Contacts of the strand formed by residues 54 - 60 (chain F) in PDB entry 2ZHX
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 ASN 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E ARG* 3.0 31.5 - - - +
96E ASN* 5.2 4.6 + - - +
194E PRO* 3.4 26.6 - - + +
45F THR* 4.5 4.3 - - + -
46F ALA 3.9 3.6 - - - -
47F TYR* 3.5 9.6 - - - -
52F ASP 4.1 1.2 + - - +
53F GLU* 1.3 70.2 - - - +
55F VAL* 1.3 62.9 + - - +
56F MET* 3.7 4.9 + - + +
71F VAL 3.7 4.0 - - - +
72F ILE* 3.7 1.6 - - - -
73F GLN* 2.9 61.3 + - + +
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Residues in contact with VAL 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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8F ILE* 3.8 34.0 - - + +
12F THR* 5.2 5.2 - - + +
14F LYS* 6.2 0.7 - - + -
16F LEU* 3.4 28.7 - - + -
44F HIS 3.6 0.7 - - - +
45F THR* 3.3 1.7 - - - -
46F ALA* 2.6 46.5 + - + +
48F ASP* 4.3 6.3 - - + +
53F GLU* 3.5 18.1 + - + +
54F ASN* 1.3 74.5 - - - +
56F MET* 1.3 61.4 + - - +
70F LEU* 4.6 14.1 - - + -
71F VAL 3.9 2.5 - - - -
72F ILE* 4.8 11.2 - - + -
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Residues in contact with MET 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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194E PRO* 3.8 6.5 - - - -
195E LEU* 3.6 41.1 - - + -
43F VAL* 4.5 4.5 - - + -
44F HIS 3.1 3.1 - - - +
45F THR* 3.8 23.3 - - + +
54F ASN* 3.8 11.9 - - + +
55F VAL* 1.3 79.0 - - - +
57F LEU* 1.3 60.6 + - - +
58F LEU* 4.2 8.7 - - + -
70F LEU* 3.4 10.4 - - - +
71F VAL* 2.9 61.5 + - + +
73F GLN* 3.7 36.8 - - + +
79F ASN* 4.7 0.2 - - - +
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Residues in contact with LEU 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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4F LEU* 3.2 34.8 - - + -
7F ILE* 3.7 35.0 - - + -
8F ILE* 4.3 23.1 - - + +
44F HIS* 2.7 50.0 + - + +
56F MET* 1.3 75.5 - - - +
58F LEU* 1.3 67.1 + - - +
59F THR* 3.9 12.1 - - + -
67F PRO* 4.8 5.8 - - + -
69F ALA 3.4 19.5 - - - +
70F LEU* 4.8 9.6 - - + -
84F LEU* 5.2 2.7 - - + -
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Residues in contact with LEU 58 (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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195E LEU* 3.8 18.8 - - + -
29F VAL* 3.7 20.0 - - + -
33F ILE* 3.6 23.6 - - + -
41F ILE* 3.6 18.4 - - + -
42F LEU 3.2 3.6 - - - -
43F VAL* 4.4 11.7 - - + -
56F MET* 4.2 6.7 - - + -
57F LEU* 1.3 85.4 - - - +
59F THR* 1.3 60.4 + - - +
67F PRO* 3.8 1.0 - - - +
68F TRP* 2.9 38.5 + - + +
69F ALA* 2.9 19.3 + - + +
71F VAL* 3.8 23.8 - - + -
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Residues in contact with THR 59 (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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4F LEU* 4.4 9.4 - - + -
41F ILE* 3.4 12.5 - - - +
42F LEU* 3.0 25.2 + - - +
44F HIS* 3.2 35.3 - - + +
57F LEU* 3.9 22.2 - - + -
58F LEU* 1.3 77.7 - - - +
60F SER* 1.3 70.5 + - - +
65F TYR* 3.8 13.8 - - + +
66F LYS 3.2 18.6 - - - -
67F PRO* 4.6 5.6 - - + -
68F TRP* 4.5 2.2 - - - +
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Residues in contact with SER 60 (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 SER* 6.3 2.0 - - - -
40F ASP 4.1 8.7 - - - -
41F ILE* 4.9 1.8 - - - -
42F LEU* 3.8 7.9 - - - +
59F THR* 1.3 88.3 + - - +
61F ASP* 1.3 71.7 + - - +
64F GLU* 2.7 41.0 + - - +
65F TYR* 4.0 1.2 - - - -
66F LYS* 2.8 21.9 + - - +
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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