Contacts of the helix formed by residues 20 - 35 (chain E) in PDB entry 1MVW
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 ASP 20 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E PHE* 1.3 74.7 - - - +
21E GLU* 1.3 63.3 + - - +
22E THR* 3.1 12.6 + - - -
23E GLU* 3.0 59.6 + - - +
24E ILE* 3.2 12.6 + - - +
93E PRO* 4.4 18.5 - - - +
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Residues in contact with GLU 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 PHE 4.0 0.6 + - - -
20E ASP* 1.3 73.7 - - - +
22E THR* 1.3 58.7 + - - +
24E ILE* 3.2 15.1 + - + +
25E GLU* 2.9 50.5 + - + +
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Residues in contact with THR 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 ASP* 3.1 8.8 + - - -
21E GLU* 1.3 77.0 - - - +
23E GLU* 1.3 56.8 + - - +
25E GLU* 3.1 18.7 + - + +
26E ASP* 2.9 46.0 + - - +
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Residues in contact with GLU 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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19E PHE* 3.3 27.1 - - + -
20E ASP* 3.0 43.7 + - - +
22E THR* 1.3 77.2 - - - +
24E ILE* 1.3 56.3 + - - +
26E ASP* 3.2 14.5 + - + +
27E PHE* 3.1 50.8 + - + -
88E LEU* 5.8 1.6 - - - +
91E ALA* 5.0 12.3 - - - +
93E PRO* 5.8 5.0 - - - +
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Residues in contact with ILE 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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19E PHE* 3.9 37.2 - - + +
20E ASP 3.2 15.0 + - - +
21E GLU* 3.2 16.6 + - + +
23E GLU* 1.3 78.0 - - - +
25E GLU* 1.3 57.8 + - + +
27E PHE* 3.2 10.0 + - - +
28E LYS* 2.9 26.4 + - - +
77E PHE* 3.9 19.4 - - + -
81E LEU* 4.4 15.7 - - + -
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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 GLU* 2.9 48.4 + - + +
22E THR* 3.1 19.4 + - + +
24E ILE* 1.3 76.9 - - + +
26E ASP* 1.3 59.2 + - - +
28E LYS* 3.2 23.7 + - - +
29E GLU* 3.0 41.7 + - - +
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Residues in contact with ASP 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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835D PHE* 5.2 15.9 - - + -
839D MLY 5.4 9.3 - - - -
22E THR* 2.9 40.7 + - - +
23E GLU* 3.2 13.3 + - + +
25E GLU* 1.3 78.1 - - - +
27E PHE* 1.3 62.7 + - + +
29E GLU* 3.2 19.7 + - - +
30E ALA* 3.0 27.5 + - - +
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Residues in contact with PHE 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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832D MET* 5.9 7.2 - - + -
835D PHE* 6.2 6.1 - + - -
19E PHE* 3.5 32.8 - + - -
23E GLU* 3.1 36.1 + - + -
24E ILE* 3.2 7.4 + - - +
26E ASP* 1.3 78.6 - - + +
28E LYS* 1.3 58.2 + - - +
30E ALA* 3.4 9.4 + - + +
31E PHE* 2.9 29.6 + - - +
77E PHE* 4.1 3.9 - - - -
80E PHE* 4.6 11.2 - + + -
81E LEU* 4.0 23.6 - - + -
84E PHE* 4.3 38.6 - + + -
88E LEU* 4.5 11.0 - - + -
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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 ILE 2.9 12.8 + - - +
25E GLU* 3.2 26.8 + - - +
27E PHE* 1.3 75.2 - - - +
29E GLU* 1.3 78.9 + - - +
31E PHE* 3.3 5.8 + - + +
32E THR* 2.9 36.8 + - - +
77E PHE* 3.5 30.3 - - + -
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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
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25E GLU* 3.0 23.0 + - - +
26E ASP* 3.3 23.9 - - - +
28E LYS* 1.3 90.7 + - - +
30E ALA* 1.3 58.9 + - - +
32E THR* 3.2 7.9 + - - -
33E VAL* 3.0 35.4 + - + +
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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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835D PHE* 4.8 21.1 - - + -
26E ASP 3.0 15.9 + - - +
27E PHE* 3.4 13.2 + - + +
29E GLU* 1.3 75.4 - - - +
31E PHE* 1.3 61.8 + - - +
33E VAL* 3.2 6.9 + - - +
34E ILE* 3.1 38.4 + - + +
80E PHE* 4.9 5.6 - - + -
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Residues in contact with PHE 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 PHE 2.9 17.8 + - - +
28E LYS* 3.4 11.7 - - + +
30E ALA* 1.3 77.3 - - - +
32E THR* 1.3 61.3 + - - +
34E ILE 3.4 1.2 + - - -
35E ASP* 2.9 37.4 + - + +
40E GLY* 3.1 42.2 - - - -
41E ILE 4.2 0.7 - - - -
42E ILE* 3.5 25.6 - - + +
75E ILE* 3.4 20.6 - - + -
76E ASN 3.5 11.0 - - - -
77E PHE* 3.6 28.7 - + + -
80E PHE* 3.7 23.5 - + + -
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Residues in contact with THR 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 22.5 + - - +
29E GLU* 3.2 7.7 + - - -
31E PHE* 1.3 82.9 - - - +
33E VAL* 1.3 63.8 + - + +
35E ASP* 3.3 23.7 - - - +
36E GLN* 4.3 2.3 + - - +
38E ALA* 6.2 4.3 - - + -
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Residues in contact with VAL 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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834D LEU* 5.6 1.1 - - + -
838D ILE* 5.7 5.8 - - + -
29E GLU* 3.0 20.3 + - + +
30E ALA* 3.2 7.6 + - - +
32E THR* 1.3 80.1 - - + +
34E ILE* 1.3 62.2 + - + +
36E GLN* 3.5 13.7 + - - +
50E THR* 3.4 13.4 + - + +
54E MET* 4.4 22.9 - - + -
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Residues in contact with ILE 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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831D TRP* 2.8 66.4 - - + -
834D LEU* 5.9 1.1 - - + -
30E ALA* 3.1 23.8 + - + +
33E VAL* 1.3 80.6 - - + +
35E ASP* 1.3 60.6 + - - +
36E GLN 3.2 3.0 + - - -
42E ILE* 3.8 15.9 - - + -
46E ASP* 3.0 25.0 - - - +
47E LEU* 3.8 11.9 - - + -
50E THR* 3.2 14.7 + - + +
80E PHE* 4.4 22.9 - - + -
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Residues in contact with ASP 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 PHE* 2.9 24.4 + - + +
32E THR* 3.3 15.0 - - - +
33E VAL 3.5 0.2 - - - -
34E ILE* 1.3 74.5 - - - +
36E GLN* 1.3 57.4 + - - +
37E ASN* 2.9 25.9 - - - +
38E ALA* 3.0 21.5 + - - +
39E ASP 3.3 3.1 + - - -
40E GLY* 3.0 25.9 + - - -
41E ILE 3.1 25.7 + - - +
42E ILE* 3.5 9.7 - - + -
46E ASP* 3.2 10.2 - - - +
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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