Contacts of the helix formed by residues 1 - 30 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0I ACE 1.3 71.9 - - - +
2I GLU* 1.3 60.2 + - - +
4I ALA* 3.6 7.4 - - - +
5I ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 2 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LYS* 5.6 5.7 + - - -
0I ACE 3.3 0.6 - - - -
1I GLY* 1.3 77.7 - - - +
3I ILE* 1.3 62.6 + - - +
5I ALA* 3.3 9.2 + - - +
6I ILE* 3.3 24.2 + - - +
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Residues in contact with ILE 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G GLU* 4.0 26.5 - - + +
3G ILE* 4.5 22.2 - - + -
6G ILE* 4.4 20.0 - - + -
0I ACE 3.4 15.4 + - + +
2I GLU* 1.3 74.6 - - - +
4I ALA* 1.3 63.7 + - - +
6I ILE* 3.2 8.1 + - + +
7I LYS* 2.9 38.6 + - - +
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Residues in contact with ALA 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0I ACE 3.0 19.5 + - - +
1I GLY* 3.6 9.4 - - - +
3I ILE* 1.3 79.5 - - - +
5I ALA* 1.3 56.7 + - - +
7I LYS* 3.3 11.0 + - - +
8I GLN* 2.9 40.5 + - - +
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Residues in contact with ALA 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I GLY 3.0 17.9 + - - +
2I GLU* 3.5 9.6 - - - +
3I ILE 3.2 0.2 - - - -
4I ALA* 1.3 72.5 - - - +
6I ILE* 1.3 61.9 + - + +
8I GLN* 3.3 14.7 + - - +
9I GLU* 3.0 34.7 + - + +
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Residues in contact with ILE 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.0 21.5 - - + -
3H ILE* 6.2 1.3 - - + -
6H ILE* 5.2 4.7 - - + -
7H LYS* 4.0 32.3 - - + -
10H ILE* 3.8 22.6 - - + +
2I GLU 3.3 11.1 + - - +
3I ILE* 3.2 12.7 + - + +
5I ALA* 1.3 75.8 - - + +
7I LYS* 1.3 65.4 + - - +
9I GLU* 3.2 16.7 + - - +
10I ILE* 3.1 39.5 + - + +
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Residues in contact with LYS 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G GLU* 2.6 45.2 + - - -
6G ILE* 4.5 18.2 - - + -
9G GLU* 6.2 0.2 - - - +
3I ILE* 2.9 33.3 + - + +
4I ALA* 3.6 8.3 - - - +
6I ILE* 1.3 76.1 - - - +
8I GLN* 1.3 58.1 + - + +
10I ILE* 3.7 7.9 + - - +
11I ALA* 3.1 26.3 + - - +
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Residues in contact with GLN 8 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ALA* 2.9 31.6 + - - +
5I ALA* 3.5 10.9 - - - +
6I ILE 3.2 0.2 - - - -
7I LYS* 1.3 76.1 - - + +
9I GLU* 1.3 60.0 + - - +
11I ALA* 3.3 7.1 + - + +
12I ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 9 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ILE* 4.1 23.3 - - + +
14H LYS* 2.7 34.1 + - - +
5I ALA* 3.0 15.9 + - + +
6I ILE* 3.5 32.8 + - - +
8I GLN* 1.3 75.4 - - - +
10I ILE* 1.3 58.1 - - + +
12I ALA* 3.1 8.8 + - - +
13I ILE* 2.8 33.2 + - - +
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Residues in contact with ILE 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.8 35.7 - - + +
9G GLU* 3.9 28.9 - - + +
10G ILE* 4.6 10.5 - - + -
13G ILE* 4.2 14.1 - - + -
10H ILE* 4.2 20.9 - - + -
6I ILE* 3.1 27.6 + - + +
7I LYS* 4.0 6.5 - - - +
9I GLU* 1.3 78.7 - - - +
11I ALA* 1.3 58.4 + - - +
13I ILE* 3.1 9.6 + - + +
14I LYS* 2.8 39.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LYS 3.1 19.4 + - - +
8I GLN* 3.5 8.5 - - + +
10I ILE* 1.3 78.0 - - - +
12I ALA* 1.3 60.8 + - - +
14I LYS* 3.4 10.3 + - - +
15I LYS* 3.2 28.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLN 2.9 13.9 + - - +
9I GLU* 3.4 11.4 - - - +
11I ALA* 1.3 75.4 - - - +
13I ILE* 1.3 64.0 + - + +
15I LYS* 3.4 9.2 + - - +
16I GLU* 3.2 30.7 + - - +
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Residues in contact with ILE 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ILE* 4.0 23.1 - - + -
