Contacts of the helix formed by residues 10 - 35 (chain Z) in PDB entry 5GAG
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 SER 10 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z GLU 4.4 0.2 + - - -
9Z LYS* 1.3 77.3 - - - +
11Z VAL* 1.3 65.2 + - - +
12Z GLU* 3.6 15.3 + - - +
13Z GLU* 3.6 26.6 + - - +
14Z LEU* 3.0 23.4 + - - +
60Z LYS* 5.0 3.1 - - - +
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Residues in contact with VAL 11 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z SER* 1.3 74.6 - - - +
12Z GLU* 1.3 56.3 + - - +
14Z LEU* 3.2 8.2 - - - +
15Z ASN* 2.7 50.0 + - - +
57Z LEU* 4.3 9.0 - - + -
60Z LYS* 4.2 26.2 - - + +
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Residues in contact with GLU 12 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z SER* 3.8 10.6 + - - +
11Z VAL* 1.3 79.4 - - - +
13Z GLU* 1.3 63.5 + - + +
15Z ASN* 3.3 8.0 + - - +
16Z THR* 3.0 32.8 + - - +
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Residues in contact with GLU 13 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Z LYS* 3.2 38.6 - - + +
10Z SER* 3.6 26.2 + - - +
11Z VAL 3.5 0.2 - - - -
12Z GLU* 1.3 79.6 - - + +
14Z LEU* 1.3 61.2 - - - +
16Z THR* 3.4 9.4 - - - -
17Z GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 14 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Z LEU* 3.6 27.4 - - + +
9Z LYS* 3.8 18.8 - - + +
10Z SER 3.0 20.5 + - - +
11Z VAL* 3.2 10.8 - - - +
13Z GLU* 1.3 76.2 - - - +
15Z ASN* 1.3 58.3 + - - +
17Z GLU* 3.1 8.4 + - + +
18Z LEU* 2.8 26.8 + - - +
53Z VAL* 4.0 14.8 - - + +
56Z LEU* 3.8 29.4 - - + -
57Z LEU* 3.5 29.6 - - + +
60Z LYS* 4.0 12.6 - - - -
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Residues in contact with ASN 15 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z VAL* 2.7 40.6 + - - +
12Z GLU* 3.8 6.8 - - - +
14Z LEU* 1.3 75.8 - - - +
16Z THR* 1.3 63.4 + - - +
18Z LEU* 3.2 15.4 - - - +
19Z LEU* 2.9 27.9 + - - +
57Z LEU* 3.6 28.8 - - - +
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Residues in contact with THR 16 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLU* 3.0 21.8 + - - +
13Z GLU* 3.4 13.5 - - - -
14Z LEU 3.2 0.2 - - - -
15Z ASN* 1.3 76.3 - - - +
17Z GLU* 1.3 58.1 + - - +
19Z LEU* 3.3 7.6 + - - +
20Z ASN* 3.0 46.3 + - - +
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Residues in contact with GLU 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z LEU* 5.7 5.8 - - + -
9Z LYS* 5.0 16.6 + - + +
13Z GLU 2.9 17.4 + - - +
14Z LEU* 3.7 6.5 - - + +
16Z THR* 1.3 73.2 - - - +
18Z LEU* 1.3 60.7 + - - +
20Z ASN* 3.8 19.8 + - - +
21Z LEU* 2.8 44.2 + - + +
24Z GLU* 4.3 7.4 - - - +
53Z VAL* 5.0 10.8 - - + -
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Residues in contact with LEU 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U GLU* 4.4 10.1 - - - +
14Z LEU 2.8 13.6 + - - +
15Z ASN* 3.2 18.8 + - - +
17Z GLU* 1.3 76.2 - - - +
19Z LEU* 1.3 65.4 + - + +
21Z LEU* 3.0 6.9 + - + +
22Z LEU* 2.9 41.4 + - + +
50Z VAL* 4.2 19.1 - - + -
53Z VAL* 4.0 20.1 - - + +
54Z LYS* 3.9 34.3 - - + +
57Z LEU* 3.8 24.9 - - + -
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Residues in contact with LEU 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U GLU* 3.4 34.3 - - + +
