Contacts of the helix formed by residues 3 - 32 (chain D) in PDB entry 1CE9
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 VAL 3 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.8 11.0 - - - +
1C MET* 4.1 18.6 - - + +
3C VAL* 4.0 24.7 - - + -
6C LEU* 3.8 14.5 - - + +
2D SER* 1.3 73.4 - - - +
4D LYS* 1.3 59.0 + - - +
6D LEU* 3.2 5.5 + - - +
7D GLU* 2.8 54.9 + - - +
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Residues in contact with LYS 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 5.7 2.9 - - - +
2D SER* 3.2 11.8 - - - +
3D VAL* 1.3 80.1 - - - +
5D GLU* 1.3 64.8 + - + +
7D GLU* 3.1 14.4 + - - +
8D ASP* 2.9 48.4 + - - +
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Residues in contact with GLU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.0 32.2 - - + +
2D SER* 3.1 23.6 + - - +
4D LYS* 1.3 84.0 - - + +
6D LEU* 1.3 58.1 + - - +
8D ASP* 3.3 12.5 + - - +
9D LYS* 3.1 26.3 + - - +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 4.2 13.5 - - + -
6C LEU* 4.0 20.4 - - + -
7C GLU* 4.0 22.2 - - + +
10C VAL* 4.1 24.2 - - + +
1D MET* 3.4 50.0 - - + +
2D SER 3.4 8.2 + - - +
3D VAL* 3.2 9.5 + - - +
4D LYS 3.2 0.6 - - - -
5D GLU* 1.3 76.9 - - - +
7D GLU* 1.3 65.1 + - - +
9D LYS* 3.4 6.4 + - + +
10D VAL* 3.2 28.2 + - - +
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Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.9 39.7 - - + +
21B GLU* 4.8 0.3 - - - +
22B ASN* 2.8 39.7 + - - +
1C MET* 4.3 7.8 - - - +
6C LEU* 3.8 18.8 - - + -
3D VAL* 2.8 32.0 + - + +
4D LYS* 3.1 10.8 + - - +
6D LEU* 1.3 76.5 - - - +
8D ASP* 1.3 65.1 + - - +
10D VAL* 3.5 3.4 + - - +
11D GLU* 3.2 31.5 + - - +
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Residues in contact with ASP 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LYS* 2.9 37.1 + - - +
5D GLU* 3.5 12.5 - - - +
6D LEU 3.2 0.2 - - - -
7D GLU* 1.3 79.8 - - - +
9D LYS* 1.3 57.3 + - - +
11D GLU* 3.5 14.0 + - - +
12D GLU* 3.0 29.7 + - - +
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.9 28.9 - - + -
5D GLU 3.1 16.1 + - - +
6D LEU* 3.8 9.2 - - + +
7D GLU 3.3 0.2 - - - -
8D ASP* 1.3 76.5 - - - +
10D VAL* 1.3 60.1 + - - +
12D GLU* 3.9 28.8 + - - +
13D LEU* 3.0 40.8 + - + +
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Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.3 10.5 - - + -
18B TYR* 3.2 30.7 - - + +
6C LEU* 4.2 8.5 - - + +
9C LYS* 3.7 34.5 - - + -
10C VAL* 3.8 17.0 - - + +
13C LEU* 3.5 15.6 - - + +
6D LEU 3.2 16.6 + - - +
7D GLU 3.7 8.1 - - - +
8D ASP 3.3 0.2 - - - -
9D LYS* 1.3 77.4 - - - +
11D GLU* 1.3 62.0 + - - +
13D LEU* 3.4 1.3 + - - -
14D LEU* 3.1 20.6 + - - +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 5.5 4.1 - - - +
14B LEU* 3.9 26.2 - - + -
15B SER* 3.6 28.5 + - - +
18B TYR* 3.2 25.2 - - + +
7D GLU* 3.2 18.4 + - - +
8D ASP* 3.9 13.6 - - - +
10D VAL* 1.3 77.3 - - - +
12D GLU* 1.3 61.7 + - - +
14D LEU* 3.5 4.3 + - - +
15D SER* 3.2 23.2 + - - -
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASP 3.0 19.3 + - - +
9D LYS* 3.7 30.0 + - - +
11D GLU* 1.3 78.2 - - - +
13D LEU* 1.3 63.0 + - - +
15D SER* 3.4 7.2 + - - -
16D LYS* 3.1 50.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 41.3 - - + +