10H ILE* 4.2 27.8 - - + -
13H ILE* 3.9 34.1 - - + -
14H LYS* 4.2 19.3 - - + -
17H ILE* 3.9 12.3 - - + -
9I GLU 2.8 19.2 + - - +
10I ILE* 3.1 11.4 + - + +
12I ALA* 1.3 75.0 - - + +
14I LYS* 1.3 59.5 + - - +
16I GLU* 3.1 17.0 + - - +
17I ILE* 2.9 28.8 + - + +
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Residues in contact with LYS 14 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLU* 3.4 34.8 + - - +
12G ALA* 6.5 0.4 - - - -
13G ILE* 4.2 22.0 - - + -
10I ILE* 2.8 31.0 + - + +
11I ALA* 3.4 8.0 + - - +
13I ILE* 1.3 73.6 - - - +
15I LYS* 1.3 57.7 + - + +
17I ILE* 3.4 8.5 + - - +
18I ALA* 3.0 27.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 15 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ALA* 3.2 17.7 + - + +
12I ALA* 3.7 10.8 - - - +
13I ILE 3.2 0.2 - - - -
14I LYS* 1.3 76.2 - - + +
16I GLU* 1.3 59.5 + - + +
18I ALA* 3.4 7.5 + - + +
19I ALA* 3.0 27.7 + - - +
28L LYS* 5.2 11.5 + - - -
29L GLN* 5.9 1.0 - - - +
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Residues in contact with GLU 16 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LYS* 5.9 1.6 - - - +
17H ILE* 3.9 28.2 - - + +
21H LYS* 2.8 34.3 + - - +
12I ALA* 3.2 17.8 + - - +
13I ILE* 3.1 15.9 + - - +
15I LYS* 1.3 74.1 - - + +
17I ILE* 1.3 58.5 + - - +
19I ALA* 3.3 7.3 + - - +
20I ILE* 2.9 38.5 + - + +
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Residues in contact with ILE 17 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ILE* 4.7 10.8 - - + +
16G GLU* 3.8 29.2 - - + -
17G ILE* 3.9 28.5 - - + -
20G ILE* 4.1 13.2 - - + -
17H ILE* 4.1 17.5 - - + -
20H ILE* 6.1 0.9 - - + -
13I ILE* 2.9 28.5 + - + +
14I LYS* 3.6 11.0 - - - +
16I GLU* 1.3 76.1 - - - +
18I ALA* 1.3 57.3 + - - +
20I ILE* 3.2 7.4 + - + +
21I LYS* 2.9 43.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLN* 4.5 2.1 - - - +
14I LYS 3.0 17.9 + - - +
15I LYS* 3.7 8.3 - - + +
17I ILE* 1.3 76.7 - - - +
19I ALA* 1.3 62.9 + - - +
21I LYS* 3.6 12.6 + - - +
22I PHI 3.2 23.2 + - - +
29L GLN* 3.6 10.7 - - + +
----------------------------------------------------------
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Residues in contact with ALA 19 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LYS 3.0 17.6 + - - +
16I GLU* 3.6 9.0 - - - +
17I ILE 3.3 0.2 - - - -
18I ALA* 1.3 77.2 - - - +
20I ILE* 1.3 58.5 + - + +
22I PHI 3.2 5.4 + - - +
23I GLU* 2.9 36.8 + - - +
29L GLN* 4.0 19.0 + - + +
31L TYR* 4.4 5.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE 20 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 3.7 22.9 - - + -
17H ILE* 4.2 26.9 - - + -
20H ILE* 3.9 17.3 - - + -
21H LYS* 4.5 14.1 - - + -
24H ILE* 3.9 14.4 - - + -
16I GLU* 2.9 26.5 + - + +
17I ILE* 3.2 9.4 + - + +
19I ALA* 1.3 73.2 - - + +
21I LYS* 1.3 66.9 + - - +
23I GLU* 3.2 14.0 + - - +
24I ILE* 2.9 45.1 + - + +
----------------------------------------------------------
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Residues in contact with LYS 21 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLY 3.2 22.7 + - - +
28F LYS* 3.3 20.5 + - - +
29F GLN* 3.3 25.0 + - - +
16G GLU* 3.1 30.7 + - - +
19G ALA* 6.4 1.1 - - + -
20G ILE* 4.1 20.9 - - + -
17I ILE* 2.9 30.3 + - + +
18I ALA* 3.8 9.9 - - - +
20I ILE* 1.3 76.6 - - - +
22I PHI 1.3 56.8 + - - +
24I ILE* 3.8 7.4 - - - +
25I ALA* 3.1 28.4 + - - +
----------------------------------------------------------
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Residues in contact with PHI 22 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA* 3.2 42.6 - - + +
19C ALA* 3.7 13.1 - - + +
22C PHI 3.8 25.3 - + + -
29F GLN* 3.6 13.6 + - + +
31F TYR* 4.1 18.6 - - - +
