Contacts of the helix formed by residues 19 - 32 (chain E) in PDB entry 2B05
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 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E ALA* 2.8 15.2 + - - +
17E ALA* 4.5 5.8 - - + +
18E GLU* 1.3 75.1 - - - +
20E TYR* 1.3 61.2 + - - +
21E ASP* 3.4 3.4 - - - -
22E ASP* 3.3 10.7 + - + +
23E MET* 3.0 21.9 + - - +
85F TYR* 3.6 22.9 - - - +
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Residues in contact with TYR 20 (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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15E GLU* 4.4 7.4 + - + +
18E GLU* 3.8 45.7 + - + +
19E ARG* 1.3 69.8 - - - +
21E ASP* 1.3 63.9 + - - +
23E MET* 3.0 40.1 - - + +
24E ALA* 2.8 30.0 + - - +
47E VAL* 4.6 4.5 - - + -
48E ALA* 4.1 2.5 - - - +
51E ASN* 3.4 52.8 + - + -
52E VAL* 3.6 15.2 - - + +
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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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19E ARG* 3.4 0.9 - - - -
20E TYR* 1.3 78.3 + - - +
22E ASP* 1.3 55.5 - - - +
24E ALA* 3.3 4.3 + - - +
25E ALA* 2.9 29.1 + - - +
52E VAL* 3.5 30.0 - - - +
56E ARG* 3.7 15.2 + - - -
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Residues in contact with ASP 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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14E ALA* 4.0 12.8 - - + -
19E ARG* 3.3 18.8 + - + +
21E ASP* 1.3 77.8 - - - +
23E MET* 1.3 56.8 + - - +
25E ALA* 3.6 6.9 - - - +
26E ALA* 3.0 30.8 + - - +
85F TYR* 4.4 9.2 - - + +
88F LYS* 5.7 7.2 - - - -
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Residues in contact with MET 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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11E ALA* 3.3 30.4 - - + +
14E ALA* 3.7 8.4 - - + +
15E GLU* 3.1 42.0 - - + +
19E ARG 3.0 10.3 + - - +
20E TYR* 3.0 46.2 - - + +
21E ASP 3.2 0.4 - - - -
22E ASP* 1.3 77.5 - - - +
24E ALA* 1.3 57.0 + - - +
26E ALA* 3.5 2.4 + - - +
27E MET* 3.0 28.6 + - - +
44E LEU* 4.0 11.7 - - - +
47E VAL* 4.5 4.7 - - + -
48E ALA* 3.6 26.8 - - + +
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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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20E TYR 2.8 18.5 + - - +
21E ASP* 3.7 4.5 - - - +
23E MET* 1.3 73.0 - - - +
25E ALA* 1.3 60.7 + - - +
27E MET* 5.2 1.1 - - - -
28E LYS* 2.8 32.8 + - - +
48E ALA* 3.7 11.4 - - + +
49E TYR* 3.5 36.9 - - + -
52E VAL* 4.2 12.1 - - + -
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Residues in contact with ALA 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 2.9 17.0 + - - +
22E ASP* 3.6 8.5 - - - +
23E MET 3.3 0.2 - - - -
24E ALA* 1.3 73.4 - - - +
26E ALA* 1.3 65.8 + - - +
28E LYS* 3.3 16.2 + - - +
29E ASN* 3.0 23.9 + - - +
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Residues in contact with ALA 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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7E LEU* 3.6 30.4 - - + +
10E LYS* 4.2 9.6 - - + -
11E ALA* 4.0 13.7 - - + +
22E ASP 3.0 16.9 + - - +
23E MET 3.7 4.0 - - - +
25E ALA* 1.3 77.3 - - - +
27E MET* 1.3 58.1 + - - +
29E ASN* 3.2 9.9 + - - +
30E VAL* 3.0 30.8 + - - +
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Residues in contact with MET 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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8E VAL* 5.3 4.5 - - + -
11E ALA* 3.8 23.8 - - + -
23E MET 3.0 16.0 + - - +
24E ALA* 4.6 1.3 - - - +
26E ALA* 1.3 74.5 - - - +
28E LYS* 1.3 61.2 + - - +
30E VAL* 3.4 16.8 + - + +
31E THR* 2.9 31.5 + - - -
41E GLU* 4.6 7.4 - - + +
44E LEU* 4.1 21.8 - - + +
45E LEU* 4.1 27.5 - - + +
48E ALA* 5.5 0.2 - - + -
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Residues in contact with LYS 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 2.8 16.3 + - - +
25E ALA* 3.5 16.5 - - - +
27E MET* 1.3 75.0 - - - +
29E ASN* 1.3 61.6 + - - +
31E THR* 3.2 8.7 + - - -
32E GLU* 2.9 29.6 + - - +
45E LEU* 4.4 0.8 - - - +
49E TYR* 3.6 8.1 - - + +
99E ASP* 3.1 31.2 + - - +
103E LEU* 3.7 33.1 - - + +
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Residues in contact with ASN 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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7E LEU* 3.9 20.0 - - + -
25E ALA 3.0 14.2 + - - +
26E ALA* 3.4 11.9 - - - +
28E LYS* 1.3 74.3 - - - +
30E VAL* 1.3 64.2 + - - +
32E GLU* 3.3 13.7 + - - +
33E LEU* 3.3 22.4 + - - +
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Residues in contact with VAL 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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4E ARG* 4.7 9.0 - - + +
7E LEU* 3.6 24.9 - - + -
8E VAL* 4.2 24.7 - - + -
26E ALA 3.0 18.5 + - - +
27E MET* 3.7 17.9 - - + +
28E LYS 3.3 0.4 - - - -
29E ASN* 1.3 74.6 - - - +
31E THR* 1.3 63.8 - - - +
33E LEU* 3.0 31.5 + - + +
34E ASN 4.3 0.9 + - - -
35E GLU* 4.9 5.4 - - - +
37E LEU* 6.5 0.7 - - + -
41E GLU* 4.5 17.5 - - + +
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Residues in contact with THR 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 MET 2.9 17.5 + - - -
28E LYS* 3.4 11.7 - - - -
30E VAL* 1.3 74.8 - - - +
32E GLU* 1.3 57.6 + - - +
34E ASN* 3.0 21.5 + - - -
35E GLU 4.6 5.9 + - - +
45E LEU* 4.0 19.8 - - - +
103E LEU* 4.2 15.0 - - + -
107E TYR* 3.7 32.3 - - + +
108E LEU* 3.8 27.6 - - + +
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Residues in contact with GLU 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 LYS 2.9 16.6 + - - +
29E ASN* 3.6 11.2 - - - +
30E VAL 3.2 0.6 - - - -
31E THR* 1.3 71.9 - - - +
33E LEU* 1.3 60.1 + - + +
34E ASN* 3.0 12.8 + - - +
103E LEU* 5.6 3.6 - - + +
107E TYR* 4.9 8.1 - - - -
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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