Contacts of the strand formed by residues 56 - 64 (chain F) in PDB entry 4KYI
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 ALA 56 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E GLN* 2.5 21.7 + - - +
453E HIS* 3.6 9.1 - - - -
53F THR* 4.0 6.3 - - - +
54F ILE 2.7 9.8 + - - +
55F GLY* 1.3 76.4 - - - +
57F ALA* 1.3 63.1 + - - +
75F TRP* 4.3 9.4 - - + -
76F ASP 3.2 13.0 - - - +
77F THR* 4.1 5.2 - - - -
90F TYR* 3.3 34.8 - - + +
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453E HIS* 4.0 6.1 - - - -
53F THR* 4.4 7.2 - - + -
56F ALA* 1.3 78.4 - - - +
58F PHE* 1.3 62.0 + - - +
59F LEU* 4.2 8.5 + - + -
74F ILE 3.5 1.9 - - - +
75F TRP* 3.5 5.0 - - - -
76F ASP* 2.7 56.3 + - + +
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Residues in contact with PHE 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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453E HIS* 3.6 41.2 + + + +
454E LEU* 4.5 7.9 - - + -
457E GLN* 3.4 36.6 + - + -
473E TYR* 4.5 13.0 - + - -
57F ALA* 1.3 75.1 - - - +
59F LEU* 1.3 75.8 + - - +
60F THR* 3.7 17.0 - - - -
73F GLU* 4.1 24.2 - - + -
74F ILE 3.4 6.1 - - - -
75F TRP* 3.3 51.1 - + + -
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Residues in contact with LEU 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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457E GLN* 5.5 2.7 - - - +
38F VAL* 3.9 28.5 - - + -
39F LEU* 6.4 0.7 - - - -
42F VAL* 3.8 28.5 - - + -
43F LYS* 5.2 10.1 - - + -
57F ALA* 4.2 12.1 + - + -
58F PHE* 1.3 89.7 - - - +
60F THR* 1.3 70.6 + - - +
74F ILE* 3.0 36.4 + - + +
76F ASP* 5.6 3.1 - - + -
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Residues in contact with THR 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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457E GLN* 4.5 13.8 + - - +
461E GLU* 5.4 1.1 - - - +
473E TYR* 4.7 4.6 + - - +
42F VAL* 4.7 6.6 - - - +
58F PHE* 3.7 16.8 - - - -
59F LEU* 1.3 89.6 + - - +
61F GLN* 1.3 71.7 + - - +
62F THR* 4.8 2.0 - - - +
71F LYS* 3.6 35.0 - - + -
72F PHE 3.4 17.6 + - - +
73F GLU* 4.4 1.3 - - + +
74F ILE* 4.9 1.1 - - - +
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Residues in contact with GLN 61 (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 PHE* 3.7 39.3 - - + +
42F VAL* 2.9 55.0 + - + +
60F THR* 1.3 76.9 + - - +
62F THR* 1.3 85.8 + - - +
63F VAL* 4.2 2.5 + - + -
70F VAL 4.6 0.2 - - - +
72F PHE* 3.3 32.4 + - - +
74F ILE* 4.8 4.2 - - + +
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Residues in contact with THR 62 (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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19F ILE* 5.8 0.2 - - + -
60F THR* 4.8 1.7 - - - +
61F GLN* 1.3 91.7 + - - +
63F VAL* 1.3 68.1 + - - +
64F CYS* 5.7 2.5 - - - -
69F THR* 3.5 30.5 - - + -
70F VAL 3.7 7.0 - - - +
71F LYS* 3.9 23.3 - - + +
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Residues in contact with VAL 63 (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 PHE* 3.7 31.9 - - + -
61F GLN* 4.9 3.6 - - + -
62F THR* 1.3 79.0 - - - +
64F CYS* 1.3 64.7 + - - +
69F THR* 3.9 4.5 - - - +
70F VAL* 3.4 44.9 + - + +
72F PHE* 4.7 16.2 - - + -
172F ASN* 4.7 2.9 - - - +
176F MET* 3.6 32.5 - - + -
179F ALA* 5.3 0.7 - - + -
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Residues in contact with CYS 64 (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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62F THR* 5.7 1.6 - - - -
63F VAL* 1.3 77.7 - - - +
65F LEU* 1.3 61.5 + - - +
68F THR 4.1 0.7 - - - -
69F THR* 5.2 1.3 - - - -
176F MET* 3.5 13.6 - - - +
64H CYS* 2.0 49.1 - - + -
67H ASP* 3.4 20.2 - - - +
68H THR* 3.6 21.3 - - - +
69H THR* 2.7 31.0 - - - -
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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