18I ALA 3.2 15.2 + - - +
19I ALA 3.5 2.9 - - - +
20I ILE 3.1 0.2 - - - -
21I LYS* 1.3 77.5 + - - +
23I GLU* 1.3 70.9 + - + +
25I ALA* 3.3 2.5 + - + +
26I ALA* 2.9 30.7 + - + +
22L PHI 3.8 34.0 - + + -
29L GLN* 3.8 15.7 - - - +
31L TYR* 3.3 46.8 - + + -
----------------------------------------------------------
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Residues in contact with GLU 23 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LYS* 6.1 0.9 - - - +
24H ILE* 3.5 17.9 - - + +
28H LYS* 2.7 36.9 + - - +
19I ALA* 2.9 19.4 + - - +
20I ILE* 3.5 20.1 - - - +
22I PHI 1.3 81.5 + - + -
24I ILE* 1.3 58.6 + - + +
26I ALA* 3.3 4.3 + - - +
27I ILE* 3.0 37.2 + - + +
31L TYR* 3.4 21.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 24 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 3.6 39.5 - - + +
23G GLU* 3.6 28.7 - - + -
24G ILE* 4.2 12.1 - - + -
27G ILE* 4.0 15.6 - - + +
24H ILE* 4.0 20.0 - - + -
20I ILE* 2.9 27.1 + - + +
21I LYS* 3.8 5.6 - - - +
23I GLU* 1.3 73.7 - - - +
25I ALA* 1.3 67.5 + - - +
27I ILE* 3.3 10.7 + - + +
28I LYS* 3.0 28.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 25 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHI 4.5 7.6 - - + -
25F ALA* 4.1 19.1 - - + -
28F LYS* 6.1 2.2 - - - -
29F GLN* 3.5 20.0 - - - +
21I LYS 3.1 18.1 + - - +
22I PHI 3.3 5.1 + - + +
24I ILE* 1.3 78.1 - - - +
26I ALA* 1.3 61.7 + - - +
28I LYS* 3.2 6.1 + - - +
29I GLN* 2.8 36.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA* 5.0 8.1 - - + +
21C LYS* 6.0 1.6 - - - +
22C PHI 3.8 27.9 - - + -
22I PHI 2.9 37.3 + - + +
23I GLU* 3.6 5.8 - - - +
24I ILE 3.3 0.2 - - - -
25I ALA* 1.3 75.4 - - - +
27I ILE* 1.3 64.9 + - + +
29I GLN* 3.3 2.3 + - - +
30I GLY* 3.1 21.7 + - - +
----------------------------------------------------------
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Residues in contact with ILE 27 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 4.4 22.9 - - + -
24H ILE* 4.4 11.2 - - + -
27H ILE* 4.6 19.5 - - + -
28H LYS* 3.9 37.2 - - + -
23I GLU 3.0 24.4 + - - +
24I ILE* 3.6 11.4 - - + +
26I ALA* 1.3 77.9 - - + +
28I LYS* 1.3 64.2 + - - +
30I GLY* 3.5 9.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 28 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLU* 5.7 1.4 + - - +
19E ALA* 4.4 16.0 - - - +
20E ILE* 6.1 1.4 - - - +
23E GLU* 3.5 17.7 + - - -
21F LYS* 2.8 46.7 + - - +
25F ALA* 6.5 0.2 - - - -
28F LYS* 6.0 0.9 - - - +
23G GLU* 3.2 28.1 + - - +
26G ALA* 5.7 2.8 - - + +
27G ILE* 4.0 22.0 - - + -
24I ILE* 3.0 26.6 + - + +
25I ALA* 3.2 5.1 + - - +
27I ILE* 1.3 78.0 - - - +
29I GLN* 1.3 76.5 + - - +
30I GLY* 4.7 0.3 - - - -
----------------------------------------------------------
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Residues in contact with GLN 29 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHI 3.9 22.4 - - + -
25C ALA* 4.2 17.5 - - + -
18F ALA 4.6 1.4 - - - +
21F LYS* 3.3 41.2 + - - +
22F PHI 3.4 16.0 + - + +
25F ALA* 3.8 19.0 - - + +
25I ALA* 2.8 31.1 + - - +
26I ALA 3.3 4.0 + - - +
28I LYS* 1.3 94.5 - - - +
30I GLY* 1.3 59.0 + - - +
31I TYR* 2.9 28.3 - - + -
----------------------------------------------------------
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Residues in contact with GLY 30 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 3.7 29.6 - - - +
22C PHI 4.8 0.5 + - - -
25C ALA* 4.2 2.8 - - - +
26I ALA 3.1 14.1 + - - +
27I ILE* 3.5 7.8 + - - -
28I LYS 3.4 2.4 - - - -
29I GLN* 1.3 79.9 - - - +
31I TYR* 1.3 68.5 + - - +
----------------------------------------------------------
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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