13C LEU* 3.9 14.6 - - + +
14C LEU* 3.9 20.6 - - + +
17C ASN* 4.4 26.5 - - + +
9D LYS* 3.0 32.0 + - + +
10D VAL 3.9 3.6 - - - +
12D GLU* 1.3 76.4 - - - +
14D LEU* 1.3 60.6 + - - +
16D LYS* 3.4 15.9 + - + +
17D ASN* 2.9 35.8 + - - +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 6.1 4.7 - - - -
10B VAL* 4.0 23.6 - - + -
11B GLU* 4.7 10.8 - - + -
14B LEU* 3.7 27.6 - - + -
13C LEU* 4.0 21.5 - - + +
10D VAL 3.1 16.6 + - - +
11D GLU* 3.9 5.4 - - - +
12D GLU 3.3 0.2 - - - -
13D LEU* 1.3 74.2 - - - +
15D SER* 1.3 61.1 + - - +
17D ASN* 3.3 8.5 + - + +
18D TYR* 2.9 54.9 + - + +
----------------------------------------------------------
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Residues in contact with SER 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 4.0 26.8 + - - -
11D GLU 3.2 14.9 + - - -
12D GLU* 3.6 7.2 - - - -
13D LEU 3.3 0.2 - - - -
14D LEU* 1.3 77.3 - - - +
16D LYS* 1.3 65.8 + - - +
18D TYR* 3.4 3.5 + - - +
19D HIS* 3.1 21.7 + - - +
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Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN* 4.0 13.9 - - - +
12D GLU* 3.1 44.7 + - + +
13D LEU* 3.6 19.1 - - + +
14D LEU 3.3 0.2 - - - -
15D SER* 1.3 77.6 - - - +
17D ASN* 1.3 61.8 + - - +
19D HIS* 3.3 8.5 + - - +
20D LEU* 3.0 28.6 + - + +
----------------------------------------------------------
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.5 29.7 + - - +
16C LYS* 3.5 27.1 - - - +
17C ASN* 3.2 32.2 + - - +
20C LEU* 3.6 10.8 - - + +
13D LEU 2.9 22.5 + - - +
14D LEU* 3.5 10.5 - - + +
15D SER 3.2 0.2 - - - -
16D LYS* 1.3 74.8 - - - +
18D TYR* 1.3 67.5 + - + +
20D LEU* 3.1 4.2 + - - +
21D GLU* 2.9 28.8 + - + +
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Residues in contact with TYR 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.6 33.2 - - + +
6A LEU* 3.4 17.8 - - + +
9A LYS* 4.4 6.2 - - - +
7B GLU* 3.7 46.8 - - + +
10B VAL* 3.3 25.2 - - + +
11B GLU* 3.7 20.9 - - + +
14D LEU* 2.9 43.5 + - + +
15D SER* 3.7 5.4 - - - +
16D LYS 3.3 0.2 - - - -
17D ASN* 1.3 78.9 - - + +
19D HIS* 1.3 58.4 + - - +
21D GLU* 3.3 7.8 + - + +
22D ASN* 3.0 33.9 + - - +
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Residues in contact with HIS 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D SER 3.1 13.6 + - - +
16D LYS* 3.6 11.3 + - - +
17D ASN 3.2 0.2 - - - -
18D TYR* 1.3 78.5 - - - +
20D LEU* 1.3 65.3 + - + +
22D ASN* 3.1 16.3 + - + +
23D GLU* 3.0 51.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN* 3.4 42.4 - - - +
20C LEU* 3.6 21.3 - - + -
21C GLU* 3.5 34.3 - - + +
24C VAL* 3.8 16.0 - - + +
16D LYS* 3.0 15.0 + - + +
17D ASN 3.5 7.9 - - - +
19D HIS* 1.3 88.1 - - + +
21D GLU* 1.3 61.9 + - - +
23D GLU* 3.4 9.3 + - + +
24D VAL* 3.1 29.3 + - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 47.0 + - + +
7B GLU* 5.2 1.8 - - - +
16C LYS* 4.4 10.9 - - - -
20C LEU* 3.9 24.9 - - + +
17D ASN* 2.9 20.2 + - + +
18D TYR* 3.5 11.9 - - + +
19D HIS 3.2 0.2 - - - -
20D LEU* 1.3 74.3 - - - +
22D ASN* 1.3 67.6 + - - +
24D VAL* 3.4 11.5 + - - +
25D ALA* 3.1 22.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.2 9.2 - - - +
