Contacts of the helix formed by residues 12 - 35 (chain D) in PDB entry 2ZUQ
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 ARG 12 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLY* 1.3 65.6 - - - -
13D GLY* 1.3 51.9 + - - +
14D ALA 3.6 0.2 - - - -
15D TRP* 3.4 4.1 + - - +
16D LEU* 2.6 57.3 + - + +
62D ALA* 4.2 9.9 - - - +
64D ALA 6.0 0.4 - - - +
65D PRO* 3.3 33.7 - - + +
66D LYS* 6.0 2.5 - - - +
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Residues in contact with GLY 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLY 2.5 7.2 + - - -
12D ARG* 1.3 71.9 - - - +
14D ALA* 1.3 51.0 + - - -
15D TRP 2.8 10.7 + - - -
16D LEU* 4.1 6.5 - - - -
17D LEU* 2.7 37.4 + - - +
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN* 3.5 32.3 - - - +
11D GLY 2.8 13.8 + - - +
13D GLY* 1.3 70.3 - - - -
15D TRP* 1.3 64.4 + - + +
17D LEU* 4.6 7.1 - - - +
18D MET* 3.8 21.7 - - - +
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Residues in contact with TRP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN* 4.7 3.2 - - - +
11D GLY* 4.1 24.8 - - - +
12D ARG 3.4 2.2 + - - +
13D GLY 2.8 1.2 + - - -
14D ALA* 1.3 82.9 - - + +
16D LEU* 1.3 59.2 + - - +
17D LEU 3.2 1.8 - - - -
18D MET* 3.0 8.9 + - - +
19D ALA* 2.9 24.1 + - - +
57D ALA 4.0 1.1 - - - -
58D ALA* 3.5 31.5 - - + +
61D GLY* 3.1 23.1 + - - -
62D ALA* 3.5 22.0 - - - +
65D PRO 5.4 0.4 - - - -
70D ARG* 4.2 28.7 - - + +
73D ALA* 3.7 28.7 - - + -
74D MET* 3.8 20.2 - - + -
77D TRP* 4.2 17.0 - + - -
161D VAL* 4.3 21.8 - - + -
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 2.6 47.7 + - + +
13D GLY* 4.0 4.3 - - - +
15D TRP* 1.3 67.8 - - - +
17D LEU* 1.3 63.6 + - - +
18D MET 3.2 1.3 - - - -
19D ALA* 4.1 7.6 - - + +
20D PHE* 3.1 27.9 + - + +
59D LEU* 6.4 1.6 - - + -
62D ALA* 3.9 19.0 - - + +
63D ILE* 5.4 8.5 - - + -
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY* 2.7 22.4 + - - +
14D ALA* 4.5 6.1 - - - +
16D LEU* 1.3 72.8 - - - +
18D MET* 1.3 77.0 + - + +
20D PHE* 3.6 9.1 - - + +
21D THR* 3.0 26.6 + - + +
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Residues in contact with MET 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA 3.8 17.5 - - - +
15D TRP* 3.0 12.6 + - + +
17D LEU* 1.3 96.2 - - + +
19D ALA* 1.3 55.6 + - - +
20D PHE 2.6 5.9 + - - -
21D THR* 2.5 47.8 + - + +
22D ALA* 3.2 6.7 + - - +
54D VAL* 5.3 0.9 - - - -
58D ALA* 3.6 5.6 - - + -
77D TRP* 3.1 34.5 - - + -
153D TYR* 5.0 8.7 - - + -
156D VAL* 4.4 20.4 - - + -
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TRP 2.9 14.8 + - - +
16D LEU* 4.5 11.2 - - + +
18D MET* 1.3 71.3 - - - +
20D PHE* 1.3 60.1 + - - +
22D ALA* 4.1 1.5 + - - +
23D LEU* 3.6 16.3 + - - +
54D VAL 4.3 8.7 - - - -
55D LEU* 3.6 15.2 - - - +
58D ALA* 3.5 7.1 - - - +
59D LEU* 3.6 49.1 - - + +
62D ALA* 5.2 0.7 - - + -
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.1 22.1 + - + +
17D LEU* 3.6 8.5 - - + +
18D MET 2.6 4.8 + - - -
19D ALA* 1.3 75.1 - - - +
21D THR* 1.3 57.5 + - - +
23D LEU* 3.3 7.8 + - + +
24D ALA* 2.7 48.1 + - + +
27D LEU* 6.0 5.2 - - + -
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Residues in contact with THR 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 3.0 10.9 + - + +
18D MET* 2.5 59.8 + - + +
20D PHE* 1.3 75.9 - - - +
22D ALA* 1.3 54.5 + - - -
24D ALA* 3.3 11.0 - - - +
25D LEU* 2.9 30.3 + - - +
153D TYR* 3.3 22.8 + - + +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET 3.2 9.7 + - - +
19D ALA 4.5 2.5 - - - +
21D THR* 1.3 75.6 - - - +
23D LEU* 1.3 60.5 + - - +
25D LEU* 3.2 15.0 + - + +
26D GLU* 2.8 32.8 + - - +
51D LEU* 4.1 11.2 - - + +
54D VAL* 4.2 28.0 - - + +
55D LEU* 5.0 1.8 - - + +
153D TYR* 3.9 20.0 - - + +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA 3.6 9.5 + - - +
20D PHE* 3.3 12.3 + - + +
22D ALA* 1.3 73.5 - - - +
24D ALA* 1.3 60.5 + - - +
25D LEU 3.1 1.3 - - - -
26D GLU* 3.7 18.2 - - + +
27D LEU* 2.8 43.3 + - + +
30D LEU* 6.4 0.9 - - + -
52D PHE* 5.1 9.4 - - + -
