Contacts of the helix formed by residues 25 - 49 (chain F) in PDB entry 2EHO
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 ASN 25 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LYS* 5.9 0.2 - - - -
8F GLU* 6.1 0.5 - - - +
9F LEU* 3.2 31.6 - - - +
12F GLU* 3.3 20.3 + - - +
23F ALA* 3.1 6.6 + - + +
24F PHE* 1.3 76.4 - - - +
26F GLU* 1.3 63.1 + - - +
27F ASP* 3.2 4.0 - - + +
28F GLY* 4.0 11.2 - - - +
29F LEU* 3.3 16.3 + - - +
79F TYR* 3.0 20.2 + - - -
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Residues in contact with GLU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D HIS* 3.7 27.0 + - - -
111D LYS* 4.9 13.8 - - - +
24F PHE* 3.3 28.1 + - + +
25F ASN* 1.3 71.3 - - - +
27F ASP* 1.3 65.4 + - - +
29F LEU* 3.9 4.0 - - - +
30F ARG* 2.8 33.3 + - - +
107F ALA* 6.0 1.7 - - - +
1014F SO4 4.0 20.5 + - - +
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Residues in contact with ASP 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS* 5.0 0.9 - - - +
25F ASN* 3.2 3.8 - - + +
26F GLU* 1.3 82.9 - - - +
28F GLY* 1.3 67.0 + - - +
30F ARG* 3.6 13.0 + - - +
31F GLN* 2.8 39.2 + - + +
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Residues in contact with GLY 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS* 3.8 19.2 - - - +
9F LEU* 3.8 22.7 - - - -
25F ASN* 3.4 12.2 + - - +
27F ASP* 1.3 80.6 - - - +
29F LEU* 1.3 59.2 + - - +
31F GLN* 3.7 2.3 - - - +
32F VAL* 2.9 32.5 + - - +
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Residues in contact with LEU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E VAL* 3.7 23.3 - - + +
145E ALA* 4.3 9.2 - - + -
9F LEU* 4.3 14.3 - - + +
24F PHE* 4.0 26.9 - - + -
25F ASN* 3.3 15.1 + - - +
26F GLU* 3.9 4.7 - - - +
27F ASP 3.2 0.4 - - - -
28F GLY* 1.3 73.2 - - - +
30F ARG* 1.3 67.3 + - - +
32F VAL* 3.3 4.4 + - + +
33F LEU* 2.9 35.7 + - + +
76F THR* 3.3 28.5 - - - +
79F TYR* 5.4 4.0 - - + -
80F LEU* 4.8 8.3 - - + -
1014F SO4 4.1 11.2 - - - +
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F GLU* 2.8 24.5 + - - +
27F ASP* 3.3 13.6 + - - +
29F LEU* 1.3 72.9 - - - +
31F GLN* 1.3 51.6 + - + +
33F LEU* 3.0 11.4 + - + +
34F GLU* 2.7 46.2 + - + +
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Residues in contact with GLN 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS* 3.5 44.0 + - + +
27F ASP* 2.8 29.7 + - + +
28F GLY 3.7 4.0 - - - +
30F ARG* 1.3 75.3 - - + +
32F VAL* 1.3 57.7 + - - +
34F GLU* 3.0 10.5 + - + +
35F GLU* 2.8 39.0 + - + +
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS* 4.0 7.9 - - + -
6F ALA* 3.9 30.1 - - + +
9F LEU* 4.1 10.1 - - + -
28F GLY 2.9 19.4 + - - +
29F LEU* 3.6 9.0 - - + +
31F GLN* 1.3 75.6 - - - +
33F LEU* 1.3 60.6 + - + +
35F GLU* 3.3 9.8 + - - +
36F MSE 3.1 36.0 + - + +
72F ASN* 3.4 42.4 - - + +
76F THR* 4.8 7.6 - - - -
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E VAL 4.7 0.2 - - - +
145E ALA* 4.1 13.9 - - + +
