Contacts of the strand formed by residues 71 - 76 (chain C) in PDB entry 5J13
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 PHE 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 4.0 12.3 - - + -
63C TYR* 3.3 22.9 - - + -
67C VAL* 3.1 41.0 + - + +
69C GLY 4.7 4.3 + - - -
70C ARG* 1.3 109.6 + - + +
72C THR* 1.3 67.2 + - - +
84C LEU* 4.1 12.8 - - + -
85C GLN 3.3 3.1 - - - +
86C MET* 3.7 48.9 - - + -
87C ASN 4.1 2.5 - - - -
89C LEU* 3.9 13.2 - - + -
93C ASP* 4.1 14.6 - - - -
97C TYR* 4.0 16.8 - + - -
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Residues in contact with THR 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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61C LYS* 4.8 4.9 - - + +
63C TYR* 3.4 8.6 + - - +
70C ARG 4.9 1.9 + - - -
71C PHE* 1.3 78.0 + - - +
73C ILE* 1.3 63.9 + - - +
74C THR* 4.0 22.5 + - + +
83C ASN 3.9 0.3 - - - +
84C LEU* 3.5 5.2 - - - -
85C GLN* 2.8 52.5 + - + +
87C ASN* 5.4 4.0 + - - -
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Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C MET 3.9 9.6 - - - +
39C TRP* 3.5 24.2 - - + -
52C ALA* 4.1 7.2 - - + +
53C VAL* 3.7 26.5 - - - +
54C ILE* 3.6 30.5 - - + +
61C LYS* 3.2 33.3 + - + +
63C TYR* 3.0 32.5 + - + +
72C THR* 1.3 73.1 - - - +
74C THR* 1.3 64.0 + - - +
82C LEU* 3.9 9.9 - - + -
83C ASN 3.5 12.1 - - - +
84C LEU* 4.3 3.8 - - + -
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Residues in contact with THR 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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22C ARG* 4.7 6.1 + - - +
54C ILE* 3.9 8.7 - - - -
61C LYS* 3.5 16.8 - - - +
72C THR* 4.0 16.4 + - + +
73C ILE* 1.3 80.3 - - - +
75C ARG* 1.3 62.3 + - - +
82C LEU* 3.4 8.2 - - - +
83C ASN* 2.9 48.2 + - - +
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PHE* 2.8 52.3 + - + -
35C TYR 3.0 20.6 + - - -
37C MET* 3.7 12.9 - - - +
54C ILE* 3.5 31.9 + - + +
55C TRP 2.8 36.8 + - - -
56C TYR 3.4 9.4 + - - -
58C GLY* 3.9 13.7 - - - +
74C THR* 1.3 79.7 - - - +
76C ASP* 1.3 60.4 + - - +
77C ASN* 2.8 23.0 + - - +
81C THR 3.3 11.2 - - - +
82C LEU* 4.3 3.1 - - + -
83C ASN* 4.9 1.3 - - - +
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Residues in contact with ASP 76 (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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32C PHE* 4.0 0.6 - - - -
75C ARG* 1.3 74.0 - - - +
77C ASN* 1.3 60.4 + - - +
78C SER* 2.6 26.7 + - - -
79C LYS* 3.3 39.7 - - + +
80C ASN* 2.8 24.9 + - - -
81C THR* 2.8 26.1 + - + +
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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