55D LEU* 3.7 33.8 - - + +
59D LEU* 5.6 2.7 - - + -
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 2.7 32.4 + - + +
21D THR* 3.3 17.0 - - - +
23D LEU* 1.3 75.7 - - - +
25D LEU* 1.3 51.3 + - - +
27D LEU* 3.9 12.2 - - - +
28D THR* 2.6 31.2 + - - -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D THR* 2.9 17.4 + - - +
22D ALA* 3.2 12.3 - - + +
23D LEU 3.1 0.2 - - - -
24D ALA* 1.3 77.0 - - - +
26D GLU* 1.3 56.9 + - - +
27D LEU 3.1 4.5 - - - -
28D THR* 3.3 8.8 + - - +
29D ALA* 3.0 24.6 + - - +
51D LEU* 4.1 12.1 - - + -
146D LEU* 5.8 1.6 - - + -
149D ILE* 4.0 26.7 - - + -
153D TYR* 3.3 37.2 - - + +
177D UQ1 3.7 19.5 - - + +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ALA 2.8 23.9 + - - +
23D LEU* 3.4 17.1 + - + +
25D LEU* 1.3 69.4 - - - +
27D LEU* 1.3 58.8 + - - +
29D ALA* 3.6 11.5 - - + +
30D LEU* 3.2 34.5 + - + +
48D ARG* 2.8 33.1 - - - +
51D LEU* 2.9 31.0 - - + +
52D PHE* 3.1 50.6 + - + -
55D LEU* 5.1 2.4 - - - +
177D UQ1 5.1 1.5 - - + +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 6.0 5.8 - - + -
23D LEU* 2.8 30.0 + - + +
24D ALA* 3.9 11.2 - - + +
26D GLU* 1.3 74.8 - - - +
28D THR* 1.3 56.8 + - - +
29D ALA 3.0 4.5 - - - -
30D LEU* 3.3 5.8 + - + +
31D TRP* 2.9 30.2 + - - +
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA 2.6 22.7 + - - -
25D LEU* 3.5 10.9 - - - +
27D LEU* 1.3 77.3 - - - +
29D ALA* 1.3 60.1 + - - +
31D TRP* 3.5 13.9 - - + +
32D PHE* 3.3 36.9 - - + -
177D UQ1 4.8 3.1 - - - +
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU 3.0 12.9 + - - +
26D GLU* 3.6 13.5 - - + +
27D LEU 3.0 0.2 - - - -
28D THR* 1.3 74.2 - - - +
30D LEU* 1.3 63.6 + - - +
31D TRP 3.0 3.8 - - - -
32D PHE* 3.0 16.5 + - - +
33D GLN* 3.0 10.6 + - - +
48D ARG* 3.4 29.1 + - - +
177D UQ1 3.5 34.2 - - + +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 6.4 1.3 - - + -
26D GLU* 3.2 23.3 + - + +
27D LEU* 3.3 5.8 + - + +
29D ALA* 1.3 77.7 - - + +
31D TRP* 1.3 61.8 + - - +
33D GLN* 3.4 37.6 - - - +
34D HIS* 3.1 32.6 + - + +
35D VAL* 4.8 1.0 - - - +
48D ARG* 5.2 2.7 - - - +
52D PHE* 4.7 13.0 - - + -
122D GLN* 5.1 6.1 - - + +
123D VAL* 3.7 26.0 - - + -
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Residues in contact with TRP 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU 2.9 17.3 + - - +
28D THR* 3.5 13.5 - - + +
29D ALA 3.0 0.2 - - - -
30D LEU* 1.3 77.1 - - - +
32D PHE* 1.3 105.0 + + - +
33D GLN 3.2 0.2 - - - -
35D VAL* 2.9 79.1 + - + +
36D MET* 3.5 14.6 + - + -
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Residues in contact with PHE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 3.3 31.4 + - + -
29D ALA 3.0 3.7 + - - +
31D TRP* 1.3 111.7 - + - +
33D GLN* 1.3 58.6 + - - +
34D HIS 3.4 0.4 - - - -
36D MET* 3.7 18.4 - - + -
37D LEU 5.0 0.2 - - - -
38D LEU* 3.1 58.0 - - + +
40D PRO* 4.3 4.1 - - - +
137D PHE* 6.1 7.0 - + - -
177D UQ1 3.6 40.6 - - - +
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ALA 3.0 4.6 + - - -
30D LEU* 3.4 26.0 - - - +
31D TRP 3.2 0.4 - - - -
32D PHE* 1.3 78.9 - - - +
34D HIS* 1.3 89.4 + - + +
37D LEU* 4.7 4.0 - - - +
38D LEU 3.0 16.3 - - - +
39D LYS* 4.8 4.6 + - - +
40D PRO* 5.5 9.0 - - - +
45D ILE* 6.2 0.4 - - - +
48D ARG* 3.1 34.2 - - - +
122D GLN 3.5 16.9 - - - +
123D VAL* 3.5 25.4 + - - +
125D VAL 6.1 1.6 - - - -
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Residues in contact with HIS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.1 15.1 + - + +
33D GLN* 1.3 112.6 + - + +
35D VAL* 1.3 71.0 + - + +
36D MET 3.1 4.0 + - - -
37D LEU* 3.3 31.4 + - + +
122D GLN* 3.2 42.0 + - + +
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU 4.8 0.4 - - - +
31D TRP* 2.9 72.2 + - + +
34D HIS* 1.3 75.9 - - + +
36D MET* 1.3 73.4 + - + +
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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
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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