19B GLU* 1.3 79.4 + - - +
21B GLU* 1.3 64.3 + - - +
23B ALA* 3.8 3.6 - - - +
24B ARG* 2.8 64.0 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.8 8.9 - - + +
26A LYS* 2.7 37.2 + - - -
17B HIS* 3.0 23.0 + - - +
18B LEU* 3.2 9.2 + - - +
20B ASN* 1.3 76.0 - - - +
22B VAL* 1.3 52.8 + - - +
24B ARG* 3.2 7.8 + - - +
25B LEU* 2.6 43.6 + - + +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.8 8.7 - - + +
21A GLU* 3.7 22.9 - - + +
22A VAL* 3.6 36.8 - - + +
25A LEU* 3.8 10.3 - - + -
18B LEU* 2.8 26.7 + - + +
19B GLU* 3.2 20.2 - - + +
21B GLU* 1.3 73.6 - - - +
23B ALA* 1.3 57.8 + - + +
25B LEU* 3.8 6.1 - - - -
26B LYS* 2.7 44.1 + - - +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU 2.9 20.4 + - - +
20B ASN* 3.8 6.1 - - - +
22B VAL* 1.3 77.2 - - + +
24B ARG* 1.3 61.8 + - + +
26B LYS* 3.1 29.5 - - + +
27B LYS* 3.1 11.1 + - - +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASN* 2.8 52.4 + - - +
21B GLU* 3.8 4.7 - - - +
23B ALA* 1.3 77.6 - - + +
25B LEU* 1.3 57.4 + - - +
27B LYS* 3.3 11.7 - - + +
28B LEU* 3.1 35.3 + - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.0 16.2 - - + +
25A LEU* 3.8 17.9 - - + -
26A LYS* 3.5 42.8 - - + +
29A VAL* 4.2 23.8 - - + -
21B GLU* 2.6 27.6 + - + +
22B VAL* 3.6 4.0 - - - +
24B ARG* 1.3 71.5 - - - +
26B LYS* 1.3 60.4 + - - +
27B LYS 3.1 0.2 - - - -
28B LEU* 2.9 13.6 + - + +
29B VAL* 2.8 26.9 + - - +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 2.7 38.1 + - - -
25A LEU* 3.6 11.6 - - + +
22B VAL* 2.7 41.1 + - - +
23B ALA* 3.1 18.6 - - + +
25B LEU* 1.3 69.8 - - - +
27B LYS* 1.3 63.8 + - - +
29B VAL* 3.2 15.7 + - + +
30B GLY* 3.1 16.6 + - - -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 3.1 14.8 + - - +
24B ARG* 3.3 16.4 - - + +
25B LEU 3.1 0.2 - - - -
26B LYS* 1.3 79.2 - - - +
28B LEU* 1.3 60.9 + - + +
30B GLY* 2.9 17.5 + - - -
31B GLU* 2.7 47.9 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.0 7.9 - - + -
24B ARG* 3.1 24.7 + - + +
25B LEU* 2.9 21.2 + - + +
27B LYS* 1.3 78.6 - - + +
29B VAL* 1.3 60.1 + - - +
31B GLU* 3.0 25.4 + - + +
32B ARG* 2.9 46.9 + - - +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.5 23.3 - - + -
28A LEU* 5.1 4.3 - - + -
29A VAL* 3.3 27.4 - - + -
32A ARG* 3.6 25.0 + - - +
25B LEU 2.8 20.9 + - - +
26B LYS* 3.3 18.4 - - + +
27B LYS 3.1 0.2 - - - -
28B LEU* 1.3 76.5 - - - +
30B GLY* 1.3 59.3 - - - +
32B ARG* 3.3 22.3 - - - +
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS 3.1 9.1 + - - -
27B LYS* 2.9 10.2 + - - -
29B VAL* 1.3 76.1 - - - +
31B GLU* 1.3 65.2 + - - +
32B ARG 3.7 0.5 + - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 2.7 54.6 + - - +
28B LEU* 3.2 32.9 + - + +
30B GLY* 1.3 83.0 - - - +
32B ARG* 1.3 57.8 + - + +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.1 23.2 + - + +
32A ARG* 2.6 78.1 + - + +
28B LEU* 2.9 30.4 + - - +
29B VAL* 3.3 13.2 - - - +
30B GLY 3.4 0.9 - - - +
31B GLU* 1.3 81.9 - - + +
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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