4B LYS* 6.0 4.0 - - - +
7B GLU* 3.1 32.9 + - - +
18D TYR 3.0 17.7 + - - -
19D HIS* 3.3 20.6 - - + +
21D GLU* 1.3 79.9 - - - +
23D GLU* 1.3 57.1 + - + +
25D ALA* 3.5 6.8 + - - +
26D ARG* 3.0 27.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 4.3 12.6 - - + -
28C LYS* 3.6 6.4 + - - -
34C ARG* 3.4 14.9 + - - -
19D HIS* 3.0 42.5 + - + +
20D LEU* 3.6 13.9 - - + +
21D GLU 3.2 0.2 - - - -
22D ASN* 1.3 76.8 - - - +
24D VAL* 1.3 59.3 + - - +
26D ARG* 3.0 44.6 + - - +
27D LEU* 2.9 40.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.5 11.9 - - + -
23C GLU* 4.2 21.5 - - + -
24C VAL* 3.5 20.4 - - + +
27C LEU* 3.9 20.6 - - + +
20D LEU 3.1 16.8 + - - +
21D GLU* 3.6 15.9 - - - +
23D GLU* 1.3 76.6 - - - +
25D ALA* 1.3 57.1 + - - +
27D LEU* 4.7 0.4 - - - -
28D LYS* 3.1 49.6 + - + +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLU 3.1 16.6 + - - +
22D ASN* 3.8 7.0 - - - +
24D VAL* 1.3 77.4 - - - +
26D ARG* 1.3 61.5 + - - +
28D LYS* 3.6 8.3 + - - +
29D LYS* 2.9 32.4 + - - +
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LYS* 3.7 1.8 - - - +
33C GLU* 2.8 44.2 + - - -
34C ARG* 3.6 6.7 - - - +
22D ASN 3.0 17.6 + - - +
23D GLU* 3.0 42.4 + - - +
25D ALA* 1.3 78.7 - - - +
27D LEU* 1.3 71.8 + - - +
29D LYS* 3.4 11.2 - - - +
30D LEU* 3.4 38.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.9 29.8 - - + +
27C LEU* 3.9 20.2 - - + -
28C LYS* 3.9 21.3 - - + +
31C VAL* 3.9 23.0 - - + +
33C GLU* 3.8 13.0 - - - +
23D GLU* 2.9 24.7 + - + +
24D VAL 4.2 2.9 - - - +
26D ARG* 1.3 101.4 - - - +
28D LYS* 1.3 62.7 + - - +
29D LYS 3.1 1.8 - - - -
30D LEU* 3.3 8.1 + - + +
31D VAL* 3.0 29.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 4.9 8.0 + - - -
26C ARG* 5.9 1.1 - - - +
27C LEU* 4.0 18.6 - - + -
24D VAL* 3.1 42.0 + - + +
25D ALA* 3.9 8.5 - - - +
26D ARG 3.3 0.2 - - - -
27D LEU* 1.3 77.5 - - - +
29D LYS* 1.3 62.5 + - + +
31D VAL* 3.7 17.7 + - - +
32D GLY 4.3 2.4 + - - -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA* 2.9 25.6 - - - +
26D ARG* 3.4 11.6 - - - +
27D LEU 3.1 0.2 - - - -
28D LYS* 1.3 80.4 - - + +
30D LEU* 1.3 59.6 + - + +
31D VAL 3.6 0.5 + - - -
32D GLY 3.8 2.4 + - - -
33D GLU* 3.0 31.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 3.4 24.7 - - + +
33C GLU* 3.9 8.5 - - - +
26D ARG* 3.4 42.5 + - + +
27D LEU* 3.3 12.2 + - + +
29D LYS* 1.3 78.8 - - + +
31D VAL* 1.3 64.4 + - - +
32D GLY 3.2 1.9 + - - -
33D GLU* 3.4 35.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.7 15.5 - - + +
30C LEU* 4.4 32.3 - - + +
31C VAL* 3.9 18.1 - - + +
27D LEU 3.0 20.0 - - - +
28D LYS* 4.0 11.4 - - - +
29D LYS 3.4 1.0 - - - -
30D LEU* 1.3 75.1 - - - +
32D GLY* 1.3 57.5 + - - +
33D GLU 3.7 0.4 + - - -
----------------------------------------------------------
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Residues in contact with GLY 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LYS 4.3 3.2 + - - -
29D LYS 3.8 6.5 + - - -
30D LEU 3.2 0.4 - - - -
31D VAL* 1.3 78.7 - - - +
33D GLU* 1.3 65.0 + - - +
34D ARG* 3.5 7.1 + - - +
----------------------------------------------------------
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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