Contacts of the helix formed by residues 20 - 43 (chain D) in PDB entry 1RXQ
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 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D SER* 4.3 0.8 + - - -
19D ILE* 1.3 78.5 - - - +
21D LYS* 1.3 63.7 + - - +
22D GLU* 3.4 17.6 + - - +
23D GLN* 2.9 26.1 + - - +
24D LYS* 3.0 22.6 + - - -
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Residues in contact with LYS 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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19D ILE 3.8 0.6 + - - -
20D SER* 1.3 73.4 - - - +
22D GLU* 1.3 70.9 + - - +
24D LYS* 3.3 16.2 + - + +
25D ASP* 3.0 39.8 + - - +
130D LEU 6.0 0.4 + - - -
131D THR* 6.1 0.4 - - - +
132D ASP* 2.6 38.5 + - - +
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Residues in contact with GLU 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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20D SER* 3.1 18.4 - - - +
21D LYS* 1.3 85.9 + - - +
23D GLN* 1.3 55.9 + - - +
25D ASP* 3.4 8.1 + - - +
26D LYS* 3.1 36.5 + - + +
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Residues in contact with GLN 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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16D ARG* 5.1 7.1 - - - +
19D ILE* 3.7 18.4 - - + -
20D SER* 2.9 22.1 + - - +
22D GLU* 1.3 73.9 - - - +
24D LYS* 1.3 67.2 + - - +
26D LYS* 3.2 35.1 + - - +
27D TRP* 2.9 62.3 + - + +
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Residues in contact with LYS 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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19D ILE* 2.9 33.7 + - + +
20D SER 3.0 17.1 + - - +
21D LYS* 3.6 17.0 - - + +
23D GLN* 1.3 79.3 - - - +
25D ASP* 1.3 60.4 + - - +
27D TRP* 3.2 6.0 + - + +
28D ILE* 2.9 34.9 + - + +
132D ASP* 4.6 17.2 + - - +
135D PHE* 3.6 40.8 - - + -
151D GLU* 2.9 36.0 + - + -
154D LEU* 3.9 15.4 - - + +
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Residues in contact with ASP 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 LYS* 3.0 36.8 + - - +
22D GLU* 3.7 6.8 - - - +
24D LYS* 1.3 79.0 - - - +
26D LYS* 1.3 63.8 + - + +
28D ILE* 3.3 16.9 + - - +
29D GLN* 3.1 22.7 + - - +
128D ARG* 5.3 1.6 + - - +
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Residues in contact with LYS 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 GLU* 3.1 23.8 + - + +
23D GLN* 3.2 37.2 + - - +
25D ASP* 1.3 75.0 - - - +
27D TRP* 1.3 59.0 + - + +
29D GLN* 3.2 6.9 + - - +
30D VAL* 2.9 34.2 + - + +
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Residues in contact with TRP 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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13D TYR* 3.5 27.6 - + - -
16D ARG* 4.5 17.5 - - - -
19D ILE* 3.6 25.1 - - + -
23D GLN* 2.9 47.4 + - + +
24D LYS* 3.7 4.3 - - + +
26D LYS* 1.3 75.4 - - + +
28D ILE* 1.3 60.5 + - - +
30D VAL* 3.7 7.1 - - + +
31D LEU* 2.9 30.7 + - - +
151D GLU 3.6 13.9 - - - -
154D LEU* 3.8 22.6 - - + +
155D GLY* 3.5 31.2 - - - -
158D VAL* 3.8 29.7 - - + +
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Residues in contact with ILE 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 LYS* 2.9 26.0 + - + +
