Contacts of the strand formed by residues 142 - 148 (chain C) in PDB entry 2ZOT
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 ARG 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C GLU* 3.1 26.7 + - - -
81C THR* 3.5 19.0 - - - +
82C LEU 3.3 8.7 - - - +
83C SER* 4.2 11.4 - - - -
90C PHE* 4.1 1.9 - - - -
121C GLU* 5.7 2.9 - - - +
140C ARG* 3.5 9.7 - - - +
141C THR* 1.3 87.0 - - - +
143C ILE* 1.3 76.0 + - - +
144C GLN* 3.3 40.8 + - - +
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Residues in contact with ILE 143 (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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80C VAL 5.3 0.9 - - - +
81C THR* 3.3 5.4 - - - -
82C LEU* 2.8 54.7 + - + +
90C PHE* 3.9 11.0 - - + -
93C PHE* 3.4 47.8 - - + -
95C LEU* 4.8 9.2 - - + -
118C ASP* 6.0 0.2 - - - -
121C GLU* 4.6 6.7 - - + -
122C THR* 4.1 17.3 - - + -
140C ARG* 3.7 25.1 - - - +
142C ARG* 1.3 85.1 - - - +
144C GLN* 1.3 70.6 + - - +
145C VAL* 4.8 3.4 - - + +
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Residues in contact with GLN 144 (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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79C ARG* 2.6 43.1 + - + +
80C VAL 3.2 10.5 - - - +
81C THR* 4.1 7.6 - - + -
117C ILE* 3.8 17.5 - - + +
118C ASP* 3.5 30.3 + - - +
122C THR* 4.3 12.0 + - - +
142C ARG* 3.3 33.2 + - - +
143C ILE* 1.3 80.5 - - - +
145C VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 145 (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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79C ARG 3.7 0.5 - - - -
80C VAL* 2.7 41.1 + - + +
95C LEU* 3.6 30.7 - - + -
114C PHE* 3.8 17.7 - - + -
115C GLN 3.2 25.4 - - - +
116C ILE* 4.2 10.3 - - + -
117C ILE* 3.6 9.6 - - - +
122C THR* 4.8 3.4 - - - +
132C VAL* 3.9 31.6 - - + -
143C ILE* 4.8 3.8 - - + +
144C GLN* 1.3 76.2 - - - +
146C PHE* 1.3 57.0 + - - +
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Residues in contact with PHE 146 (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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77C SER* 4.4 22.4 - - - -
78C TYR 3.4 16.4 - - - -
79C ARG* 3.9 37.5 - - + -
114C PHE* 3.3 11.4 - - - -
115C GLN* 3.0 68.2 + - + +
116C ILE 5.1 1.1 - - - -
117C ILE* 3.5 28.2 - - + +
145C VAL* 1.3 71.4 - - - +
147C TRP* 1.3 60.2 + - - +
148C ILE* 4.3 1.3 - - + -
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Residues in contact with TRP 147 (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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65C VAL* 6.1 0.9 - - + -
72C TYR* 4.3 14.1 - + + -
77C SER* 3.5 0.6 - - - -
78C TYR* 2.8 57.1 + + + -
80C VAL* 3.6 22.7 - - + -
97C ALA* 3.5 6.4 - - + +
111C ALA 3.2 20.0 + - - -
112C GLY* 3.8 0.4 - - - -
113C THR 3.8 10.1 - - - -
114C PHE* 3.6 30.1 - + + -
145C VAL 3.8 0.6 + - - -
146C PHE* 1.3 74.7 - - - +
148C ILE* 1.3 67.8 + - - +
149C ALA* 3.7 23.7 + - + -
150C PRO* 3.7 23.3 - - + -
157C VAL* 3.7 29.8 - - + -
159C LEU* 4.1 14.4 - - + -
181C LEU* 4.5 15.0 - - + -
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Residues in contact with ILE 148 (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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75C GLY* 3.5 24.9 - - - +
76C THR 3.7 3.1 - - - +
77C SER* 4.1 14.8 - - - +
112C GLY* 3.0 26.9 - - - -
113C THR* 2.8 36.1 + - - +
114C PHE 5.2 0.7 - - - +
115C GLN* 4.4 28.5 - - + +
146C PHE* 5.4 1.1 - - + -
147C TRP* 1.3 78.5 - - - +
149C ALA* 1.3 68.0 + - - +
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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