Contacts of the strand formed by residues 58 - 64 (chain C) in PDB entry 1O94
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 GLU 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET 3.0 15.8 + - - +
2C LYS* 3.2 23.4 + - + +
3C ILE 2.8 28.4 + - - +
50C LYS* 4.7 0.2 - - - +
56C ASP 4.3 0.2 - - - -
57C VAL* 1.3 71.7 - - - +
59C VAL* 1.3 65.7 + - - +
60C VAL* 4.6 1.3 - - + +
82C ASP* 3.5 18.2 - - + -
83C ARG* 2.7 45.0 + - - -
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 3.5 7.6 - - + +
5C VAL* 4.4 4.7 - - + -
43C LEU* 3.8 28.0 - - + -
46C ALA* 3.9 40.2 - - + +
47C MET* 4.3 8.5 - - - -
50C LYS* 4.2 13.5 - - + -
57C VAL* 4.2 14.1 - - + +
58C GLU* 1.3 73.9 - - - +
60C VAL* 1.3 62.5 + - - +
81C ALA* 3.8 8.3 - - + -
82C ASP* 2.8 43.4 + - - +
83C ARG 3.3 5.4 + - - +
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Residues in contact with VAL 60 (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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2C LYS* 4.1 13.9 - - + -
3C ILE 3.0 15.9 + - - +
4C LEU* 3.4 21.7 - - + +
5C VAL* 2.9 25.6 + - - +
58C GLU* 3.9 2.2 + - - +
59C VAL* 1.3 75.0 - - - +
61C VAL* 1.3 78.7 + - - +
62C VAL* 4.1 4.5 - - + -
83C ARG* 3.4 35.4 - - + +
85C VAL* 3.9 17.7 - - + -
111C GLU* 4.1 14.4 - - - +
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Residues in contact with VAL 61 (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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5C VAL* 3.3 16.6 - - + +
7C VAL* 4.4 11.0 - - + -
43C LEU* 3.8 19.1 - - + -
59C VAL* 4.9 0.2 - - + -
60C VAL* 1.3 76.7 - - - +
62C VAL* 1.3 61.3 + - - +
73C LEU* 3.9 11.4 - - + +
76C CYS* 3.8 26.2 - - + -
81C ALA* 3.7 20.6 - - + -
83C ARG 2.9 18.9 + - - +
84C ALA* 3.3 16.4 - - + -
85C VAL 2.7 32.4 + - - +
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Residues in contact with VAL 62 (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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4C LEU* 3.8 40.4 - - + -
5C VAL 3.1 5.7 + - - -
6C ALA* 3.4 4.5 - - - +
7C VAL 2.9 24.0 + - - +
60C VAL* 4.1 9.6 - - + -
61C VAL* 1.3 82.6 - - - +
63C SER* 1.3 65.2 + - - +
73C LEU* 4.4 1.3 - - - -
85C VAL* 3.3 16.2 - - + +
87C VAL* 4.4 11.7 - - + -
104C LEU* 4.0 20.0 - - + +
107C VAL* 4.3 23.3 - - + -
108C ILE* 6.4 0.9 - - + -
111C GLU* 5.1 0.9 - - + -
1236C AMP 3.6 2.8 - - - -
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Residues in contact with SER 63 (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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7C VAL* 2.7 25.4 + - - +
8C LYS* 4.1 4.9 - - - -
9C GLN 4.4 1.0 + - - -
62C VAL* 1.3 76.6 - - - +
64C VAL* 1.3 69.1 + - - +
65C GLY 3.9 1.0 + - - -
69C VAL* 3.3 30.1 - - - +
73C LEU* 3.9 15.9 - - - -
85C VAL 3.0 6.7 + - - -
86C ARG* 3.4 5.8 - - - +
87C VAL 3.0 23.9 + - - +
1236C AMP 3.7 3.7 + - - -
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Residues in contact with VAL 64 (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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63C SER* 1.3 76.4 + - - +
65C GLY* 1.3 59.5 + - - +
69C VAL* 4.9 1.7 - - - +
87C VAL* 3.4 20.0 - - + +
88C TRP* 4.1 15.6 - - + -
92C ALA* 5.2 0.9 - - + -
95C SER* 6.2 0.7 - - - -
100C VAL* 4.2 12.1 - - + -
103C ILE* 3.8 44.9 - - + -
104C LEU* 3.8 30.1 - - + -
1236C AMP 2.9 38.3 + - - +
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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