25D ASP* 3.3 16.8 + - - +
27D TRP* 1.3 75.7 - - - +
29D GLN* 1.3 59.1 + - - +
31D LEU* 3.3 4.2 + - - -
32D GLU* 2.9 24.1 + - - +
124D THR* 3.5 24.2 - - + +
127D LEU* 3.9 35.4 - - + +
128D ARG* 3.6 40.4 - - + +
135D PHE* 4.4 11.2 - - + -
154D LEU* 4.0 12.1 - - + -
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Residues in contact with GLN 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 ASP 3.1 13.8 + - - +
26D LYS* 3.6 9.9 - - - +
28D ILE* 1.3 75.3 - - - +
30D VAL* 1.3 66.1 + - + +
32D GLU* 3.2 16.6 + - - +
33D GLU* 2.8 58.7 + - - +
128D ARG* 3.2 24.2 + - - +
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Residues in contact with VAL 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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26D LYS* 2.9 23.2 + - + +
27D TRP* 3.7 12.3 - - + +
29D GLN* 1.3 75.9 - - + +
31D LEU* 1.3 63.8 + - - +
33D GLU* 3.0 24.6 + - - +
34D VAL* 3.2 13.3 + - + +
158D VAL* 3.9 12.8 - - + -
162D HIS* 3.1 41.1 - - + +
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Residues in contact with LEU 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 TRP 2.9 16.3 + - - +
28D ILE* 3.6 5.8 - - - +
30D VAL* 1.3 78.6 - - - +
32D GLU* 1.3 60.9 + - - +
33D GLU 3.3 0.7 + - - -
34D VAL* 3.3 9.2 + - + -
72D HIS* 5.2 0.4 - - + -
120D HIS* 2.7 49.2 + - + +
123D TRP* 3.9 30.7 - - + -
124D THR* 4.2 6.7 - - + -
127D LEU* 3.9 17.7 - - + -
154D LEU* 3.7 22.2 - - + -
157D TYR* 4.2 18.6 - - + +
158D VAL* 4.3 8.5 - - + +
161D SER* 4.2 13.0 - - - +
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Residues in contact with GLU 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 ILE 2.9 14.2 + - - +
29D GLN* 3.2 23.6 + - - +
31D LEU* 1.3 75.9 - - - +
33D GLU* 1.3 60.9 + - + +
35D PRO* 3.4 12.0 - - - +
36D ALA* 5.8 0.2 - - - +
117D GLN* 4.8 11.0 + - - +
120D HIS* 4.8 6.9 - - - +
121D GLY* 4.4 11.1 - - - +
124D THR* 3.2 24.7 + - + +
128D ARG* 3.2 26.9 + - - +
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Residues in contact with GLU 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 GLN* 2.8 46.5 + - - +
30D VAL* 3.0 18.8 + - + +
32D GLU* 1.3 76.5 - - + +
34D VAL* 1.3 64.0 + - - +
35D PRO* 3.4 1.8 - - - -
36D ALA* 3.3 10.6 + - + +
37D LYS* 3.2 49.1 + - + +
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Residues in contact with VAL 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 VAL* 3.2 16.3 + - + +
31D LEU* 3.3 14.6 + - + +
33D GLU* 1.3 75.7 - - - +
35D PRO* 1.3 71.4 - - + +
37D LYS* 3.1 10.3 + - - +
38D LEU* 2.9 26.4 + - + +
68D LEU* 5.9 3.4 - - + -
72D HIS* 5.0 2.9 - - + -
116D LEU* 6.0 3.4 - - + -
120D HIS* 3.7 13.5 - - + +
158D VAL* 5.8 0.4 - - - -
161D SER* 3.5 39.5 - - - +
162D HIS* 4.5 12.1 - - + +
165D ILE* 4.0 12.3 - - + +
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Residues in contact with PRO 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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32D GLU 3.4 15.5 - - - +
33D GLU 3.5 0.7 - - - -
34D VAL* 1.3 97.2 - - + +
36D ALA* 1.3 55.5 + - - +
38D LEU* 3.3 8.0 + - + +
39D LYS* 2.9 30.1 + - - +
113D LEU* 4.6 6.4 - - + +
116D LEU* 3.5 32.1 - - + +
117D GLN* 3.5 33.2 - - + +
120D HIS* 3.6 22.2 - - + +
