Contacts of the strand formed by residues 66 - 71 (chain F) in PDB entry 5B6N
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 VAL 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F TRP* 3.6 22.7 - - + -
35F ILE* 3.4 31.4 - - + +
61F PHE* 3.0 44.1 + - + +
62F ALA* 4.0 6.2 + - - +
64F ARG* 3.4 20.9 - - + +
65F ASN* 1.3 76.9 - - - +
67F LYS* 1.3 70.0 + - - +
68F LEU* 4.0 1.3 + - + +
164F VAL* 4.3 9.6 - - + -
168F GLN* 3.7 13.0 - - - +
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Residues in contact with LYS 67 (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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28F PHE* 3.3 61.9 + - + +
29F LEU* 4.7 5.3 - - + +
30F GLY* 4.6 4.4 - - - +
32F SER* 4.2 17.5 - - - +
33F TRP 3.1 13.6 + - - +
34F GLY* 3.1 4.7 - - - -
35F ILE 2.9 24.0 + - - +
65F ASN 4.3 0.2 - - - -
66F VAL* 1.3 75.6 - - - +
68F LEU* 1.3 63.7 + - - +
69F ILE* 4.0 1.4 + - - +
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Residues in contact with LEU 68 (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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28F PHE* 4.6 2.8 - - - -
35F ILE* 3.5 31.9 - - + -
37F PHE* 4.3 10.8 - - + -
54F ALA* 3.9 24.0 - - + +
58F ALA* 4.4 8.7 - - + -
61F PHE* 3.8 47.8 - - + -
66F VAL 4.0 0.8 + - - -
67F LYS* 1.3 76.2 - - - +
69F ILE* 1.3 63.9 + - - +
100F PHE* 3.1 43.3 - - + +
101F PRO* 3.7 6.4 - - - +
157F PHE* 5.2 4.9 - - + -
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Residues in contact with ILE 69 (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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14F PHE* 6.2 0.2 - - + -
18F THR* 4.5 0.4 - - + -
23F ILE* 4.3 15.3 - - + -
25F PHE* 4.3 13.5 - - + -
28F PHE* 3.8 29.2 - - + -
29F LEU* 5.5 2.2 - - + -
34F GLY 5.9 0.4 - - - -
35F ILE 2.7 18.0 + - - +
36F LEU* 3.2 28.4 - - + +
37F PHE* 2.9 28.6 + - - -
67F LYS 5.0 2.2 - - - +
68F LEU* 1.3 78.5 - - - +
70F ALA* 1.3 64.5 + - - +
100F PHE* 4.7 0.9 - - - -
101F PRO* 3.6 29.2 - - + +
103F ILE* 3.6 30.5 - - + -
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Residues in contact with ALA 70 (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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37F PHE* 3.1 35.9 - - + +
39F HIS* 4.5 6.1 - - - +
51F LEU* 4.6 6.7 - - + -
69F ILE* 1.3 77.6 - - - +
71F LEU* 1.3 57.5 + - - +
100F PHE* 4.6 4.2 - - + -
101F PRO 3.2 7.6 + - - +
102F ILE* 3.2 16.1 - - + -
103F ILE* 2.6 37.3 + - - +
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Residues in contact with LEU 71 (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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36F LEU* 4.1 19.1 - - + -
37F PHE 3.1 22.8 + - - +
38F SER* 3.3 10.2 - - - +
39F HIS* 3.0 28.7 + - - -
70F ALA* 1.3 79.6 - - - +
72F SER* 1.3 61.6 + - - +
102F ILE* 4.3 1.8 - - - -
103F ILE* 3.6 30.1 - - + +
105F ASP* 4.2 24.5 - - + +
110F LEU* 4.4 14.1 - - + -
111F ALA* 5.4 0.7 - - + -
114F LEU* 5.7 0.7 - - + -
116F MET* 3.6 34.8 - - + -
130F THR* 4.8 3.0 + - + +
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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