Contacts of the strand formed by residues 78 - 83 (chain F) in PDB entry 2ZUQ
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 THR 78 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F SER* 6.1 1.3 - - - -
22F CYS 3.4 4.5 - - - +
23F ALA* 4.2 20.2 - - + -
29F PHE* 3.3 16.5 - - - -
72F ARG* 3.6 1.9 - - - -
73F ASP* 3.4 22.4 + - - +
76F LYS* 3.5 21.4 + - + +
77F ASN* 1.3 77.6 - - - +
79F LEU* 1.3 60.1 + - - +
80F TYR* 2.3 41.7 + - + +
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Residues in contact with LEU 79 (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 SER* 3.2 3.1 - - - -
22F CYS* 2.8 44.8 + - + +
29F PHE* 4.3 4.6 - - + -
34F MET* 3.5 42.8 - - + -
35F SER 4.0 9.6 - - - +
36F TRP* 3.8 23.1 - - - +
51F ILE* 3.5 28.7 - - + -
70F ILE* 4.1 6.3 - - + -
71F SER 3.8 3.1 - - - +
72F ARG* 3.7 16.4 - - + -
78F THR* 1.3 71.0 - - - +
80F TYR* 1.3 72.8 + - - +
96F CYS* 3.9 9.4 - - - -
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Residues in contact with TYR 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LYS* 4.3 27.4 - - + -
20F LEU 3.2 7.4 - - - +
21F SER* 3.6 19.7 - - - -
36F TRP* 3.7 4.9 - - - -
70F ILE* 3.3 12.3 - - - +
71F SER* 2.7 67.8 + - - +
72F ARG 4.4 0.7 - - - -
73F ASP* 4.1 21.7 + - + +
76F LYS* 5.3 1.0 - - - +
78F THR* 2.3 47.4 + - + +
79F LEU* 1.3 85.7 - - - +
81F LEU* 1.3 60.8 + - - +
82F GLN 4.1 0.7 - - - +
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Residues in contact with LEU 81 (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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18F LEU 3.5 2.9 - - - +
19F LYS* 3.4 1.9 - - - -
20F LEU* 2.6 47.1 + - + +
36F TRP* 3.4 45.4 - - + +
48F VAL* 4.0 15.0 - - + -
49F ALA* 4.0 20.4 - - + -
60F TYR* 5.4 0.2 - - + -
68F PHE* 3.8 24.5 - - + -
69F THR 3.5 20.9 - - - +
70F ILE* 4.4 0.7 - - - +
80F TYR* 1.3 71.0 - - - +
82F GLN* 1.3 59.8 + - - +
83F MET* 3.7 13.0 + - + +
94F TYR* 4.1 14.4 - - + -
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Residues in contact with GLN 82 (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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17F SER* 4.8 5.6 + - - -
18F LEU 3.5 4.6 + - - +
19F LYS* 3.4 47.3 - - + +
67F ARG 4.0 0.5 - - - +
68F PHE* 3.3 4.3 - - - -
69F THR* 2.7 53.2 + - - +
71F SER* 5.5 4.5 + - - +
80F TYR* 4.1 0.8 - - - +
81F LEU* 1.3 70.6 - - - +
83F MET* 1.3 95.1 + - - +
84F SER* 4.3 6.2 + - - +
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Residues in contact with MET 83 (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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17F SER* 3.0 7.1 + - - -
18F LEU* 2.9 42.6 + - + +
20F LEU* 3.5 30.5 - - + -
67F ARG 3.8 2.5 - - - -
68F PHE* 3.3 37.0 - - + -
81F LEU* 4.0 11.7 - - + +
82F GLN* 1.3 80.2 + - - +
84F SER* 1.3 62.4 + - - +
86F LEU* 3.6 24.7 - - + -
90F ASP* 4.4 3.4 - - + -
94F TYR* 3.5 33.7 - - + +
115F VAL* 4.4 11.4 - - + -
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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