Contacts of the helix formed by residues 5 - 34 (chain B) in PDB entry 2L6W
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 PRO 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B SER 3.9 1.8 - - - +
4B LEU* 1.3 95.8 - - + +
6B PHE* 1.3 60.5 + - + +
7B LYS* 3.1 18.6 - - + +
8B VAL* 3.1 46.0 - - + +
9B VAL* 3.7 3.6 - - - +
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Residues in contact with PHE 6 (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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1A GLY* 4.9 24.0 - - - +
2A HIS* 5.0 11.9 - - + -
4A LEU 5.7 3.6 - - - -
6A PHE* 4.9 17.7 - - + -
9A VAL* 5.7 5.8 - - + -
1B GLY* 6.2 2.7 - - - -
4B LEU 3.8 0.6 + - - -
5B PRO* 1.3 74.1 - - + +
7B LYS* 1.3 79.0 + - + +
8B VAL 3.4 0.2 - - - -
9B VAL* 3.2 16.3 + - + +
10B VAL* 3.2 36.5 + - + +
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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
----------------------------------------------------------
5B PRO* 3.1 14.8 - - + -
6B PHE* 1.3 94.9 - - + +
8B VAL* 1.3 65.8 + - + +
9B VAL 3.2 0.3 + - - -
10B VAL* 3.3 7.3 + - + +
11B ILE* 3.1 48.8 + - + +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.3 21.1 - - + -
5B PRO* 3.1 35.4 - - + +
7B LYS* 1.3 78.7 - - + +
9B VAL* 1.3 66.1 + - + +
11B ILE* 4.1 8.5 - - + +
12B SER* 2.9 33.1 + - - -
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 6.1 1.3 - - + -
9A VAL* 3.5 33.9 - - + +
10A VAL* 3.5 27.4 - - + +
13A ALA* 3.7 9.9 - - + +
14A ILE* 6.5 0.2 - - + -
1B GLY* 5.7 6.1 - - - -
4B LEU* 5.7 0.9 - - + +
5B PRO 3.7 13.9 - - - +
6B PHE* 3.4 17.9 - - + +
8B VAL* 1.3 80.7 - - + +
10B VAL* 1.3 60.7 + - - +
12B SER* 3.3 5.9 + - - -
13B ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.5 23.6 - - + -
6B PHE* 3.2 30.7 + - + +
7B LYS* 3.3 7.8 + - + +
9B VAL* 1.3 75.4 - - - +
11B ILE* 1.3 65.4 + - + +
13B ALA* 3.1 5.2 + - + +
14B ILE* 3.0 30.5 + - + +
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.1 41.1 + - + +
8B VAL* 4.1 7.4 - - + +
10B VAL* 1.3 77.9 - - + +
12B SER* 1.3 57.1 + - - +
14B ILE* 3.1 9.9 - - + +
15B LEU* 3.0 40.6 + - + +
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Residues in contact with SER 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 4.7 10.1 + - - +
17A LEU* 5.4 10.4 - - - +
8B VAL 2.9 20.6 + - - -
9B VAL* 3.6 6.1 - - - -
11B ILE* 1.3 74.6 - - - +
13B ALA* 1.3 59.8 + - - +
15B LEU* 3.9 6.8 - - - +
16B ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.5 4.9 - - + +
12A SER* 4.3 12.1 - - - +
13A ALA* 3.7 30.2 - - + +
16A ALA* 4.9 0.2 - - - -
9B VAL 2.9 16.2 + - - +
10B VAL* 3.5 7.0 - - - +
12B SER* 1.3 74.9 - - - +
14B ILE* 1.3 67.2 + - - +
16B ALA* 3.0 12.8 + - - +
17B LEU* 3.1 22.5 + - + +
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Residues in contact with ILE 14 (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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10B VAL* 3.0 19.0 + - + +
11B ILE* 3.1 22.2 - - + +
13B ALA* 1.3 76.6 - - - +
15B LEU* 1.3 66.4 + - + +
17B LEU* 3.4 9.7 + - + +
18B VAL* 3.1 36.8 + - + +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.0 25.0 + - + +
