Contacts of the strand formed by residues 68 - 75 (chain C) in PDB entry 5Y39
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 68 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET* 3.5 29.2 - - - +
75B ASP 3.3 9.6 + - - -
76B CYS* 3.6 15.0 - - - -
53C PHE* 4.0 2.4 - - - -
57C THR* 2.9 34.8 + - - +
60C GLY 4.0 7.2 - - - -
61C SER* 2.8 17.2 + - - +
67C LYS* 1.3 77.3 - - - +
69C LYS* 1.3 61.4 + - - +
70C SER 3.3 27.4 + - - +
71C ILE* 3.9 7.2 - - - +
84C ASN* 3.3 22.7 + - - +
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASP* 2.7 37.8 + - - +
76B CYS 3.7 5.9 + - - -
77B MET* 3.7 38.7 - - + +
80B ARG* 5.8 1.2 - - - +
67C LYS 4.0 1.8 - - - +
68C ASN* 1.3 77.1 - - - +
70C SER* 1.3 59.4 + - - +
83C PHE* 3.6 1.4 - - + -
84C ASN* 2.7 36.9 + - - +
85C ARG* 3.6 14.7 + - - +
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP* 2.9 42.8 + - - +
101B PHE* 5.5 1.2 - - - -
53C PHE* 4.6 0.9 - - - -
68C ASN* 3.3 5.6 + - - -
69C LYS* 1.3 80.3 - - - +
71C ILE* 1.3 71.6 + - - +
72C ILE* 5.5 5.0 - - - +
81C VAL* 5.4 1.9 - - - +
82C GLN 3.1 15.3 - - - -
83C PHE* 3.6 28.2 - - - -
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 4.9 1.6 - - + -
56B TYR* 4.4 7.6 - - + +
72B ILE* 3.9 13.2 - - + -
73B LEU 3.4 9.9 - - - +
74B MET* 3.8 25.6 - - + -
53C PHE* 3.8 22.0 - - + -
56C ALA* 3.6 32.5 - - + -
68C ASN* 3.9 11.4 - - - +
70C SER* 1.3 82.0 - - - +
72C ILE* 1.3 66.8 - - - +
73C CYS* 3.7 25.7 - - - -
80C VAL 3.7 1.2 - - - +
81C VAL* 3.4 4.0 - - - +
82C GLN* 2.9 33.2 + - + +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE 3.9 0.3 - - - +
72B ILE* 3.3 8.1 - - - +
73B LEU* 2.7 59.2 + - + +
101B PHE* 4.7 16.6 - - + -
70C SER* 5.5 5.2 - - - +
71C ILE* 1.3 76.3 - - - +
73C CYS* 1.3 64.1 + - - +
74C TYR* 3.5 39.9 - - + +
79C GLN* 4.6 0.7 - - + +
80C VAL 3.4 6.3 - - - +
81C VAL* 3.8 22.9 - - + -
100C THR* 3.8 24.0 - - + -
104C VAL* 4.8 7.9 - - + -
111E LEU* 4.7 6.1 - - + -
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Residues in contact with CYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 3.5 39.5 - - + -
69B LEU* 4.0 4.7 - - + -
71B PHE 3.5 4.0 - - - -
72B ILE* 3.8 11.4 - - - -
71C ILE* 3.7 22.4 - - - -
72C ILE* 1.3 73.4 - - - +
74C TYR* 1.3 63.4 - - - +
75C TYR* 3.8 20.5 - - + -
79C GLN* 3.2 4.7 - - - -
80C VAL* 2.8 44.8 + - + +
82C GLN* 5.5 0.7 - - - -
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Residues in contact with TYR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.4 4.4 - - - +
70B LYS* 2.7 48.4 + - - -
71B PHE* 2.9 38.1 + + + +
73B LEU* 3.9 17.4 - - + +
105B LYS* 3.9 17.9 - - + -
72C ILE* 3.5 18.7 - - + +
73C CYS* 1.3 71.2 - - - +
75C TYR* 1.3 57.4 + - - +
78C TYR 4.1 1.8 - - - -
79C GLN* 3.7 21.5 - - + -
96C SER* 5.0 3.6 - - - -
100C THR* 2.9 34.6 + - - +
109E GLN* 3.4 27.3 + - - -
111E LEU* 3.3 22.1 - - + +
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 2.7 43.0 + - - -
57B ASP* 4.6 0.2 - - - -
59B ASN 4.0 4.3 - - - -
68B ASN* 3.1 43.5 - - - +
69B LEU* 3.7 19.1 - - + -
70B LYS* 3.3 16.5 - - - -
49C PHE* 3.4 15.7 - + - -
73C CYS* 3.8 23.8 - - + -
74C TYR* 1.3 74.8 - - - +
76C ASN* 1.3 65.6 + - - +
77C THR 3.3 1.3 + - - -
78C TYR* 2.9 71.8 + + + +
80C VAL* 4.4 6.3 - - + -
96C SER* 3.9 5.0 - - - -
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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