5U GLU* 4.7 13.0 - - + +
8U LEU* 4.4 12.7 - - + +
15Z ASN 2.9 14.0 + - - +
16Z THR* 3.5 11.0 - - - +
18Z LEU* 1.3 76.0 - - + +
20Z ASN* 1.3 63.3 + - - +
22Z LEU* 3.0 14.4 + - + +
23Z ARG* 2.9 45.7 + - - +
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Residues in contact with ASN 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z THR* 3.0 37.2 + - - +
17Z GLU* 3.9 16.1 + - - +
19Z LEU* 1.3 74.2 - - - +
21Z LEU* 1.3 62.9 + - - +
23Z ARG* 2.7 33.2 + - - +
24Z GLU* 3.0 39.1 + - - +
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Residues in contact with LEU 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z GLU* 2.8 30.1 + - + +
18Z LEU* 3.0 6.3 + - - +
20Z ASN* 1.3 77.0 - - - +
22Z LEU* 1.3 57.4 - - - +
24Z GLU* 3.3 18.8 + - - +
25Z GLN* 2.9 28.2 + - - +
46Z VAL* 3.5 36.7 - - + +
49Z ASP* 3.6 19.7 - - + +
50Z VAL* 3.4 39.0 - - + +
53Z VAL* 3.9 15.0 - - + -
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Residues in contact with LEU 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U GLU* 3.7 33.4 - - + +
8U LEU* 3.6 25.7 - - + +
9U LYS* 5.3 12.1 - - + -
18Z LEU* 2.9 28.4 + - + +
19Z LEU* 3.0 11.0 + - + +
21Z LEU* 1.3 73.3 - - - +
23Z ARG* 1.3 65.0 - - - +
25Z GLN* 3.1 21.9 + - - +
26Z PHE* 2.9 25.9 + - - +
50Z VAL* 3.8 26.0 - - + -
54Z LYS* 5.9 0.2 - - - +
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Residues in contact with ARG 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U GLU* 3.3 25.2 + - - +
8U LEU* 4.1 23.3 - - + +
19Z LEU* 2.9 33.2 + - - +
20Z ASN* 2.7 53.4 + - - +
22Z LEU* 1.3 75.1 - - - +
24Z GLU* 1.3 58.3 + - + +
26Z PHE* 3.7 3.8 - - - +
27Z ASN* 2.9 32.5 + - - +
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Residues in contact with GLU 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z GLU* 4.3 6.2 - - - +
20Z ASN* 3.0 33.0 + - - +
21Z LEU* 3.4 26.3 - - - +
22Z LEU 3.1 0.2 - - - -
23Z ARG* 1.3 78.5 - - + +
25Z GLN* 1.3 56.8 + - - +
27Z ASN* 3.4 6.8 + - - +
28Z LEU* 2.9 33.3 + - - +
46Z VAL* 4.8 8.4 - - + +
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Residues in contact with GLN 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U LYS* 6.2 0.3 - - - -
21Z LEU 2.9 15.9 + - - +
22Z LEU* 3.1 26.0 + - - +
24Z GLU* 1.3 73.1 - - - +
26Z PHE* 1.3 67.7 + - - +
28Z LEU* 3.2 7.8 + - - +
29Z ARG* 2.9 40.2 + - + +
43Z LEU* 5.5 1.2 - - + +
46Z VAL* 3.6 20.6 - - + +
47Z ARG* 4.1 34.6 - - + +
50Z VAL* 4.4 3.8 - - - +
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Residues in contact with PHE 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U LEU* 3.3 38.8 - - + +
11U LEU* 3.6 33.7 - - + -
50U LEU* 3.8 34.8 - - + -
51U PHE* 4.9 7.2 - + - -
22Z LEU 2.9 16.6 + - - +
23Z ARG* 3.7 7.6 - - - +
25Z GLN* 1.3 77.6 - - - +
27Z ASN* 1.3 69.7 - - + +
29Z ARG* 3.0 22.1 + - - +
30Z MET* 2.9 49.9 + - + +
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Residues in contact with ASN 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U VAL* 3.5 34.5 - - - +
23Z ARG 2.9 18.5 + - - +
24Z GLU* 3.6 7.6 + - - +
26Z PHE* 1.3 83.9 - - + +
28Z LEU* 1.3 63.9 + - - +
30Z MET* 3.3 6.7 - - - +
31Z GLN* 3.0 40.5 + - - +
