Contacts of the strand formed by residues 70 - 76 (chain C) in PDB entry 2J3W
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 TRP 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C SER* 3.6 34.8 - - - -
5C PHE* 5.6 0.4 - - - -
6C TYR* 6.0 0.7 - - + -
27C LYS* 5.4 6.1 - - - -
37C LEU* 5.5 5.9 - - + +
38C ASN* 5.7 9.0 - - - -
41C ILE* 4.4 23.8 - - + -
66C LYS* 3.3 3.5 - - - -
67C PHE* 2.9 43.2 + + + +
68C ASN* 3.3 3.3 - - + -
69C GLU* 1.3 107.6 + - + +
71C PHE* 1.3 67.6 + - - +
72C VAL* 4.1 2.3 - - - +
86C LEU* 4.4 17.3 - - + -
87C HIS* 3.6 19.5 - - - -
88C ASP* 3.5 24.2 - - + -
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Residues in contact with PHE 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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63C THR* 3.8 21.3 - - + -
65C ASP 3.9 2.9 - - - -
66C LYS* 3.3 44.4 - - + -
69C GLU 3.8 10.3 - - - -
70C TRP* 1.3 75.6 - - - +
72C VAL* 1.3 60.1 + - - +
86C LEU* 3.4 5.2 - - - -
87C HIS* 2.8 59.6 + + + +
88C ASP 4.7 5.8 - - - -
90C ARG* 3.1 69.5 - - + -
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Residues in contact with VAL 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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41C ILE* 3.9 15.5 - - + -
45C ALA* 3.5 27.4 - - + -
63C THR* 3.5 2.5 - - - +
64C VAL* 2.9 33.7 + - + +
65C ASP* 2.9 31.8 + - + +
66C LYS* 4.6 0.7 - - - +
70C TRP 4.1 6.5 - - - +
71C PHE* 1.3 75.7 - - - +
73C SER* 1.3 67.3 + - - +
84C ILE* 4.3 9.9 - - + -
85C MET 3.4 4.0 - - - +
86C LEU* 3.3 31.0 - - + -
87C HIS* 3.9 0.2 - - - -
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Residues in contact with SER 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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60C TYR* 4.7 2.6 + - - -
62C LYS* 3.3 17.1 + - - -
63C THR* 3.7 9.2 - - - +
72C VAL* 1.3 76.3 - - - +
74C ALA* 1.3 63.7 + - - +
83C PHE 3.7 0.3 - - - +
84C ILE* 3.7 2.3 - - - -
85C MET* 2.9 35.9 + - - +
87C HIS* 2.7 30.9 + - - -
95C ILE* 4.2 22.3 - - - +
99C PHE* 4.0 4.0 - - - -
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Residues in contact with ALA 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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49C VAL* 3.8 31.4 - - + -
60C TYR* 3.6 8.1 - - - -
61C LEU* 2.8 47.2 + - + +
62C LYS 3.2 6.3 + - - -
64C VAL* 4.5 7.0 - - + -
72C VAL 4.4 0.2 + - - -
73C SER* 1.3 78.3 - - - +
75C PHE* 1.3 57.7 + - - +
82C ARG* 6.5 0.2 - - + -
83C PHE 3.1 9.9 - - - +
84C ILE* 4.0 4.5 - - + -
99C PHE* 3.8 3.8 - - - -
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Residues in contact with PHE 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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59C MET* 3.2 41.3 - - + -
60C TYR* 3.7 25.6 - + + -
74C ALA* 1.3 74.8 - - - +
76C VAL* 1.3 66.3 + - - +
77C THR* 4.2 7.4 - - + -
81C MET 3.5 2.1 - - - +
82C ARG* 3.6 1.0 - - - -
83C PHE* 2.7 59.2 + + + +
96C LYS* 5.2 1.6 - - - -
99C PHE* 3.4 30.3 - + + -
100C THR* 4.0 26.0 - - + -
103C TYR* 3.7 33.7 - + + -
76F GLY* 6.0 0.2 - - - -
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Residues in contact with VAL 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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49C VAL* 3.8 17.0 - - + -
53C MET* 4.1 21.8 - - + -
59C MET* 2.8 34.3 + - - +
61C LEU* 3.8 26.2 - - + -
75C PHE* 1.3 77.4 - - - +
77C THR* 1.3 67.9 + - - +
80C HIS* 3.9 20.9 - - + -
81C MET 3.4 5.4 - - - +
82C ARG* 4.5 4.7 - - + -
78F ARG* 3.6 31.9 + - - +
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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