Contacts of the helix formed by residues 1 - 32 (chain D) in PDB entry 1VZJ
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 ASP 1 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D THR* 1.3 65.7 + - - +
3D LEU* 3.2 13.2 - - + +
4D ASP* 4.1 27.1 + - - +
5D GLU* 3.3 21.0 + - - +
19H SER* 5.1 14.6 + - - -
23H HIS* 6.1 0.4 - - - +
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Residues in contact with THR 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASP* 1.3 75.8 - - - +
3D LEU* 1.3 68.7 + - - +
5D GLU* 3.3 8.3 - - - +
6D ALA* 2.8 27.2 + - - +
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Residues in contact with LEU 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASP* 3.2 7.5 - - + +
2D THR* 1.3 84.8 + - - +
4D ASP* 1.3 55.7 + - - +
5D GLU 3.0 1.3 - - - -
6D ALA* 2.9 7.7 + - + +
7D GLU* 2.7 36.2 + - - +
14I PHE* 5.2 3.4 - - + +
15I PHE* 4.0 37.3 - - + +
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Residues in contact with ASP 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASP* 3.7 29.5 + - - +
2D THR 3.5 0.2 - - - -
3D LEU* 1.3 77.0 - - - +
5D GLU* 1.3 57.9 + - - +
7D GLU* 3.2 6.7 + - - +
8D ARG* 2.9 27.2 + - - +
19H SER 5.5 0.7 - - - +
22H VAL* 3.8 10.9 - - + +
23H HIS* 2.5 44.3 + - + +
26H ASN* 3.0 32.8 + - - +
27H GLN* 4.6 2.6 + - - -
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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 ASP 3.3 13.4 + - - +
2D THR* 3.3 13.9 - - - +
3D LEU 3.0 0.4 - - - -
4D ASP* 1.3 80.6 - - - +
6D ALA* 1.3 57.0 + - - +
8D ARG* 2.6 41.3 + - - +
9D GLN* 3.1 32.3 + - - +
19H SER* 5.6 3.1 + - - -
22H VAL* 4.0 18.1 - - - +
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Residues in contact with ALA 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D THR 2.8 15.2 + - - +
3D LEU* 2.9 16.8 + - + +
5D GLU* 1.3 74.1 - - - +
7D GLU* 1.3 66.6 + - - +
9D GLN* 3.5 7.4 + - - +
10D TRP* 3.0 25.6 + - - +
14I PHE 4.4 6.5 - - - +
15I PHE* 4.2 13.9 - - + -
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Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 3.5 15.8 + - - +
3D LEU 2.7 16.2 + - - +
4D ASP* 3.2 15.0 + - - +
6D ALA* 1.3 74.4 - - - +
8D ARG* 1.3 62.7 + - - +
10D TRP* 3.7 1.2 - - - +
11D LYS* 3.0 59.0 + - - +
26H ASN* 3.6 31.6 + - - +
27H GLN* 5.6 1.4 + - - -
15I PHE* 3.5 44.0 - - + -
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Residues in contact with ARG 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP 2.9 16.6 + - - +
5D GLU* 2.6 40.7 + - - +
6D ALA 3.3 0.2 - - - -
7D GLU* 1.3 78.5 - - - +
9D GLN* 1.3 99.2 + - - +
11D LYS* 3.8 4.6 - - - +
12D ALA* 3.0 36.7 + - + +
16G ARG* 6.1 1.0 - - - +
22H VAL* 3.9 28.5 - - + -
25H LYS* 6.4 3.1 - - + -
26H ASN* 4.1 9.8 + - - +
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Residues in contact with GLN 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLU* 3.1 17.6 + - - +
6D ALA* 4.0 6.9 - - - +
8D ARG* 1.3 104.3 + - - +
10D TRP* 1.3 58.0 + - - +
12D ALA* 3.9 1.2 - - - +
13D GLU* 3.1 60.8 + - + +
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Residues in contact with TRP 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 5.2 9.2 - - - -
6C ALA* 3.9 27.6 - - + -
9C GLN* 4.9 3.6 - - - -
10C TRP* 4.3 4.7 - + + -
6D ALA 3.0 18.6 + - - +
7D GLU 3.7 2.5 - - - +
9D GLN* 1.3 75.2 - - - +
11D LYS* 1.3 77.8 + - + +
13D GLU* 3.2 6.0 + - - +
14D PHE* 2.8 77.5 + + - +
10I PHE* 3.3 17.8 - + - -
11I PRO* 3.0 25.6 + - + -
12I PRO 3.8 2.9 + - - -
13I PRO* 3.5 42.5 - - + +
14I PHE 4.9 2.2 - - - -
15I PHE* 3.9 22.7 - + + -
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Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 4.3 8.2 + - - -
6C ALA* 5.4 6.5 - - - -
9C GLN* 5.8 4.9 - - - +
7D GLU* 3.0 53.4 + - + +
8D ARG* 3.8 4.5 - - - +
