Contacts of the helix formed by residues 1 - 29 (chain B) in PDB entry 4DZL
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 GLY 1 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B ACE 1.3 70.3 - - - +
2B GLU* 1.3 61.8 + - - +
4B ALA* 3.7 7.7 - - - +
5B ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 4.5 16.3 + - - -
0B ACE 3.5 0.2 - - - -
1B GLY* 1.3 76.9 - - - +
3B ILE* 1.3 62.0 + - - +
5B ALA* 3.2 18.0 + - - +
6B ILE* 3.2 17.6 + - - +
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Residues in contact with ILE 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B ACE 3.3 18.8 + - + +
2B GLU* 1.3 75.8 - - - +
4B ALA* 1.3 68.8 + - - +
6B ILE* 3.3 10.1 + - + +
7B LYS* 3.2 27.9 + - + +
2C GLU* 3.9 36.3 - - + +
3C ILE* 5.3 8.7 - - + -
6C ILE* 4.4 18.6 - - + -
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Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B ACE 3.1 15.1 + - - +
1B GLY* 3.7 8.5 - - - +
2B GLU 3.3 0.2 - - - -
3B ILE* 1.3 84.5 - - + +
5B ALA* 1.3 56.0 + - - +
7B LYS* 3.2 15.2 + - + +
8B GLN* 2.9 40.3 + - - +
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Residues in contact with ALA 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY 3.0 14.3 + - - +
2B GLU* 3.2 16.3 + - - +
4B ALA* 1.3 77.2 - - - +
6B ILE* 1.3 58.0 + - + +
8B GLN* 3.2 14.6 + - - +
9B GLU* 3.0 34.2 + - + +
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 6.2 0.2 - - + -
6A ILE* 5.0 4.3 - - + -
7A LYS* 3.9 36.6 - - + -
10A ILE* 3.6 24.0 - - + -
2B GLU 3.2 13.1 + - - +
3B ILE* 3.3 13.4 + - + +
5B ALA* 1.3 76.0 - - + +
7B LYS* 1.3 57.2 + - - +
9B GLU* 3.4 22.2 + - - +
10B ILE* 3.2 34.7 + - + +
6C ILE* 4.5 19.1 - - + -
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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
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3B ILE* 3.2 27.8 + - + +
4B ALA* 3.2 12.1 + - - +
6B ILE* 1.3 75.2 - - - +
8B GLN* 1.3 59.4 + - - +
10B ILE* 3.5 8.2 + - - +
11B ALA* 3.1 26.0 + - - +
2C GLU* 2.7 36.1 + - - -
6C ILE* 4.4 22.9 - - + -
9C GLU* 6.0 1.3 - - - +
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 2.9 27.7 + - - +
5B ALA* 3.2 14.5 + - - +
7B LYS* 1.3 74.5 - - - +
9B GLU* 1.3 62.1 + - + +
11B ALA* 3.2 6.3 + - - +
12B ALA* 2.9 30.9 + - - +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.0 24.3 - - + +
14A LYS* 2.7 32.4 + - - +
5B ALA* 3.0 14.9 + - - +
6B ILE* 3.6 34.1 + - - +
7B LYS 3.4 0.2 - - - -
8B GLN* 1.3 77.0 - - + +
10B ILE* 1.3 57.7 + - - +
12B ALA* 3.5 5.7 + - - +
13B ILE* 3.0 35.8 + - + +
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.6 11.7 - - + -
6B ILE* 3.2 22.1 + - + +
7B LYS* 3.8 8.1 - - + +
8B GLN 3.1 0.6 - - - -
9B GLU* 1.3 76.1 - - - +
11B ALA* 1.3 59.8 + - - +
13B ILE* 3.4 10.0 + - + +
14B LYS* 3.0 37.0 + - + +
6C ILE* 3.7 34.5 - - + +
9C GLU* 3.8 34.8 - - + +
10C ILE* 4.3 17.3 - - + -
13C ILE* 4.3 13.2 - - + +
