Contacts of the strand formed by residues 78 - 85 (chain C) in PDB entry 2WZJ
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 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 4.9 6.4 - - + +
69C LEU* 4.4 24.4 - - + +
70C ALA 3.4 11.7 - - - +
71C ARG* 4.7 10.5 - - + -
76C GLY 4.0 1.2 + - - +
77C LYS* 1.3 79.7 - - - +
79C VAL* 1.3 66.2 + - - +
116C PHE* 5.5 0.9 - - - -
131C TYR* 3.8 36.5 + - + +
133C SER* 5.3 2.1 - - - -
360C LEU* 5.1 1.2 - - - +
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 3.5 31.4 - - + -
69C LEU* 3.7 3.6 - - - +
70C ALA* 2.8 48.3 + - + +
72C HIS 4.7 0.2 - - - +
77C LYS 4.3 5.4 - - - +
78C GLU* 1.3 81.0 - - - +
80C ALA* 1.3 58.8 - - - +
81C VAL* 4.4 1.8 - - + -
116C PHE* 4.0 13.5 - - + -
128C VAL* 3.9 10.5 - - + -
129C MET 3.5 8.5 - - - +
131C TYR* 3.9 8.5 - - - -
360C LEU* 3.8 35.7 - - + -
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Residues in contact with ALA 80 (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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59C ILE* 4.9 3.1 - - + -
67C VAL* 4.1 16.8 - - + -
68C LYS 3.6 4.7 - - - +
69C LEU* 4.8 1.1 - - - +
79C VAL* 1.3 73.4 - - - +
81C VAL* 1.3 60.9 + - - +
82C ARG 4.0 0.4 - - - -
128C VAL* 3.6 0.9 - - - -
129C MET* 2.7 53.9 + - + +
130C GLU 4.0 13.0 - - - +
131C TYR* 3.8 16.6 - - + +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 5.2 3.6 - - + -
53C TYR* 4.8 6.1 - - + -
55C LEU* 4.4 12.8 - - + -
67C VAL* 3.4 3.3 - - - -
68C LYS* 2.7 41.9 + - + +
70C ALA* 3.7 26.5 - - + -
79C VAL* 4.4 6.1 - - + -
80C ALA* 1.3 76.6 - - - +
82C ARG* 1.3 69.9 + - - +
83C ILE* 3.6 7.6 + - + +
126C TYR* 4.1 30.5 - - + -
127C LEU 3.6 6.1 - - - +
128C VAL* 4.2 18.4 - - + -
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA* 4.0 13.3 - - - +
66C LYS 3.5 24.3 - - - +
67C VAL* 3.8 9.8 - - + +
80C ALA 4.0 1.2 + - - -
81C VAL* 1.3 71.0 - - - +
83C ILE* 1.3 76.3 + - - +
84C ILE* 4.0 15.9 - - + +
125C LEU 3.6 1.9 - - - +
126C TYR* 3.5 4.9 - - - -
127C LEU* 2.9 44.2 + - + +
129C MET* 4.5 3.1 - - + +
196C PHE* 2.9 37.2 - - + -
197C SER 3.3 20.1 + - - -
198C ASN* 2.9 27.9 - - - +
200C PHE 3.4 16.8 + - - -
201C THR* 4.6 4.6 - - - +
202C PHE* 4.2 12.3 - - - -
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Residues in contact with ILE 83 (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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55C LEU* 4.6 18.4 - - + -
66C LYS* 2.8 59.1 + - + +
68C LYS* 4.8 9.9 - - + -
81C VAL* 4.0 13.5 - - + +
82C ARG* 1.3 85.1 + - - +
84C ILE* 1.3 69.4 + - - +
85C ASP* 4.3 0.7 - - + +
124C THR* 3.8 22.2 - - + -
125C LEU 4.0 1.6 - - - -
126C TYR* 3.6 27.6 - - + +
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Residues in contact with ILE 84 (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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82C ARG* 4.0 21.1 - - + +
83C ILE* 1.3 83.0 - - - +
85C ASP* 1.3 72.4 + - - +
86C LYS* 3.6 3.5 + - + +
89C LEU* 4.1 11.2 - - + -
97C LEU* 3.6 44.2 - - + -
124C THR* 3.4 8.5 - - - +
125C LEU* 2.9 50.3 + - + +
127C LEU* 5.0 2.5 - - + -
196C PHE* 4.1 17.0 - - + -
202C PHE* 4.2 9.6 - - + -
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 4.3 0.8 - - - +
84C ILE* 1.3 75.7 - - - +
86C LYS* 1.3 66.0 + - - +
87C THR* 3.0 32.2 + - - +
88C GLN* 3.3 32.9 + - + +
89C LEU* 3.9 14.9 - - - +
123C LYS* 3.1 12.1 - - - +
124C THR* 4.8 4.0 - - - +
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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