12B SER* 3.9 7.0 - - - +
14B ILE* 1.3 80.8 - - + +
16B ALA* 1.3 64.7 + - - +
18B VAL* 3.3 11.8 + - + +
19B VAL* 3.1 40.0 + - + +
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Residues in contact with ALA 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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13A ALA 4.9 1.3 - - - +
16A ALA* 3.3 39.6 - - + +
17A LEU* 4.4 8.5 - - + +
20A LEU* 4.5 2.1 - - + +
12B SER* 2.9 20.0 + - - +
13B ALA* 3.0 2.2 + - - +
15B LEU* 1.3 77.4 - - - +
17B LEU* 1.3 56.7 + - - +
19B VAL* 3.0 11.8 - - + +
20B LEU* 3.0 29.3 + - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 5.0 8.7 - - - +
16A ALA* 3.5 23.3 - - + -
19A VAL* 6.3 0.2 - - + -
13B ALA* 3.1 27.0 + - - +
14B ILE* 3.7 14.6 - - + +
15B LEU 3.3 0.2 - - - -
16B ALA* 1.3 74.1 - - - +
18B VAL* 1.3 65.6 + - + +
20B LEU* 3.6 19.8 + - + +
21B THR* 3.4 23.6 + - - -
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Residues in contact with VAL 18 (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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14B ILE* 3.1 28.4 + - + +
15B LEU* 3.6 15.9 - - + +
16B ALA 3.3 0.2 - - - -
17B LEU* 1.3 78.9 - - + +
19B VAL* 1.3 64.7 + - + +
21B THR* 3.5 7.0 + - - -
22B ILE* 3.2 33.4 + - + +
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.6 22.4 - - + -
15B LEU* 3.1 31.3 + - + +
16B ALA* 3.0 23.3 - - - +
18B VAL* 1.3 74.7 - - + +
20B LEU* 1.3 59.6 + - - +
22B ILE* 3.0 17.4 + - + +
23B ILE* 2.8 37.0 + - + +
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Residues in contact with LEU 20 (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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19A VAL* 3.7 40.6 - - + +
20A LEU* 3.7 9.9 - - + -
23A ILE* 3.5 41.4 - - + +
16B ALA 3.0 19.1 + - - +
17B LEU* 3.7 23.1 - - + +
18B VAL 3.3 0.2 - - - -
19B VAL* 1.3 78.2 - - - +
21B THR* 1.3 62.0 + - - +
23B ILE* 3.4 0.7 + - - +
24B SER* 3.3 17.3 + - - -
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Residues in contact with THR 21 (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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17B LEU 3.4 11.4 + - - -
18B VAL* 3.5 9.7 + - - -
19B VAL 3.2 0.4 - - - -
20B LEU* 1.3 75.7 - - - +
22B ILE* 1.3 61.0 + - + +
24B SER* 3.2 8.6 + - - -
25B LEU* 2.9 51.0 + - + +
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Residues in contact with ILE 22 (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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18B VAL* 3.2 29.2 - - + +
19B VAL* 3.0 19.2 + - + +
21B THR* 1.3 76.2 - - + +
23B ILE* 1.3 67.8 + - + +
25B LEU* 3.1 16.3 + - + +
26B ILE* 3.1 36.8 + - + +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.6 28.7 - - + -
23A ILE* 3.4 27.6 - - + +
24A SER* 4.5 4.7 - - - +
27A ILE* 3.5 25.2 - - + +
19B VAL* 2.8 22.1 + - + +
20B LEU 3.6 7.4 - - - +
21B THR 3.3 0.2 - - - -
22B ILE* 1.3 79.1 - - + +
24B SER* 1.3 58.6 + - - +
26B ILE* 3.5 21.8 + - + +
27B ILE* 3.1 18.7 + - - +
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Residues in contact with SER 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.6 19.7 - - - +
20B LEU 3.3 4.7 + - - -