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Residues in contact with ALA 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 17.4 + - - +
8B GLN* 3.2 6.5 + - - +
10B ILE* 1.3 74.1 - - - +
12B ALA* 1.3 64.8 + - - +
14B LYS* 3.3 12.9 + - - +
15B LYS* 3.1 30.1 + - + +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN 2.9 17.6 + - - +
9B GLU* 3.7 6.3 - - - +
11B ALA* 1.3 73.9 - - - +
13B ILE* 1.3 66.4 + - + +
15B LYS* 3.1 11.7 + - - +
16B GLU* 3.0 31.9 + - + +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.1 21.1 - - + -
13A ILE* 3.8 32.1 - - + -
14A LYS* 4.0 31.4 - - + -
17A ILE* 4.7 5.2 - - + -
9B GLU 3.0 24.2 + - - +
10B ILE* 3.8 9.9 - - + +
11B ALA 3.4 0.2 - - - -
12B ALA* 1.3 75.6 - - + +
14B LYS* 1.3 57.8 + - - +
16B GLU* 3.2 15.7 + - - +
17B ILE* 2.9 35.9 + - + +
13C ILE* 3.9 23.1 - - + -
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Residues in contact with LYS 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 ILE* 3.0 34.6 + - + +
11B ALA* 3.6 11.4 - - - +
12B ALA 3.2 0.4 - - - -
13B ILE* 1.3 76.5 - - - +
15B LYS* 1.3 57.3 + - + +
17B ILE* 3.5 7.2 + - - +
18B ALA* 3.1 28.2 + - - +
9C GLU* 3.3 25.8 + - - +
13C ILE* 4.3 19.5 - - + -
16C GLU* 5.7 3.1 - - - +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.1 18.7 + - + +
12B ALA* 3.1 11.9 + - - +
14B LYS* 1.3 74.3 - - + +
16B GLU* 1.3 65.5 + - + +
18B ALA* 3.5 5.7 + - - +
19B ALA* 3.2 22.5 + - - +
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Residues in contact with GLU 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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14A LYS* 5.6 3.5 - - - +
17A ILE* 3.7 27.6 - - + +
21A LYS* 2.9 30.7 + - + +
12B ALA* 3.0 19.2 + - + +
13B ILE* 3.6 22.6 + - - +
15B LYS* 1.3 75.5 - - + +
17B ILE* 1.3 59.2 + - - +
19B ALA* 3.3 7.5 + - - +
20B ILE* 2.9 34.3 + - + +
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.3 15.5 - - + -
13B ILE* 2.9 30.3 + - + +
14B LYS* 3.8 7.6 - - - +
15B LYS 3.3 0.2 - - - -
16B GLU* 1.3 77.3 - - - +
18B ALA* 1.3 57.7 + - - +
20B ILE* 3.2 7.1 + - + +
21B LYS* 2.9 34.9 + - - +
13C ILE* 4.9 4.0 - - + -
16C GLU* 3.8 34.3 - - + +
17C ILE* 3.1 37.7 - - + +
20C ILE* 3.9 19.7 - - + -
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Residues in contact with ALA 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 LYS 3.1 17.6 + - - +
15B LYS* 4.0 6.3 - - - +
17B ILE* 1.3 77.1 - - - +
19B ALA* 1.3 61.8 + - - +
21B LYS* 3.4 13.4 + - - +
22B PHI 3.1 21.7 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS 3.2 16.0 + - - +
16B GLU* 3.6 6.5 - - - +
18B ALA* 1.3 76.5 - - - +
20B ILE* 1.3 59.9 + - - +
22B PHI 3.1 10.4 + - - +
23B GLU* 2.9 36.0 + - - +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.1 25.4 - - + -
20A ILE* 3.9 18.8 - - + -
21A LYS* 4.8 10.1 - - + -
24A ILE* 3.8 20.4 - - + -
16B GLU* 2.9 26.9 + - + +
17B ILE* 3.2 19.5 + - + +
19B ALA* 1.3 75.9 - - + +
21B LYS* 1.3 58.7 + - - +
23B GLU* 2.9 15.3 + - - +
24B ILE* 2.9 29.6 + - + +
