Contacts of the strand formed by residues 66 - 71 (chain C) in PDB entry 2UZL
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 LEU 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ILE* 4.1 20.6 - - + +
55C LEU* 4.0 33.3 + - + +
56C LYS* 4.3 11.9 - - + -
59C ASN* 5.4 1.5 + - - +
64C VAL 3.7 3.8 + - - -
65C LYS* 1.3 79.3 + - - +
67C LEU* 1.3 60.2 + - - +
68C ASP 3.7 15.7 - - - +
69C VAL* 4.0 18.2 - - + -
78C LEU* 3.7 33.9 - - + -
79C VAL 3.7 6.1 - - - +
80C PHE* 3.9 16.5 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.4 34.8 - - - +
30C VAL* 4.0 9.9 - - + -
65C LYS* 3.5 36.1 - - + +
66C LEU* 1.3 72.6 - - - +
68C ASP* 1.3 63.1 + - + +
79C VAL* 2.7 19.3 + - + +
80C PHE 3.7 7.6 - - - +
81C GLU* 3.7 33.2 - - + +
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Residues in contact with ASP 68 (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 PHE* 5.7 2.4 - - + -
66C LEU* 3.6 5.8 - - - +
67C LEU* 1.3 81.9 - - + +
69C VAL* 1.3 80.1 + - - +
70C ILE* 4.0 19.9 - - - +
78C LEU* 3.4 1.2 - - - -
79C VAL* 2.7 50.1 + - + +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.8 40.2 - - + -
56C LYS* 6.1 1.1 - - + -
66C LEU* 4.0 13.7 - - + -
68C ASP* 1.3 88.2 + - - +
70C ILE* 1.3 62.0 + - - +
71C HIS* 3.6 7.0 + - + +
76C LEU* 3.7 25.4 - - + -
77C TYR 3.4 5.2 - - - +
78C LEU* 4.8 2.7 - - + -
304D PHE* 3.8 24.7 - - + -
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Residues in contact with ILE 70 (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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1C MET* 3.9 41.5 - - + +
4C PHE* 3.7 29.6 - - + -
68C ASP* 4.0 19.1 - - - +
69C VAL* 1.3 72.8 - - - +
71C HIS* 1.3 59.5 + - - +
72C THR* 3.4 20.4 + - + +
75C LYS 3.9 0.3 - - - +
76C LEU* 3.6 3.3 - - - -
77C TYR* 2.8 39.0 + - + +
79C VAL* 4.1 12.8 - - + -
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Residues in contact with HIS 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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37C LEU* 4.9 3.7 - - + +
44C VAL* 4.1 14.6 - - - +
69C VAL* 3.6 9.5 + - + +
70C ILE* 1.3 69.9 - - - +
72C THR* 1.3 71.3 + - - +
76C LEU* 3.4 24.2 - - + +
296D HIS* 3.3 52.6 + + + +
299D LEU* 4.0 21.3 - - + +
300D LYS* 4.9 11.4 + - + +
304D PHE* 3.4 33.3 - + + -
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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