148E HIS* 3.9 43.2 - - + +
149E MSE 3.5 32.5 - - + -
150E PRO* 5.5 0.5 - - - +
29F LEU* 2.9 39.9 + - + +
30F ARG* 3.4 10.5 - - + +
32F VAL* 1.3 73.8 - - + +
34F GLU* 1.3 66.5 + - - +
36F MSE 3.4 12.7 + - + +
37F LYS* 3.1 22.2 + - - +
76F THR* 5.5 3.1 - - + +
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Residues in contact with GLU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 2.7 29.5 + - + +
31F GLN* 3.0 14.1 + - + +
33F LEU* 1.3 74.0 - - - +
35F GLU* 1.3 58.0 + - + +
37F LYS* 3.2 27.2 + - - +
38F ALA* 3.0 26.8 + - - +
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Residues in contact with GLU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F MSE 3.1 62.1 + - + +
3F CYS* 4.4 4.0 - - - -
5F LYS* 4.2 21.2 - - - +
31F GLN* 2.8 24.3 + - + +
32F VAL* 3.5 8.3 - - - +
34F GLU* 1.3 75.2 - - + +
36F MSE 1.3 60.0 + - + +
38F ALA* 3.3 7.7 + - - +
39F LEU* 2.8 37.9 + - + +
72F ASN* 4.0 14.7 + - - +
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Residues in contact with MSE 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E MSE 3.3 47.1 - - + +
150E PRO* 3.5 16.8 - - + +
153E LEU* 4.4 4.3 - - + -
32F VAL* 3.1 21.1 + - - +
33F LEU* 3.7 13.2 - - - +
34F GLU 3.3 0.2 - - - -
35F GLU* 1.3 72.4 - - - +
37F LYS* 1.3 62.5 + - - +
39F LEU* 4.5 1.6 - - - -
40F TYR* 2.9 31.4 + - - +
69F LEU* 3.3 47.5 - - + +
72F ASN* 3.7 26.9 - - + +
73F ARG* 4.1 6.3 - - + +
76F THR* 5.0 1.8 - - - -
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Residues in contact with LYS 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E PRO* 4.1 10.5 - - + +
33F LEU 3.1 13.6 + - - +
34F GLU* 3.3 28.6 + - - +
36F MSE 1.3 75.9 - - - +
38F ALA* 1.3 62.5 + - - +
40F TYR* 3.1 5.5 + - + +
41F GLU* 3.1 49.6 + - + +
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F MSE 4.2 15.5 - - + -
34F GLU 3.0 13.4 + - - +
35F GLU* 3.5 10.1 - - - +
37F LYS* 1.3 76.3 - - - +
39F LEU* 1.3 62.7 + - - +
41F GLU* 3.2 16.4 + - - +
42F GLN* 3.0 40.2 + - - +
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F MSE 3.9 24.9 - - - +
1F MSE 3.9 20.4 - - + -
35F GLU* 2.8 24.3 + - + +
36F MSE 4.7 0.2 - - - -
38F ALA* 1.3 74.1 - - - +
40F TYR* 1.3 62.5 + - - +
42F GLN* 3.5 7.6 + - - +
43F ASN* 3.1 24.9 + - - +
65F ARG* 3.4 44.1 - - + +
68F SER* 3.8 21.8 - - - -
69F LEU* 3.9 20.8 - - + +
72F ASN* 4.2 12.6 - - - +
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E PRO* 3.7 25.8 - - + -
151E PRO* 4.1 39.1 + - + +
152E ASN* 5.2 1.4 + - - -
153E LEU* 5.1 3.4 - - + -
36F MSE 2.9 20.9 + - - +
37F LYS* 3.1 7.2 + - + +
39F LEU* 1.3 75.4 - - - +
41F GLU* 1.3 66.4 + - + +
43F ASN* 3.4 5.1 + - + +
44F GLN* 2.8 66.2 + - + +
69F LEU* 4.1 16.8 - - + +
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Residues in contact with GLU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LYS* 3.1 43.8 + - + +
38F ALA* 3.4 13.7 - - - +
40F TYR* 1.3 80.7 - - + +
42F GLN* 1.3 60.3 + - + +
