Contacts of the helix formed by residues 50 - 62 (chain E) in PDB entry 2WQU
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 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.8 5.0 - - + +
41A PRO* 4.8 1.0 - - - +
48E PHE 3.3 8.2 + - - +
49E SER* 1.3 78.9 + - - +
51E ASP* 1.3 66.9 + - - +
52E ALA* 3.0 14.8 + - - +
53E PHE* 2.9 28.8 + - + +
54E ALA* 3.1 19.4 + - - +
87E ASP 4.5 0.3 - - - +
88E ILE* 3.9 0.3 - - - -
89E LYS* 3.1 44.5 + - - +
90E SER* 3.3 31.9 + - - +
92E GLN 5.2 0.4 + - - -
1323E SO4 4.0 11.8 + - - -
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Residues in contact with ASP 51 (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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49E SER 3.6 3.9 + - - -
50E ASP* 1.3 76.2 + - - +
52E ALA* 1.3 62.5 + - - +
54E ALA* 3.6 6.4 + - - +
55E GLU* 3.3 26.7 + - - +
66E VAL* 5.3 5.4 - - - +
1323E SO4 4.1 22.2 + - - +
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Residues in contact with ALA 52 (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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50E ASP* 3.0 8.7 + - - +
51E ASP* 1.3 76.2 - - - +
53E PHE* 1.3 61.5 + - - +
55E GLU* 3.3 9.8 - - - +
56E THR* 3.0 27.6 + - - -
86E SER* 3.2 28.2 - - - +
87E ASP* 3.7 19.7 - - + +
88E ILE* 4.2 2.7 - - + -
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Residues in contact with PHE 53 (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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48E PHE* 3.5 40.6 - + + -
50E ASP* 2.9 14.7 + - + +
51E ASP 3.4 0.2 - - - -
52E ALA* 1.3 74.3 - - - +
54E ALA* 1.3 66.1 + - - +
56E THR* 3.0 11.3 + - - -
57E ILE* 3.0 27.8 + - + +
81E ILE* 3.9 30.1 - - + -
88E ILE* 3.8 28.2 - - + +
90E SER 3.6 24.9 - - - +
91E VAL* 4.0 26.9 - - + -
92E GLN 4.2 2.5 - - - -
94E ILE* 3.9 26.7 - - + -
105E LEU* 4.9 2.9 - - + -
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Residues in contact with ALA 54 (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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44E ILE* 3.4 33.5 - - + +
45E LYS* 4.7 5.2 - - + -
48E PHE* 3.6 27.9 - - - +
50E ASP 3.1 11.8 + - - +
51E ASP* 3.7 7.2 - - - +
53E PHE* 1.3 75.1 - - - +
55E GLU* 1.3 55.7 + - - +
57E ILE* 3.3 1.1 + - - -
58E LYS* 3.0 26.2 + - - +
66E VAL* 4.0 12.5 - - + +
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Residues in contact with GLU 55 (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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51E ASP* 3.3 16.8 + - - +
52E ALA* 3.3 13.9 - - - +
53E PHE 3.2 0.2 - - - -
54E ALA* 1.3 77.9 - - - +
56E THR* 1.3 59.3 + - - +
58E LYS* 2.7 35.4 + - - +
59E ASP* 3.0 31.6 + - - +
66E VAL* 3.2 24.5 - - - +
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Residues in contact with THR 56 (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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52E ALA 3.0 14.7 + - - -
53E PHE* 3.0 18.7 + - + -
55E GLU* 1.3 74.0 - - - +
57E ILE* 1.3 66.0 + - + +
59E ASP* 3.3 7.8 + - + +
60E ASN* 3.0 24.6 + - + +
81E ILE* 3.8 18.4 - - + -
82E ILE 4.8 3.8 - - - +
83E ALA* 3.6 27.2 - - + +
86E SER* 4.8 4.7 - - - -
88E ILE* 3.9 11.8 - - - +
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Residues in contact with ILE 57 (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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44E ILE* 3.9 12.1 - - + -
48E PHE* 3.7 51.1 - - + -
53E PHE* 3.0 21.7 + - + +
54E ALA 3.6 7.2 - - - +
56E THR* 1.3 76.9 - - + +
58E LYS* 1.3 57.9 + - - +
60E ASN* 3.3 4.9 + - + +
61E LEU* 3.0 52.3 + - + +
75E LEU* 4.5 2.9 - - + -
78E ILE* 3.9 20.4 - - + -
81E ILE* 4.5 13.7 - - + -
97E LEU* 4.0 10.8 - - + -
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Residues in contact with LYS 58 (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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44E ILE* 3.8 18.1 - - + +
54E ALA 3.0 13.7 + - - +
55E GLU* 2.7 34.5 + - - +
56E THR 3.2 0.2 - - - -
57E ILE* 1.3 77.8 - - - +
59E ASP* 1.3 71.6 + - - +
61E LEU 3.4 0.7 + - - -
62E LYS 2.9 23.7 + - - -
63E LYS* 3.0 31.6 + - + +
64E LYS* 3.5 24.0 - - - +
65E SER* 3.7 4.3 - - - +
66E VAL* 3.6 32.1 - - + +
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Residues in contact with ASP 59 (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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55E GLU* 3.0 16.7 + - - +
56E THR* 3.3 10.3 + - + +
58E LYS* 1.3 89.3 + - - +
60E ASN* 1.3 64.8 + - - +
62E LYS* 3.0 22.4 + - - +
63E LYS 5.5 0.6 - - - +
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Residues in contact with ASN 60 (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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56E THR* 3.0 19.0 + - + +
57E ILE* 3.6 8.7 - - + +
59E ASP* 1.3 76.3 - - - +
61E LEU* 1.3 60.9 + - - +
62E LYS* 3.5 10.4 + - - +
78E ILE* 3.3 40.1 - - + +
79E ASP 5.4 0.2 + - - -
80E GLN 4.0 15.9 + - - -
81E ILE* 5.5 4.2 - - + +
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Residues in contact with LEU 61 (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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44E ILE* 4.3 2.5 - - + -
57E ILE* 3.0 39.2 + - + +
60E ASN* 1.3 74.6 - - - +
62E LYS* 1.3 69.4 + - - +
63E LYS* 3.8 22.1 - - + +
70E VAL* 3.6 27.8 - - + -
74E GLU* 3.5 38.4 - - + +
75E LEU* 4.3 9.0 - - + -
77E SER* 4.8 3.1 - - - +
78E ILE* 4.0 16.8 - - + -
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Residues in contact with LYS 62 (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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58E LYS 2.9 7.9 + - - -
59E ASP* 3.0 15.4 + - - +
60E ASN 4.2 8.3 - - - +
61E LEU* 1.3 81.1 - - - +
63E LYS* 1.3 63.3 + - - +
64E LYS* 5.5 2.1 - - - +
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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