21B THR* 3.2 12.3 + - - -
22B ILE 3.2 0.2 - - - -
23B ILE* 1.3 79.1 - - - +
25B LEU* 1.3 65.2 + - - +
27B ILE* 3.3 11.3 + - - +
28B LEU* 3.1 23.3 + - - +
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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
----------------------------------------------------------
21B THR* 2.9 37.0 + - + +
22B ILE* 3.1 19.7 + - + +
24B SER* 1.3 78.3 - - - +
26B ILE* 1.3 63.3 + - + +
28B LEU* 3.4 17.6 + - + +
29B ILE* 3.1 38.7 + - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 5.7 6.5 - - + -
22B ILE* 3.1 28.6 + - + +
23B ILE* 3.7 21.8 - - + +
24B SER 3.2 0.2 - - - -
25B LEU* 1.3 78.5 - - + +
27B ILE* 1.3 59.2 + - + +
29B ILE* 4.2 4.0 - - - +
30B MET* 2.9 41.6 + - + +
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Residues in contact with ILE 27 (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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23A ILE* 4.2 14.4 - - + +
26A ILE* 5.8 4.0 - - + -
27A ILE* 3.4 37.9 - - + -
30A MET* 4.0 34.3 - - + -
23B ILE 3.1 17.5 - - - +
24B SER* 3.3 13.6 + - - +
26B ILE* 1.3 74.7 - - + +
28B LEU* 1.3 65.6 + - - +
30B MET* 3.6 11.7 - - + +
31B LEU* 3.0 28.5 + - + +
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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
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24B SER* 3.1 16.6 + - - +
25B LEU* 3.6 20.6 - - + +
26B ILE 3.3 0.2 - - - -
27B ILE* 1.3 78.2 - - - +
29B ILE* 1.3 62.6 + - + +
31B LEU* 3.8 4.1 - - + +
32B TRP* 2.9 31.0 + - + +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.1 24.5 + - + +
26B ILE* 4.3 3.8 - - - +
28B LEU* 1.3 79.3 - - + +
30B MET* 1.3 65.8 + - - +
32B TRP* 3.1 23.2 + - + +
33B GLN* 3.1 38.2 + - - +
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Residues in contact with MET 30 (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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27A ILE* 4.6 17.0 - - + -
30A MET* 4.3 16.4 - - + -
31A LEU* 5.1 21.1 - - + -
34A LYS* 5.7 5.8 - - + -
26B ILE* 2.9 29.3 + - + +
27B ILE* 3.6 26.9 - - + +
29B ILE* 1.3 77.2 - - - +
31B LEU* 1.3 58.7 + - + +
33B GLN* 3.6 3.4 + - - +
34B LYS* 2.9 33.6 + - - +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 5.7 9.4 - - + -
34A LYS* 5.0 18.4 - - - +
27B ILE* 3.0 21.3 + - + +
28B LEU* 4.0 4.0 - - + +
30B MET* 1.3 77.7 - - + +
32B TRP* 1.3 65.8 + - - +
33B GLN 3.2 0.2 - - - -
34B LYS* 3.4 25.8 + - + +
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Residues in contact with TRP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 2.9 21.6 + - + +
29B ILE* 3.1 19.0 + - + +
31B LEU* 1.3 78.6 - - - +
33B GLN* 1.3 90.4 + - + +
34B LYS* 4.8 2.8 - - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.1 23.6 + - - +
30B MET* 4.4 3.0 - - - +
32B TRP* 1.3 106.6 - - + +
34B LYS* 1.3 62.0 - - - +
35B LYS* 2.6 31.9 + - - +
36B PRO* 5.5 0.6 - - - +
37B ARG* 3.3 35.3 + - + +
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B MET* 2.9 23.8 + - - +
31B LEU* 3.4 23.4 + - + +
32B TRP 4.8 2.9 - - - +
33B GLN* 1.3 77.7 - - - +
35B LYS* 1.3 75.2 + - + +
36B PRO* 3.7 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