10D TRP* 1.3 92.9 - - + +
12D ALA* 1.3 62.7 + - - +
14D PHE* 3.5 3.8 - - - +
15D HIS* 3.1 42.7 + - + -
26H ASN* 4.2 18.6 + - - +
29H ASP* 4.2 22.2 - - + +
30H HIS* 5.1 4.4 + - - +
15I PHE* 4.7 7.0 - - - -
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ARG* 3.0 29.9 + - + +
9D GLN* 3.9 7.2 - - - +
11D LYS* 1.3 77.9 - - - +
13D GLU* 1.3 63.8 + - + +
15D HIS* 4.0 4.1 - - - +
16D ARG* 3.1 24.0 + - - +
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 6.1 1.3 - - - -
11A LYS* 3.2 33.6 + - - +
9D GLN* 3.1 47.5 + - + +
10D TRP* 3.9 2.6 - - - +
12D ALA* 1.3 74.2 - - + +
14D PHE* 1.3 60.2 + - - +
16D ARG* 3.3 9.4 + - - +
17D TRP* 2.8 30.0 + - - +
10I PHE* 3.4 24.0 - - + -
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Residues in contact with PHE 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLN* 3.7 35.9 - - + -
10C TRP* 3.7 26.9 - + - -
13C GLU* 3.6 33.9 - - + -
10D TRP* 2.8 42.8 + + + +
11D LYS* 3.5 5.8 - - - +
13D GLU* 1.3 72.2 - - - +
15D HIS* 1.3 69.0 + + - +
17D TRP* 2.7 18.9 + + - +
18D SER* 2.6 37.1 + - - -
10I PHE* 3.4 27.3 - + + -
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Residues in contact with HIS 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLN* 4.7 16.6 + - - -
11D LYS* 3.1 26.2 + - + +
12D ALA* 4.0 4.2 - - - +
14D PHE* 1.3 99.3 - + - +
16D ARG* 1.3 62.2 + - - +
18D SER* 3.4 12.6 + - - -
19D SER* 3.1 21.3 + - - -
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Residues in contact with ARG 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.1 11.4 - - - +
14A PHE* 5.3 5.9 - - - -
12D ALA 3.1 18.9 + - - +
13D GLU* 3.6 10.3 - - - +
14D PHE 3.1 0.8 - - - -
15D HIS* 1.3 76.8 - - - +
17D TRP* 1.3 61.5 + - - +
19D SER* 3.3 13.5 + - - -
20D TYR* 3.1 53.3 + - + -
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Residues in contact with TRP 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 3.9 19.5 - + + -
14A PHE* 3.9 17.5 - + + -
10C TRP* 5.9 0.4 - + - -
13C GLU* 3.9 38.1 - - + -
17C TRP* 3.9 4.9 - + - -
13D GLU 2.8 13.6 + - - +
14D PHE* 2.7 18.4 + + - +
16D ARG* 1.3 73.6 - - - +
18D SER* 1.3 71.1 - - - -
19D SER 2.9 4.7 - - - -
20D TYR* 2.8 26.8 + - - +
21D MSE 3.0 38.2 + - - +
7I PRO* 3.8 11.9 - - + +
8I PRO 2.9 22.4 + - - -
9I LEU* 3.8 19.5 - - + -
10I PHE* 3.4 45.8 - + + -
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 3.5 30.6 + - - +
14D PHE* 2.6 23.2 + - - -
15D HIS* 3.6 17.0 - - - -
17D TRP* 1.3 79.5 - - - +
19D SER* 1.3 57.3 + - - +
20D TYR 3.4 0.2 - - - -
21D MSE 3.3 11.1 - - - +
22D VAL* 3.2 29.9 + - - +
----------------------------------------------------------
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D HIS 3.1 11.7 + - - -
16D ARG* 3.5 13.0 - - - -
17D TRP 2.9 0.8 - - - -
18D SER* 1.3 77.7 - - - +
20D TYR* 1.3 61.2 + - - +
21D MSE 3.1 1.3 - - - -
22D VAL* 3.9 7.6 - - - +
23D HIS* 3.2 25.1 + - - +
----------------------------------------------------------
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Residues in contact with TYR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.6 37.2 - + + -
17A TRP* 3.8 29.6 - + + -
18A SER* 4.8 5.1 + - - -
16D ARG* 3.1 59.4 + - + -
17D TRP 2.8 7.2 + - - +
19D SER* 1.3 77.5 - - - +
21D MSE 1.3 59.9 + - - +
23D HIS* 3.7 13.1 - - - +
24D TRP* 2.8 31.2 + - - +
7I PRO* 4.7 4.9 - - + -
----------------------------------------------------------
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Residues in contact with MSE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 4.3 12.8 - - - +
16C ARG* 4.7 4.9 - - - -
17C TRP* 3.7 27.6 - - + -
20C TYR* 3.4 30.7 - - + +
17D TRP* 3.0 27.1 + - + +
18D SER* 3.3 16.8 - - - +
20D TYR* 1.3 78.5 - - - +
22D VAL* 1.3 52.3 + - + +
24D TRP* 3.0 3.9 + - + +
25D LYS* 2.7 36.2 + - - +
6I PRO* 3.4 15.3 - - + -
7I PRO* 2.8 47.3 - - + +