43F ASN 3.0 1.1 - - - -
44F GLN* 2.7 29.1 + - - +
45F SER* 2.9 14.3 + - - -
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Residues in contact with GLN 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F MSE 4.3 13.5 - - - +
1F MSE 3.7 13.5 - - - +
38F ALA* 3.0 36.7 + - - +
39F LEU* 3.8 6.7 - - - +
41F GLU* 1.3 76.6 - - + +
43F ASN* 1.3 62.4 + - - +
45F SER* 3.5 4.6 + - - -
46F ASP* 2.9 31.7 + - - +
65F ARG* 3.0 37.1 + - - +
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Residues in contact with ASN 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU 3.1 15.1 + - - +
40F TYR* 3.5 7.6 - - + +
41F GLU 3.0 0.6 - - - -
42F GLN* 1.3 73.8 - - - +
44F GLN* 1.3 68.9 + - - +
46F ASP* 3.9 1.0 - - - +
47F VAL* 3.0 32.4 + - + +
62F ILE* 3.2 39.5 + - - +
65F ARG* 2.7 46.5 + - - +
66F HIS* 4.1 16.0 + - - +
69F LEU* 4.8 6.2 - - + +
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Residues in contact with GLN 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F TYR* 2.8 59.2 + - + +
41F GLU* 2.7 21.1 + - - +
43F ASN* 1.3 70.2 - - - +
45F SER* 1.3 66.6 + - - +
47F VAL* 3.1 12.4 + - - +
48F ASN* 3.0 24.8 + - - +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLU 2.9 9.2 + - - -
42F GLN* 3.7 10.1 - - - -
44F GLN* 1.3 75.4 - - - +
46F ASP* 1.3 71.7 + - - +
48F ASN* 3.0 19.2 + - - +
49F GLU* 3.4 21.0 + - - +
42H ARG* 5.1 0.5 + - - -
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Residues in contact with ASP 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F GLN* 2.9 20.3 + - - +
43F ASN 4.1 2.7 - - - +
45F SER* 1.3 80.3 + - - +
47F VAL* 1.3 62.2 + - - +
49F GLU* 3.3 12.8 + - - -
50F ALA* 3.3 10.2 + - - +
58F LEU* 3.5 29.2 - - + +
61F THR* 4.3 2.3 - - - +
62F ILE* 4.1 10.1 - - + +
65F ARG* 2.7 33.5 + - - +
42H ARG* 3.1 33.9 + - - -
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ASN* 3.0 27.5 + - + +
44F GLN* 3.4 8.1 - - - +
45F SER 3.0 0.6 + - - -
46F ASP* 1.3 74.4 - - - +
48F ASN* 1.3 67.9 + - - +
50F ALA* 3.0 21.3 + - + +
51F LYS* 3.5 20.9 + - + +
62F ILE* 3.4 34.3 - - + -
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Residues in contact with ASN 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLN* 3.0 18.9 - - - +
45F SER* 3.0 8.5 + - - +
47F VAL* 1.3 77.1 - - - +
49F GLU* 1.3 56.2 + - - +
50F ALA 2.8 5.4 - - - -
51F LYS* 2.8 31.6 + - - +
52F SER* 2.7 43.9 + - - +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F SER* 3.7 19.4 + - - +
46F ASP* 3.3 13.9 + - - +
48F ASN* 1.3 76.8 - - + +
50F ALA* 1.3 56.0 + - - +
51F LYS 3.3 0.4 - - - -
52F SER* 5.1 0.2 - - - -
53F GLY* 3.2 19.7 - - - +
55F ARG* 3.1 40.2 + - + +
58F LEU* 3.9 8.1 - - + -
42H ARG* 2.9 42.5 + - - -
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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) + - + + + + + -
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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