Contacts of the helix formed by residues 20 - 37 (chain E) in PDB entry 2LPZ
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 VAL 20 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PHE* 3.3 36.3 - - + +
17E ASP* 3.1 5.4 - - - +
19E GLY* 1.3 85.3 - - - +
21E ASP* 1.3 63.4 + - - +
22E ASN 3.1 3.6 - - - +
23E LEU* 3.1 29.1 + - + +
57E TYR* 3.2 39.1 - - + -
5K TRP* 3.6 22.4 - - + +
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Residues in contact with ASP 21 (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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17E ASP* 2.5 23.5 + - - +
18E THR* 3.8 11.4 + - - +
19E GLY 3.7 1.6 - - - -
20E VAL* 1.3 74.1 - - - +
22E ASN* 1.3 69.0 + - - +
24E GLN* 3.9 11.1 + - - +
25E THR* 4.0 10.7 + - - -
57E TYR* 5.0 6.0 + - - -
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Residues in contact with ASN 22 (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* 3.1 1.2 - - - +
21E ASP* 1.3 86.0 - - - +
23E LEU* 1.3 66.3 + - - +
24E GLN 3.2 0.7 - - - -
25E THR* 3.0 9.8 + - - -
26E GLN* 2.8 34.2 + - + +
3K THR 5.5 1.4 + - - -
4K PRO* 5.3 2.2 - - - +
5K TRP* 3.8 34.6 - - + +
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Residues in contact with LEU 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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20E VAL* 3.1 28.6 + - + +
22E ASN* 1.3 79.1 - - - +
24E GLN* 1.3 64.3 + - - +
26E GLN* 3.2 4.3 + - - +
27E VAL* 3.0 21.8 + - - +
50E LYS* 3.5 31.0 - - + +
53E GLU* 3.7 31.9 - - + +
54E TYR* 4.4 5.6 - - + -
57E TYR* 3.8 24.5 - - + -
5K TRP* 3.7 36.9 - - + -
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Residues in contact with GLN 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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20E VAL 3.7 2.2 + - - -
21E ASP* 4.2 7.7 - - - +
22E ASN 3.2 0.2 - - - -
23E LEU* 1.3 77.2 - - - +
25E THR* 1.3 56.5 + - - +
27E VAL* 3.3 8.4 - - - +
28E THR* 2.7 44.0 + - - +
54E TYR* 4.0 16.9 + - + +
57E TYR* 2.8 32.9 + - + +
58E ARG* 3.6 21.9 - - - +
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Residues in contact with THR 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 ASP 4.0 8.5 + - - -
22E ASN* 3.0 14.8 + - - -
24E GLN* 1.3 80.1 - - - +
26E GLN* 1.3 60.6 + - + +
28E THR* 3.4 5.5 + - - -
29E GLU* 3.0 51.4 + - + +
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Residues in contact with GLN 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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22E ASN* 2.8 24.5 + - + +
23E LEU* 3.2 4.7 + - - +
25E THR* 1.3 79.4 - - + +
27E VAL* 1.3 57.7 + - - +
29E GLU* 3.4 8.8 + - - +
30E ALA* 2.9 28.8 + - - +
50E LYS* 2.9 40.1 + - + +
4K PRO* 4.4 9.3 - - - +
5K TRP* 3.0 57.4 + - - +
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Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU 3.0 15.0 + - - +
24E GLN 3.3 11.4 - - - +
26E GLN* 1.3 73.9 - - - +
28E THR* 1.3 67.3 + - - +
30E ALA* 4.0 4.5 - - - -
31E LEU* 3.0 21.7 + - - +
47E TYR* 3.4 29.8 - - + +
50E LYS* 3.8 13.4 - - + +
51E LEU* 3.7 36.1 - - + +
54E TYR* 3.8 29.4 - - + -
68J PHE* 6.1 3.8 - - + -
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Residues in contact with THR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLN* 2.7 33.0 + - - +
25E THR* 3.7 6.5 - - - -
27E VAL* 1.3 78.6 - - - +
29E GLU* 1.3 61.9 + - + +
31E LEU* 3.2 11.0 + - + +
32E ASP* 2.9 40.7 + - - +
54E TYR* 5.8 0.5 - - - -
68J PHE* 6.5 0.4 - - - -
