Contacts of the strand formed by residues 52 - 57 (chain F) in PDB entry 1E50
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 52 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F PHE* 4.6 20.8 - - - -
43F ARG 4.8 0.4 + - - -
46F ASN* 5.5 0.8 - - - +
47F ALA* 2.6 89.9 + - + +
48F CYS* 3.3 2.8 + - - -
50F ASP* 4.4 13.7 + - - +
51F GLY* 1.3 73.1 - - - +
53F SER* 1.3 67.1 + - - +
66F LEU 3.3 9.9 - - - +
67F GLN* 5.4 7.2 - - + +
68F PHE* 3.7 2.2 - - - -
69F PHE* 6.0 0.4 - - + -
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR* 3.7 6.1 - - - -
44F PHE* 3.5 21.0 - - - -
47F ALA* 4.8 5.4 - - - -
48F CYS* 4.7 0.7 - - - -
52F ARG* 1.3 82.4 - - - +
54F GLU* 1.3 70.0 + - - +
55F ILE* 3.5 19.8 - - - +
65F SER* 3.4 5.0 + - - -
66F LEU* 2.7 37.9 + - - +
68F PHE* 3.6 23.8 - - - -
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E MET* 3.5 30.2 - - - +
114E SER* 4.1 11.8 + - - -
29F TYR* 3.3 12.8 - - + -
30F THR* 2.8 38.3 + - - +
31F GLY* 4.2 19.4 - - - +
53F SER* 1.3 79.8 + - - +
55F ILE* 1.3 59.9 + - - +
63F ASN* 4.8 0.9 - - - +
64F LEU 3.3 4.5 - - - +
65F SER* 4.3 11.2 - - - +
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Residues in contact with ILE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 3.6 20.6 - - + -
28F LYS 3.5 11.9 - - - +
29F TYR* 4.2 2.5 - - - -
30F THR* 3.9 0.2 + - - -
44F PHE* 4.5 0.4 - - + -
53F SER* 3.5 17.9 - - - +
54F GLU* 1.3 81.0 - - - +
56F ALA* 1.3 64.9 + - - +
57F PHE* 5.8 0.5 - - - -
62F THR 4.2 0.2 - - - +
63F ASN* 3.4 3.4 - - - -
64F LEU* 2.7 33.9 + - - +
66F LEU* 4.1 11.9 - - + -
97F LEU* 4.0 16.4 - - + -
110F TRP* 3.5 46.0 + - + +
114F ILE* 3.6 23.3 - - + -
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Residues in contact with ALA 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 4.5 15.0 - - + -
27F ILE* 3.3 2.6 - - - -
28F LYS 2.9 30.7 + - - +
30F THR* 3.5 14.6 - - + -
55F ILE* 1.3 75.1 - - - +
57F PHE* 1.3 66.0 + - - +
58F VAL* 3.1 7.0 + - + +
61F GLY 5.1 0.2 - - - -
62F THR 3.0 14.1 - - - +
63F ASN* 3.2 25.3 + - + +
110F TRP* 6.2 0.2 - - - -
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Residues in contact with PHE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 3.7 40.6 - - + -
25F CYS* 3.7 23.1 - - - -
26F GLU 3.6 5.2 - - - +
27F ILE* 3.8 16.8 - - + +
55F ILE 5.8 0.4 - - - -
56F ALA* 1.3 71.4 - - - +
58F VAL* 1.3 53.7 + - - +
59F ALA* 3.5 2.0 - - + +
60F THR* 3.5 5.1 + - - +
61F GLY* 2.8 32.1 + - - -
62F THR* 2.7 29.4 + - + +
64F LEU* 3.9 14.1 - - + -
110F TRP* 3.3 34.3 - + - -
123F GLY 3.7 17.9 - - - -
124F CYS* 3.8 19.5 - - - -
125F LEU* 4.2 5.4 - - + -
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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