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Residues in contact with ALA 36 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D GLU 5.8 0.2 - - - +
33D GLU* 3.3 12.1 + - + +
35D PRO* 1.3 78.8 - - - +
37D LYS* 1.3 63.8 + - + +
39D LYS* 3.4 9.2 + - - +
40D GLN* 3.0 29.1 + - - +
117D GLN* 4.2 8.2 + - - +
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Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D GLU* 3.2 42.6 + - + +
34D VAL* 3.1 9.4 + - - +
36D ALA* 1.3 78.5 - - - +
38D LEU* 1.3 64.7 + - - +
40D GLN* 3.4 10.6 + - + +
41D ALA* 3.1 22.3 + - - +
162D HIS* 6.6 0.2 - - + -
165D ILE* 4.2 20.4 - - + +
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Residues in contact with LEU 38 (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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34D VAL* 2.9 17.9 + - + +
35D PRO* 3.7 5.2 - - + +
37D LYS* 1.3 74.4 - - - +
39D LYS* 1.3 65.8 + - - +
41D ALA* 3.1 14.6 + - + +
42D VAL* 3.2 14.6 + - + +
65D VAL* 4.3 15.3 - - + -
68D LEU* 3.7 25.1 - - + -
113D LEU* 3.6 17.3 - - + -
116D LEU* 3.5 32.5 - - + -
165D ILE* 4.0 19.4 - - + +
168D ILE* 3.7 30.5 - - + -
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Residues in contact with LYS 39 (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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35D PRO 2.9 17.5 + - - +
36D ALA* 3.7 9.0 - - - +
37D LYS 3.3 0.2 - - - -
38D LEU* 1.3 77.1 - - - +
40D GLN* 1.3 63.1 + - - +
42D VAL 3.2 0.5 + - - -
43D GLU* 2.9 60.4 + - + +
113D LEU* 4.0 31.1 - - + +
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Residues in contact with GLN 40 (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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36D ALA 3.0 18.3 + - - +
37D LYS* 3.8 12.5 - - + +
39D LYS* 1.3 77.7 - - - +
41D ALA* 1.3 59.8 + - - +
42D VAL 3.5 0.3 + - - -
43D GLU* 4.3 20.9 + - - +
44D VAL* 5.0 6.9 - - - +
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LYS 3.1 13.8 + - - +
38D LEU* 3.1 13.2 + - + +
40D GLN* 1.3 78.8 - - - +
42D VAL* 1.3 58.9 + - + +
44D VAL* 5.4 3.3 - - - +
45D MSE 3.3 22.5 - - - +
165D ILE* 4.8 4.0 - - + -
168D ILE* 3.9 20.3 - - + +
169D THR* 3.9 23.1 - - + -
172D SER* 4.6 1.7 + - - -
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Residues in contact with VAL 42 (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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38D LEU* 3.2 16.5 + - + +
39D LYS 4.1 0.7 - - - +
41D ALA* 1.3 81.8 - - - +
43D GLU* 1.3 68.9 + - - +
44D VAL 3.2 2.9 - - - -
45D MSE 3.0 30.6 + - - +
50D LEU* 4.4 8.7 - - + +
61D VAL* 3.6 27.6 - - + -
65D VAL* 4.1 15.7 - - + -
109D PRO* 4.6 7.1 - - + +
113D LEU* 3.7 31.9 - - + -
168D ILE* 3.9 14.6 - - + -
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Residues in contact with GLU 43 (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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39D LYS* 2.9 51.6 + - + +
40D GLN* 4.3 20.2 + - - +
41D ALA 3.9 0.8 - - - -
42D VAL* 1.3 80.6 - - - +
44D VAL* 1.3 69.3 + - + +
45D MSE 3.3 3.7 + - - +
113D LEU* 5.3 4.3 - - + -
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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