Contacts of the strand formed by residues 53 - 59 (chain F) in PDB entry 2ZJQ
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 53 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F LEU 3.4 19.5 + - - +
13F PRO 3.7 0.6 + - - +
14F ALA* 6.5 0.2 - - - -
41F PHE* 4.4 5.1 - - + -
45F THR* 4.5 17.9 - - + -
48F LYS* 3.3 44.4 - - + +
51F ALA 3.4 10.4 + - - +
52F ILE* 1.3 83.0 - - - +
54F PRO* 1.3 75.9 - - + +
55F VAL* 3.6 12.7 + - + +
69F THR* 4.1 17.0 - - + -
70F LYS 3.5 25.1 - - - +
71F THR 4.4 1.1 - - - -
72F PRO* 3.6 13.0 - - + -
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Residues in contact with PRO 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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10F LEU 3.7 8.1 - - - +
11F GLN* 3.6 26.9 - - + +
52F ILE 4.3 0.2 - - - -
53F ILE* 1.3 84.1 - - + +
55F VAL* 1.3 61.5 + - - +
70F LYS* 2.8 41.9 + - + +
71F THR 3.2 28.5 - - - +
73F PRO* 3.7 20.6 - - + -
111F LYS* 5.8 0.2 - - - +
1071X U 6.0 1.8 - - - +
1072X U 6.3 0.7 - - + -
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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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9F LYS* 4.9 0.2 - - - +
10F LEU* 3.1 38.3 + - + +
11F GLN* 4.8 0.2 - - - +
12F LEU* 5.7 4.0 - - + +
37F PHE* 4.7 13.5 - - + -
41F PHE* 3.5 32.8 - - + -
53F ILE* 3.6 9.6 + - + +
54F PRO* 1.3 79.7 - - - +
56F GLU* 1.3 65.6 + - - +
57F ILE* 5.0 0.4 - - + -
67F PHE* 3.5 31.9 - - + -
68F ILE 3.7 10.8 - - - +
69F THR* 4.5 14.8 - - - +
70F LYS* 3.2 4.9 - - - +
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Residues in contact with GLU 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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7F ILE* 4.9 6.4 - - + +
8F VAL 3.8 6.5 - - - +
9F LYS* 3.2 39.3 + - + +
55F VAL* 1.3 75.8 - - - +
57F ILE* 1.3 62.8 + - - +
58F THR* 3.9 5.5 + - - +
66F THR 3.7 0.2 - - - +
67F PHE* 3.4 20.3 + - - -
68F ILE* 3.8 16.1 + - + +
70F LYS* 3.3 35.1 - - - +
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Residues in contact with ILE 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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7F ILE* 3.7 5.2 - - - +
8F VAL* 2.8 50.4 + - + +
10F LEU* 3.8 26.5 - - + -
27F LEU* 4.6 16.8 - - + -
37F PHE* 3.7 39.5 - - + -
55F VAL* 4.7 3.1 - - + +
56F GLU* 1.3 75.0 - - - +
58F THR* 1.3 63.1 + - - +
59F ILE* 4.1 12.7 + - + -
65F PHE* 3.7 26.0 - - + -
66F THR 3.3 13.7 - - - +
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Residues in contact with THR 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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7F ILE* 4.7 14.1 - - + +
56F GLU* 3.9 6.1 + - - +
57F ILE* 1.3 75.8 + - - +
59F ILE* 1.3 66.8 + - - +
60F TYR* 3.9 22.1 + - + +
64F SER 3.6 1.7 - - - +
65F PHE* 3.2 3.5 - - - -
66F THR* 3.0 43.3 + - - +
68F ILE* 6.1 1.2 - - - +
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Residues in contact with ILE 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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2F LYS 5.7 4.0 - - - +
3F LYS 4.8 8.5 - - - +
4F VAL* 5.5 9.6 - - + +
8F VAL* 4.5 16.8 - - + +
27F LEU* 4.3 23.8 - - + -
30F TYR* 4.8 17.9 - - + -
57F ILE* 4.0 8.4 + - + -
58F THR* 1.3 78.1 - - - +
60F TYR* 1.3 78.9 + - - +
63F ARG* 4.6 8.3 - - - -
64F SER 3.4 15.0 - - - +
65F PHE* 3.6 23.3 - - + +
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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