Contacts of the helix formed by residues 22 - 40 (chain E) 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 THR 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E LEU* 1.3 75.6 - - - +
23E PRO* 1.3 73.6 - - - +
24E ALA* 3.4 13.2 + - + +
25E GLU* 3.2 25.7 + - + +
26E LEU* 3.0 25.3 + - - +
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Residues in contact with PRO 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU 4.6 1.8 - - - +
22E THR* 1.3 88.4 - - - +
24E ALA* 1.3 64.9 + - - +
26E LEU* 3.1 19.5 + - + +
27E ILE* 3.1 20.3 + - - +
57E GLN* 3.8 26.5 - - + +
29G ILE* 3.3 22.9 - - + +
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Residues in contact with ALA 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E THR* 3.4 10.2 + - + +
23E PRO* 1.3 78.4 - - - +
25E GLU* 1.3 61.4 + - - +
27E ILE* 3.7 3.1 + - - +
28E GLU* 3.4 20.4 + - - +
29G ILE 3.6 1.7 + - - -
30G GLY* 3.0 28.9 - - - +
31G GLY* 4.9 3.1 - - - -
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Residues in contact with GLU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 3.0 35.5 - - + +
22E THR* 3.2 22.4 + - + +
23E PRO 3.2 0.6 - - - -
24E ALA* 1.3 78.4 - - - +
26E LEU* 1.3 59.5 + - - +
27E ILE 3.4 0.2 - - - -
28E GLU* 3.3 5.5 + - - +
29E ARG* 2.8 56.1 + - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E VAL* 6.2 1.8 - - + -
21E LEU* 4.0 18.6 - - + +
22E THR 3.0 13.5 + - - +
23E PRO* 3.1 13.6 + - + +
25E GLU* 1.3 74.3 - - - +
27E ILE* 1.3 64.4 + - + +
29E ARG* 3.2 3.3 + - - +
30E LEU* 2.8 27.9 + - - +
50E ILE* 4.1 25.1 - - + +
53E CYS* 3.5 37.0 - - + -
54E VAL* 3.3 30.5 - - + +
57E GLN* 4.0 15.0 - - + -
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Residues in contact with ILE 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 3.1 16.2 + - + +
24E ALA 4.1 4.3 - - - +
26E LEU* 1.3 82.3 - - + +
28E GLU* 1.3 64.8 + - - +
30E LEU* 3.4 7.9 - - + +
31E GLU* 3.1 42.2 + - + +
54E VAL* 4.2 18.8 - - + -
57E GLN* 5.9 4.0 - - + -
85E ILE* 3.6 46.4 - - + -
12G LYS* 6.3 0.2 - - + -
29G ILE* 4.3 16.6 - - + +
30G GLY* 4.4 10.1 - - - -
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Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ALA 3.4 14.0 + - - +
25E GLU* 3.3 11.2 + - - +
26E LEU 3.2 0.2 - - - -
27E ILE* 1.3 83.0 - - - +
29E ARG* 1.3 75.0 + - - +
31E GLU* 3.3 18.9 + - - +
32E GLN* 2.8 46.7 + - - +
176E ARG* 5.6 3.1 + - - -
12G LYS* 4.7 12.2 + - - -
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Residues in contact with ARG 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 4.3 15.0 - - + -
25E GLU* 2.8 43.9 + - - +
26E LEU* 3.5 6.5 - - - +
28E GLU* 1.3 95.6 - - - +
30E LEU* 1.3 63.5 + - - +
32E GLN* 3.1 35.7 - - + +
33E ALA* 3.0 21.8 + - - +
47E LYS* 5.8 0.6 + - - +
50E ILE* 3.5 26.9 - - + +
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU 2.8 14.5 + - - +
27E ILE* 3.4 17.5 - - + +
28E GLU 3.1 0.2 - - - -
29E ARG* 1.3 75.0 - - - +
31E GLU* 1.3 60.0 + - + +
33E ALA* 2.8 10.0 + - + +
34E TRP* 2.8 24.9 + - - +
50E ILE* 4.0 23.3 - - + +
54E VAL* 3.8 31.0 - - + -
85E ILE* 4.4 16.6 - - + +
88E VAL* 4.1 20.9 - - + -
89E LEU* 4.1 26.5 - - + +
92E TYR* 4.7 14.6 - - + -
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Residues in contact with GLU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ILE* 3.1 28.8 + - + +
28E GLU* 3.8 18.7 - - - +
30E LEU* 1.3 81.2 - - + +
32E GLN* 1.3 57.3 + - - +
34E TRP* 3.3 16.9 - - + +
35E MSE 2.9 41.2 + - + +
84E ARG* 5.4 0.9 + - - -
88E VAL* 4.1 22.6 - - + +
8G PHE* 4.4 12.6 - - - -
9G LEU* 5.6 3.5 - - + +
12G LYS* 3.0 41.0 - - - +
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Residues in contact with GLN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLU* 2.8 35.9 + - - +