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Residues in contact with LEU 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z GLU 2.9 14.0 + - - +
25Z GLN* 3.2 11.0 - - - +
27Z ASN* 1.3 78.6 - - - +
29Z ARG* 1.3 59.0 + - - +
31Z GLN* 2.9 31.4 + - - +
32Z ALA* 2.9 12.8 + - - +
37Z LEU* 3.8 29.2 - - + -
42Z LEU* 3.5 39.3 - - + -
43Z LEU* 3.6 22.2 - - + +
46Z VAL* 4.0 17.9 - - + -
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Residues in contact with ARG 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U LEU 3.0 27.7 + - - -
9U LYS* 3.8 7.1 - - - +
11U LEU 2.9 30.5 + - - +
12U ARG* 3.0 61.9 + - - +
13U ALA* 5.1 0.2 - - - +
25Z GLN* 2.9 34.1 + - + +
26Z PHE* 3.3 18.1 - - - +
28Z LEU* 1.3 73.4 - - - +
30Z MET* 1.3 61.6 + - + +
32Z ALA* 3.9 8.3 - - - +
33Z ALA* 2.9 27.1 + - - +
43Z LEU* 4.6 7.6 - - + +
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Residues in contact with MET 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LEU* 5.3 3.4 - - - +
12U ARG 4.8 6.5 - - - +
13U ALA* 4.9 0.9 - - - -
14U PRO* 3.8 33.2 - - + +
32U LEU* 6.2 0.7 - - - -
51U PHE* 3.8 30.3 - - + -
95U PHE* 5.9 1.8 - - + -
96U VAL 3.6 25.6 - - - +
26Z PHE* 2.9 47.6 + - + +
27Z ASN* 3.3 11.9 - - - +
29Z ARG* 1.3 77.1 - - + +
31Z GLN* 1.3 65.1 + - - +
33Z ALA* 3.1 18.1 - - - +
34Z SER* 3.2 9.4 + - - -
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Residues in contact with GLN 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U VAL 5.2 9.1 - - - +
27Z ASN* 3.0 37.1 + - - +
28Z LEU* 2.9 17.7 + - + +
30Z MET* 1.3 76.1 - - - +
32Z ALA* 1.3 56.2 + - - +
34Z SER* 2.6 29.9 + - - -
36Z GLN* 3.1 46.7 + - - +
37Z LEU* 4.0 21.1 - - + +
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Residues in contact with ALA 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z LEU 2.9 14.1 + - - +
29Z ARG* 4.1 9.0 - - - +
31Z GLN* 1.3 76.4 - - - +
33Z ALA* 1.3 61.8 + - - +
35Z GLY* 3.3 11.8 + - - +
37Z LEU* 3.6 29.7 - - + +
43Z LEU* 4.6 14.6 - - + -
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Residues in contact with ALA 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U ALA* 3.5 30.5 - - + -
14U PRO* 4.1 14.0 - - + +
29Z ARG 2.9 17.4 + - - +
30Z MET* 3.1 17.9 - - - +
32Z ALA* 1.3 79.6 - - - +
34Z SER* 1.3 58.2 + - - +
35Z GLY 3.5 0.2 + - - -
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Residues in contact with SER 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U PRO* 5.8 5.6 - - - -
30Z MET 3.2 8.7 + - - -
31Z GLN* 2.6 22.2 + - - -
33Z ALA* 1.3 77.9 - - - +
35Z GLY* 1.3 59.0 + - - +
36Z GLN* 3.5 16.9 + - - +
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Residues in contact with GLY 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z GLN 3.2 2.6 + - - -
32Z ALA* 3.3 9.6 + - - -
33Z ALA 3.3 4.0 + - - -
34Z SER* 1.3 78.3 - - - +
36Z GLN* 1.3 56.7 + - - +
37Z LEU 3.2 12.6 + - - +
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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
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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) + - + + + + + -
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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