Contacts of the strand formed by residues 40 - 46 (chain F) in PDB entry 4BEI
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 ILE 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39F VAL* 1.3 82.5 + - + +
41F GLU* 1.3 73.2 + - - +
42F ALA 4.1 2.1 + - - +
64F ILE* 3.9 22.7 - - + -
65F ARG 3.5 6.3 - - - +
66F ASN* 4.9 2.2 - - + -
67F GLU* 5.4 1.1 - - - -
72F VAL* 3.8 28.7 - - + -
74F PHE* 4.0 24.0 - - + -
106F LEU* 5.4 0.4 - - + -
135F VAL* 4.2 16.6 - - + -
137F ALA* 4.5 8.1 - - + -
143F PHE* 3.2 50.2 - - + +
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Residues in contact with GLU 41 (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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39F VAL 4.3 0.2 + - - -
40F ILE* 1.3 75.2 - - - +
42F ALA* 1.3 60.2 + - - +
43F ASN* 5.0 7.7 - - - +
63F GLY 3.7 1.2 - - - +
64F ILE* 3.5 2.4 - - - -
65F ARG* 2.8 54.6 + - + +
67F GLU* 5.0 8.9 - - + +
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Residues in contact with ALA 42 (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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40F ILE* 4.1 2.1 + - + -
41F GLU* 1.3 72.7 - - - +
43F ASN* 1.3 70.6 + - - +
63F GLY 3.4 6.7 - - - +
64F ILE* 4.7 0.9 - - + +
133F LEU* 4.2 15.0 - - + -
135F VAL* 4.3 20.0 - - + -
143F PHE* 4.6 10.0 - - + +
144F LYS* 4.4 14.6 - - - +
145F ALA* 3.5 16.5 - - + +
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Residues in contact with ASN 43 (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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41F GLU* 5.0 6.8 - - - +
42F ALA* 1.3 82.4 + - - +
44F LEU* 1.3 63.3 - - - +
61F GLN 4.4 0.9 - - - -
62F LEU* 3.7 0.3 - - - -
63F GLY* 2.9 40.1 + - - +
65F ARG* 6.1 0.7 - - - +
133F LEU* 3.2 10.2 - - - +
145F ALA* 3.7 6.1 - - - -
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Residues in contact with LEU 44 (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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43F ASN* 1.3 80.6 - - - +
45F SER* 1.3 67.3 - - - +
46F LEU* 4.4 3.6 - - + -
60F SER* 3.9 16.2 - - - -
61F GLN 3.5 4.9 - - - +
62F LEU* 3.4 31.6 - - + -
78F LEU* 4.2 4.7 - - + -
131F VAL* 3.7 31.2 - - + +
133F LEU* 3.8 13.2 - - + +
145F ALA* 3.3 34.6 - - + +
147F GLN* 3.0 37.7 - - + +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F LEU* 1.3 76.3 - - - +
46F LEU* 1.3 67.0 + - - +
47F ASN 4.2 0.2 + - - -
60F SER* 3.4 5.4 - - - -
61F GLN* 3.0 46.9 + - - +
147F GLN* 4.1 5.6 - - - -
48G GLN* 6.2 5.2 - - - -
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Residues in contact with LEU 46 (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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44F LEU* 4.4 7.4 - - + -
45F SER* 1.3 84.4 - - - +
47F ASN* 1.3 61.6 + - - +
48F GLN* 3.4 25.8 + - - +
49F ASN* 4.5 8.7 + - - +
58F ILE* 4.3 13.0 - - + -
59F SER 3.9 1.8 - - - -
60F SER* 3.9 17.7 - - - -
118F PHE* 4.9 0.7 - - + -
131F VAL* 4.3 14.4 - - + -
147F GLN* 3.6 26.0 - - + +
148F GLU 3.6 25.6 - - - +
149F PHE* 4.2 17.5 - - + -
47G ASN 3.2 12.8 - - - +
48G GLN* 5.0 4.2 - - - +
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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