29E ARG* 3.1 46.8 - - + +
31E GLU* 1.3 78.8 - - - +
33E ALA* 1.3 58.2 + - - +
35E MSE 3.7 6.4 + - - +
36E ASN* 3.2 36.5 + - - +
176E ARG* 4.0 50.7 + - + +
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Residues in contact with ALA 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ARG 3.0 10.9 + - - +
30E LEU* 2.8 13.3 + - + +
32E GLN* 1.3 75.1 - - - +
34E TRP* 1.3 67.5 + - - +
36E ASN* 3.1 6.3 + - - +
37E GLU* 2.9 27.5 + - - +
44E LEU* 5.3 0.3 - - - +
47E LYS* 4.6 20.0 - - + +
50E ILE* 5.2 3.8 - - + -
92E TYR* 3.4 28.6 - - + +
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Residues in contact with TRP 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LEU 2.8 11.4 + - - +
31E GLU* 3.3 15.0 - - + +
33E ALA* 1.3 78.1 - - - +
35E MSE 1.3 78.6 + - + +
37E GLU* 4.0 2.6 - - - +
38E LYS* 3.2 35.8 + - + +
87E TYR* 3.9 20.9 - + - -
88E VAL* 3.7 26.5 - - + -
91E SER* 2.6 28.2 + - - -
92E TYR* 3.5 32.9 - - + -
95E CYS* 5.5 0.3 - - - -
1G MSE 5.1 4.9 - - - -
5G GLU* 3.6 43.7 - - + -
8G PHE* 4.3 10.1 - + - -
9G LEU* 3.3 33.4 - - + -
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Residues in contact with MSE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLU* 2.9 24.9 + - - +
32E GLN* 3.9 7.9 - - - +
34E TRP* 1.3 89.2 - - + +
36E ASN* 1.3 69.9 + - - +
38E LYS* 3.0 10.7 + - - +
39E PHE* 2.8 43.2 - - + -
174E ARG* 4.8 17.3 - - + -
176E ARG* 4.2 25.8 - - - +
1G MSE 5.0 10.5 - - + -
9G LEU* 4.1 24.0 - - + -
150G LEU* 5.2 9.9 - - + -
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Residues in contact with ASN 36 (chain E).
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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32E GLN* 3.2 22.8 + - - +
33E ALA* 3.1 7.2 + - - +
35E MSE 1.3 79.8 - - - +
37E GLU* 1.3 59.7 + - - +
39E PHE* 2.9 6.2 + - - +
40E ALA* 2.9 31.7 + - - +
44E LEU* 3.6 18.6 - - + -
173E LEU* 6.0 4.2 - - - +
174E ARG 5.5 4.4 + - - -
176E ARG* 5.6 7.7 - - - +
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Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ALA 2.9 16.1 + - - +
34E TRP 4.0 3.8 - - - +
36E ASN* 1.3 76.2 - - - +
38E LYS* 1.3 59.6 + - - +
39E PHE 3.3 0.2 - - - -
40E ALA 4.0 0.3 - - - +
43E LEU* 3.6 4.7 - - - +
44E LEU* 2.8 49.2 + - - +
45E GLU 4.5 1.0 - - - +
92E TYR* 3.9 18.7 + - + -
95E CYS* 3.1 16.2 - - + -
96E ARG* 3.3 42.5 + - + -
99E LYS* 2.8 47.7 + - - +
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Residues in contact with LYS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TRP* 3.2 27.7 + - + +
35E MSE 3.1 13.9 - - - +
36E ASN 2.9 0.6 - - - -
37E GLU* 1.3 79.9 - - - +
39E PHE* 1.3 57.7 + - + +
40E ALA 3.8 0.8 - - - +
91E SER* 3.4 15.0 + - - -
95E CYS* 4.1 19.9 - - - +
0G MSE 2.9 44.2 + - - +
1G MSE 3.9 14.1 - - + -
5G GLU* 3.0 40.1 + - - +
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Residues in contact with PHE 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E MSE 2.8 40.8 + - + +
36E ASN* 2.9 6.7 + - - +
38E LYS* 1.3 82.7 - - + +
40E ALA* 1.3 62.5 + - - +
41E PRO 3.8 0.3 - - - -
171E VAL* 3.1 27.3 - - + +
172E PHE* 3.6 31.0 - - + +
0G MSE 3.9 40.2 - - + +
1G MSE 3.7 42.6 - - + -
150G LEU* 5.9 3.4 - - + -
153G ILE* 5.7 2.2 - - + -
154G ASN* 3.7 15.0 - - - -
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ASN 2.9 15.0 + - - +
37E GLU 4.0 1.2 + - - +
38E LYS 3.8 0.7 - - - -
39E PHE* 1.3 79.1 + - - +
41E PRO* 1.3 66.5 - - + +
42E GLU 3.1 14.8 - - - +
44E LEU* 4.0 17.9 - - + -
99E LYS* 3.0 22.7 + - - +
208E TYR* 3.8 21.1 - - + +
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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