Contacts of the helix formed by residues 81 - 91 (chain E) in PDB entry 3E4U
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 GLU 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E PHE* 6.1 2.0 - - - -
79E ASN* 2.7 38.6 + - - +
82E GLY* 1.3 67.1 + - - +
83E PHE 3.4 2.2 - - - +
84E CYS* 3.4 15.4 + - - +
85E ILE* 3.0 39.7 + - + +
98E ARG* 3.3 27.2 + - - -
101E ASN* 2.2 39.4 + - + +
104E ALA* 5.6 3.4 - - + -
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Residues in contact with GLY 82 (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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79E ASN* 3.1 11.3 + - - -
81E GLU* 1.3 80.3 - - - +
83E PHE* 1.3 63.5 + - - +
85E ILE* 3.5 3.0 + - - +
86E LEU* 3.1 26.9 + - - +
101E ASN 5.7 0.2 - - - -
104E ALA* 4.6 3.8 - - - -
105E VAL* 4.3 29.9 - - - +
108E THR* 4.5 10.5 - - - -
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Residues in contact with PHE 83 (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 ILE* 3.7 26.9 - - + -
38E VAL* 3.6 29.8 - - + -
43E PHE* 3.5 44.6 - + + -
50E LEU* 4.9 1.1 - - + -
57E PHE* 4.1 15.3 - + - -
74E LEU* 4.4 8.3 - - + -
78E ILE* 4.0 7.4 - - + -
79E ASN 3.3 6.1 + - - -
81E GLU 3.4 0.4 - - - +
82E GLY* 1.3 72.4 - - - +
84E CYS* 1.3 54.8 + - - +
86E LEU* 3.0 5.6 + - + +
87E LEU* 2.7 52.4 + - + -
90E MET* 5.3 2.2 - - + -
108E THR* 4.3 12.9 - - + +
112E LEU* 4.0 28.5 - - + -
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Residues in contact with CYS 84 (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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43E PHE* 3.7 33.5 - - + -
81E GLU* 3.4 18.5 + - - +
83E PHE* 1.3 79.8 - - - +
85E ILE* 1.3 56.6 + - - +
87E LEU* 3.5 5.4 + - - +
88E ASP* 2.9 47.7 + - - +
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Residues in contact with ILE 85 (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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81E GLU* 3.0 41.6 + - + +
82E GLY* 3.8 4.5 - - - +
83E PHE 3.2 0.2 - - - -
84E CYS* 1.3 74.6 - - + +
86E LEU* 1.3 60.0 + - - +
88E ASP* 3.5 8.1 + - - +
89E PHE* 3.0 26.9 + - - +
94E ARG 5.0 0.7 - - - +
95E LEU* 3.8 21.1 - - + -
96E ASN* 3.7 33.4 - - + +
97E LEU* 5.9 0.4 - - - -
98E ARG* 4.6 15.9 - - - +
101E ASN* 5.1 4.7 - - + -
105E VAL* 3.6 28.5 - - + -
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Residues in contact with LEU 86 (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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82E GLY 3.1 11.0 + - - +
83E PHE* 3.0 9.7 + - + +
85E ILE* 1.3 75.8 - - - +
87E LEU* 1.3 58.3 + - - +
89E PHE* 3.4 7.6 + - + +
90E MET* 2.9 34.1 + - + +
95E LEU* 5.0 3.1 - - + -
105E VAL* 4.2 8.1 - - + +
108E THR* 3.5 27.8 - - + +
109E ALA* 3.4 33.0 - - + +
112E LEU* 4.1 18.6 - - + -
114E MET* 3.6 26.7 - - + -
117E VAL* 3.9 27.8 - - + -
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Residues in contact with LEU 87 (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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26E ARG* 3.9 23.7 - - - +
43E PHE* 3.7 37.9 - - + -
44E ARG 4.3 9.6 - - - +
45E ALA* 3.9 6.5 - - + -
50E LEU* 3.7 30.7 - - + -
83E PHE* 2.7 31.0 + - + +
84E CYS* 3.8 5.2 - - - +
86E LEU* 1.3 69.6 - - - +
88E ASP* 1.3 65.2 + - - +
90E MET* 3.3 18.3 + - - +
91E TYR* 3.3 41.6 + - + +
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Residues in contact with ASP 88 (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 ARG* 3.5 28.6 + - - +
84E CYS* 2.9 35.6 + - - +
85E ILE* 3.8 8.4 - - + +
87E LEU* 1.3 75.3 - - - +
89E PHE* 1.3 57.1 + - - +
91E TYR* 3.2 2.6 + - - -
92E THR* 2.6 41.8 + - + +
94E ARG 4.4 3.1 - - - +
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Residues in contact with PHE 89 (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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53E CYS* 5.9 0.4 - - + -
85E ILE 3.0 17.8 + - - +
86E LEU* 3.6 4.9 - - + +
88E ASP* 1.3 72.1 - - - +
90E MET* 1.3 66.6 + - - +
92E THR* 3.8 1.1 - - - -
93E SER 2.9 28.9 + - - -
94E ARG 3.5 15.4 + - - +
95E LEU* 3.8 33.2 - - + -
114E MET* 3.7 24.2 - - + -
117E VAL* 3.5 27.1 - - + -
11F PHE* 3.5 40.4 - + + -
14F HIS* 3.1 37.0 - + - -
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Residues in contact with MET 90 (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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19E LEU* 3.5 10.9 - - - +
49E VAL* 4.2 4.5 - - + +
50E LEU* 3.6 36.3 - - + -
53E CYS* 3.8 29.4 - - + -
54E SER* 4.3 8.3 - - - -
57E PHE* 4.2 5.6 - - + -
83E PHE* 5.3 2.5 - - + -
86E LEU* 2.9 25.7 + - + +
87E LEU* 3.4 14.4 - - - +
89E PHE* 1.3 77.3 - - - +
91E TYR* 1.3 64.5 + - + +
112E LEU* 3.6 31.2 - - + -
114E MET* 3.8 21.1 - - + -
14F HIS* 3.0 23.8 + - - -
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Residues in contact with TYR 91 (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 LEU* 3.7 21.9 - - + +
20E LEU* 5.0 1.7 - - - +
22E LEU* 3.6 36.6 - - + -
23E ASN* 3.3 38.4 - - - +
26E ARG* 3.6 26.9 - - + +
45E ALA* 3.7 2.7 - - + +
46E HIS* 2.8 50.6 + + - +
49E VAL* 3.6 33.8 - - + +
50E LEU* 5.1 1.3 - - + -
87E LEU* 3.3 37.9 + - + +
88E ASP 3.2 4.2 + - - +
89E PHE 3.1 0.4 - - - -
90E MET* 1.3 79.3 - - + +
92E THR* 1.3 58.6 + - - +
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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