----------------------------------------------------------
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 5.7 7.2 - - - +
20C TYR* 5.2 3.6 + - - +
18D SER 3.2 16.4 + - - +
19D SER* 4.0 8.1 - - - +
21D MSE 1.3 76.6 - - + +
23D HIS* 1.3 63.9 + - - +
25D LYS* 3.4 8.0 + - + +
26D ASN* 3.1 28.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 5.3 7.5 + - + -
19D SER 3.2 17.2 + - - +
20D TYR* 3.9 14.1 - - + +
21D MSE 3.2 0.2 - - - -
22D VAL* 1.3 81.4 - - - +
24D TRP* 1.3 62.2 + - - +
26D ASN* 3.4 9.0 - - + +
27D GLN* 3.2 48.3 + - + +
----------------------------------------------------------
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Residues in contact with TRP 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TRP* 3.6 32.1 - + + -
21A MSE 3.7 15.0 - - - -
20C TYR* 3.3 48.7 - + + -
24C TRP* 3.7 17.9 - + + -
20D TYR 2.8 19.7 + - - +
21D MSE 3.5 1.8 - - + +
23D HIS* 1.3 73.9 + - - +
25D LYS* 1.3 98.7 + - + +
27D GLN* 3.2 6.6 + - + +
28D PHE* 2.9 41.8 + + + +
3I THR* 3.2 13.7 + - - -
4I PRO 2.7 19.6 + - - -
5I PRO 3.4 2.3 + - - -
6I PRO* 3.3 35.0 - - + -
7I PRO* 4.2 3.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.5 47.1 + - + +
23C HIS* 6.4 2.9 - - - -
21D MSE 2.7 19.6 + - - +
22D VAL* 3.4 7.4 + - - +
24D TRP* 1.3 87.0 - - + +
26D ASN* 1.3 57.4 + - - +
28D PHE* 3.2 11.1 + - + +
29D ASP* 2.9 64.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL* 3.1 21.0 + - - +
23D HIS* 3.4 13.1 - - + +
25D LYS* 1.3 79.6 - - - +
27D GLN* 1.3 66.1 + - + +
29D ASP* 3.5 4.4 + - - +
30D HIS* 3.2 58.1 + - - -
----------------------------------------------------------
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Residues in contact with GLN 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MSE 6.0 4.0 - - + -
24A TRP* 3.8 33.5 - - + -
25A LYS* 3.9 29.4 + - - +
23D HIS* 3.2 39.6 + - + +
24D TRP* 3.2 8.0 + - + +
26D ASN* 1.3 80.0 - - + +
28D PHE* 1.3 62.6 + - - +
30D HIS* 3.7 12.0 + - - +
31D TYR* 3.1 23.2 + - - +
3I THR* 3.8 9.4 - - + +
----------------------------------------------------------
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Residues in contact with PHE 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 6.2 0.2 - - - -
23C HIS* 3.9 28.5 - + + -
24C TRP* 3.8 24.5 - + - -
27C GLN* 3.0 44.0 - - + -
24D TRP* 2.9 47.6 + + + +
25D LYS* 3.4 12.3 - - - +
26D ASN 3.1 0.2 - - - -
27D GLN* 1.3 75.7 - - - +
29D ASP* 1.3 79.5 + - - +
31D TYR* 3.4 11.0 + + + +
32D SER* 3.0 17.0 + - - -
2I LEU* 4.7 7.4 - - + -
3I THR* 3.9 23.5 - - + +
----------------------------------------------------------
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LYS* 2.9 58.8 + - - +
26D ASN* 3.5 4.9 + - - +
27D GLN 3.5 0.2 - - - -
28D PHE* 1.3 82.9 - - - +
30D HIS* 1.3 65.7 + - + +
32D SER* 3.6 21.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASN* 3.2 41.2 + - - +
27D GLN* 3.7 14.0 + - - +
28D PHE 3.2 0.6 - - - -
29D ASP* 1.3 79.0 - - + +
31D TYR* 1.3 69.7 + - - +
32D SER 3.8 4.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 3.8 15.3 - + + -
28A PHE* 4.2 12.9 - + - -
27C GLN* 6.1 1.1 - - - -
31C TYR* 3.3 36.6 + + - -
27D GLN 3.1 14.8 + - - +
28D PHE* 3.6 10.8 - + + +
30D HIS* 1.3 79.3 - - - +
32D SER* 1.3 64.4 + - - +
1I LEU* 2.6 47.0 + - - -
2I LEU* 3.4 28.7 - - + -
3I THR* 4.5 7.6 - - + -
----------------------------------------------------------
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Residues in contact with SER 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN* 2.7 33.6 + - - -
31C TYR* 4.1 13.7 - - - -
28D PHE 3.0 12.0 + - - -
29D ASP* 3.6 17.3 + - - +
30D HIS 3.8 4.1 - - - +
31D TYR* 1.3 84.9 - - - +
----------------------------------------------------------
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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