20C ILE* 3.6 32.8 - - + -
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Residues in contact with LYS 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 ILE* 2.9 29.5 + - + +
18B ALA* 3.8 12.1 - - - +
19B ALA 3.4 0.2 - - - -
20B ILE* 1.3 73.1 - - - +
22B PHI 1.3 61.2 + - - +
24B ILE* 3.7 7.3 + - - +
25B ALA* 3.2 21.5 + - - +
16C GLU* 3.0 34.4 + - + +
20C ILE* 4.3 20.4 - - + -
31L TYR 5.7 1.2 + - - -
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Residues in contact with PHI 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 ALA 3.1 14.8 + - - +
19B ALA* 3.4 12.1 - - - +
21B LYS* 1.3 76.8 + - - +
23B GLU* 1.3 72.5 + - + +
25B ALA* 3.1 11.3 + - + +
26B ALA* 3.0 40.6 + - + -
29K GLN* 6.2 1.6 - - - -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 5.8 4.0 - - - +
24A ILE* 4.1 27.3 - - + +
28A LYS* 2.7 33.3 + - - +
19B ALA* 2.9 19.8 + - - +
20B ILE* 2.9 18.1 + - - +
22B PHI 1.3 86.9 + - + +
24B ILE* 1.3 57.3 + - - +
26B ALA* 3.3 5.9 + - - +
27B ILE* 2.9 34.5 + - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.4 14.1 - - + -
20B ILE* 2.9 17.4 + - + +
21B LYS* 4.0 6.5 - - - +
23B GLU* 1.3 73.9 - - - +
25B ALA* 1.3 64.4 + - - +
27B ILE* 3.4 9.5 + - + +
28B LYS* 3.1 39.9 + - + +
20C ILE* 3.7 46.9 - - + +
23C GLU* 4.0 19.3 - - + +
24C ILE* 4.0 12.1 - - + -
27C ILE* 4.0 13.7 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS 3.2 13.1 + - - +
22B PHI 3.1 17.3 + - + +
24B ILE* 1.3 76.8 - - - +
26B ALA* 1.3 57.1 + - - +
28B LYS* 3.2 9.2 + - - +
29B GLN* 3.0 35.8 + - - +
29K GLN* 5.8 3.8 - - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 6.4 1.8 - - - -
22B PHI 3.0 40.6 + - + +
23B GLU* 3.6 9.6 - - - +
25B ALA* 1.3 74.9 - - - +
27B ILE* 1.3 65.0 + - - +
28B LYS 3.5 0.2 + - - -
29B GLN* 3.6 17.3 + - - +
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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
----------------------------------------------------------
24A ILE* 4.0 29.2 - - + +
27A ILE* 3.9 43.1 - - + -
28A LYS* 4.7 14.1 - - + -
23B GLU* 2.9 20.5 + - + +
24B ILE* 3.6 12.3 - - + +
26B ALA* 1.3 76.8 - - + +
28B LYS* 1.3 61.6 + - - +
29B GLN 3.7 2.3 + - - +
27C ILE* 4.0 27.4 - - + -
32C GLY 5.0 1.7 - - - +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.1 32.2 + - + +
25B ALA* 3.2 8.0 + - - +
27B ILE* 1.3 77.7 - - - +
29B GLN* 1.3 63.1 + - - +
30B GLY* 3.4 2.4 + - - -
23C GLU* 3.0 16.5 + - - +
27C ILE* 4.2 14.6 - - + -
31C TYR 5.5 0.9 + - - -
32C GLY* 4.1 39.4 - - - +
28K LYS* 4.3 7.1 - - - +
23L GLU* 2.5 34.2 + - - -
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Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.0 20.4 + - - +
26B ALA* 3.6 13.2 + - - +
27B ILE 3.4 4.3 - - - +
28B LYS* 1.3 76.9 - - - +
30B GLY* 1.3 79.4 + - - +
31B TYR 5.4 0.3 - - - -
32B GLY* 5.1 3.5 + - - -
25K ALA* 5.7 6.5 - - - +
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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