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E THR* 3.0 40.5 + - + +
26E GLN* 3.8 7.8 - - - +
28E THR* 1.3 73.9 - - + +
30E ALA* 1.3 60.8 + - - +
32E ASP* 3.3 13.3 + - - +
33E LYS* 3.0 45.5 + - - +
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Residues in contact with ALA 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 GLN 2.9 18.8 + - - +
27E VAL* 3.7 8.7 - - - +
28E THR 3.3 0.2 - - - -
29E GLU* 1.3 77.6 - - - +
31E LEU* 1.3 56.5 + - - +
33E LYS* 3.6 7.4 + - - +
34E LEU* 2.9 30.1 + - - +
43E LEU* 4.8 6.7 - - + +
46E ALA* 4.8 6.3 - - + -
47E TYR* 3.8 32.4 - - + +
50E LYS* 4.9 4.9 - - + -
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Residues in contact with LEU 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 VAL 3.0 15.5 + - - +
28E THR* 3.2 14.1 + - + +
30E ALA* 1.3 73.9 - - - +
32E ASP* 1.3 63.1 + - - +
34E LEU* 3.7 6.7 - - + -
35E ALA* 2.8 34.3 + - + +
47E TYR* 3.6 30.2 - - + +
12J VAL* 5.1 7.9 - - + +
15J LYS* 5.0 22.4 - - + -
16J PHE* 5.3 12.3 - - + +
64J THR* 4.4 14.4 - - + +
68J PHE* 3.8 31.6 - - + -
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Residues in contact with ASP 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 THR* 2.9 30.5 + - - +
29E GLU* 3.3 17.1 + - - +
31E LEU* 1.3 80.8 - - - +
33E LYS* 1.3 62.1 + - + +
35E ALA* 3.5 15.3 - - - +
36E ALA* 3.7 5.9 + - - +
15J LYS* 5.3 13.3 + - - +
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Residues in contact with LYS 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 GLU* 3.0 30.5 + - - +
30E ALA* 4.0 3.4 - - - +
32E ASP* 1.3 75.9 - - + +
34E LEU* 1.3 65.5 + - - +
36E ALA* 2.9 19.2 + - - +
37E LYS 3.2 8.0 + - - -
43E LEU* 3.5 33.6 - - + +
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Residues in contact with LEU 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 ALA 2.9 20.3 + - - +
31E LEU* 3.7 7.4 - - + +
33E LYS* 1.3 75.7 - - - +
35E ALA* 1.3 57.9 + - - +
37E LYS 3.0 13.4 - - - +
38E PRO* 2.8 55.5 - - + +
43E LEU* 3.5 29.5 - - + +
44E LEU* 3.6 25.8 - - + +
47E TYR* 3.3 38.6 - - + -
16J PHE* 5.4 6.5 - - + -
60J ALA* 6.2 2.2 - - + -
64J THR* 5.4 4.9 - - + -
79P PHE* 5.6 1.1 - - + -
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Residues in contact with ALA 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 LEU* 2.8 19.3 + - + +
32E ASP* 3.5 10.3 - - - +
33E LYS 3.1 0.2 - - - -
34E LEU* 1.3 76.9 - - - +
36E ALA* 1.3 60.6 + - - +
38E PRO* 3.6 0.5 - - - +
15J LYS 3.4 26.0 - - - +
16J PHE* 3.6 25.6 - - + +
19J GLY* 3.2 22.8 - - - +
20J VAL* 3.3 12.1 - - - +
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Residues in contact with ALA 36 (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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32E ASP 3.7 5.0 + - - +
33E LYS* 2.9 14.1 + - - +
35E ALA* 1.3 80.1 - - - +
37E LYS* 1.3 68.4 + - + +
38E PRO* 3.6 0.2 - - - -
19J GLY* 3.5 14.4 - - - +
5P TRP* 2.7 36.0 + - + +
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Residues in contact with LYS 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 LYS 3.2 3.0 + - - -
34E LEU* 3.0 11.8 + - - +
36E ALA* 1.3 89.5 - - + +
38E PRO* 1.3 67.6 - - - +
39E SER 3.0 3.3 + - - +
40E ASP* 3.1 25.9 + - + +
43E LEU* 3.7 13.3 - - + +
6P SER 3.5 23.6 - - - +
7P GLY* 4.2 1.6 - - - -
8P TYR* 4.0 25.3 - - + +
11P ASP* 2.8 21.5 + - - +
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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
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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