Contacts of the strand formed by residues 92 - 99 (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 GLY 92 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.4 12.4 - - - -
91C ARG* 1.3 78.4 - - - +
93C PHE* 1.3 60.9 + - - +
134C GLU* 3.1 20.0 - - - -
163C ILE 3.6 0.3 - - - -
164C VAL* 2.7 46.3 + - - +
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Residues in contact with PHE 93 (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 LEU* 3.7 22.4 - - + -
90C PHE* 3.9 18.4 - + + -
92C GLY* 1.3 75.6 - - - +
94C THR* 1.3 76.9 + - - +
95C LEU* 4.1 5.4 - - + -
121C GLU 4.6 0.2 - - - -
122C THR* 3.9 6.7 - - + -
132C VAL* 3.2 30.1 - - + -
133C THR* 2.9 39.2 + - - -
134C GLU* 2.8 33.3 + - + +
143C ILE* 3.4 41.5 - - + -
162C SER* 3.2 16.8 - - - +
163C ILE* 4.2 1.8 - - + +
164C VAL* 4.2 1.9 - - - +
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Residues in contact with THR 94 (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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48C LEU* 3.5 33.0 - - + +
93C PHE* 1.3 84.7 - - - +
95C LEU* 1.3 64.9 + - - +
96C ILE* 6.0 1.4 - - - +
125C MET* 3.7 28.7 - - + -
131C ALA* 5.4 3.1 - - - -
132C VAL 3.3 7.9 - - - -
133C THR* 4.3 0.2 - - - +
160C LYS 4.4 0.6 + - - -
161C ALA* 3.2 8.1 - - - +
162C SER* 3.1 49.6 + - - +
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Residues in contact with LEU 95 (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 LEU* 3.7 32.3 - - + -
80C VAL* 4.2 12.1 - - + +
82C LEU* 5.6 1.3 - - + +
93C PHE* 4.1 9.6 - - + -
94C THR* 1.3 77.7 - - - +
96C ILE* 1.3 68.7 + - - +
114C PHE* 4.0 18.2 - - + -
131C ALA* 3.3 6.9 - - - -
132C VAL* 2.7 46.9 + - + +
143C ILE* 4.8 6.7 - - + -
145C VAL* 3.6 31.6 - - + -
159C LEU* 4.7 2.9 - - + -
160C LYS 3.3 16.8 - - - +
161C ALA* 4.2 4.0 - - + -
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Residues in contact with ILE 96 (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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46C ARG* 3.6 40.6 - - + +
48C LEU* 5.6 12.8 - - + -
94C THR* 6.0 0.7 - - - +
95C LEU* 1.3 80.7 - - - +
97C ALA* 1.3 59.8 + - - +
98C LEU* 3.6 27.6 - - + -
110C HIS* 4.5 13.9 - - + +
114C PHE* 3.7 12.3 - - - -
128C CYS* 5.4 2.5 - - - -
130C VAL* 4.3 6.3 - - + +
131C ALA* 3.5 22.7 - - + -
159C LEU* 3.4 4.3 - - - +
160C LYS* 2.9 42.9 + - + +
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Residues in contact with ALA 97 (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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96C ILE* 1.3 75.3 - - - +
98C LEU* 1.3 61.2 + - - +
110C HIS* 3.0 32.8 + - + +
111C ALA 3.3 24.5 - - - +
114C PHE* 3.5 15.8 - - + -
130C VAL 5.0 1.0 + - - -
147C TRP* 3.5 17.5 - - - +
157C VAL* 4.3 3.1 - - + -
158C ILE 3.6 3.4 - - - -
159C LEU* 3.8 11.7 - - + -
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Residues in contact with LEU 98 (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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46C ARG* 4.5 5.2 - - - +
96C ILE* 3.6 27.8 - - + -
97C ALA* 1.3 72.9 - - - +
99C ARG* 1.3 63.6 + - - +
102C ARG 4.6 3.6 - - - +
103C GLU 3.8 18.8 - - - +
104C GLY* 3.8 11.4 - - - +
109C ASP* 3.7 27.8 - - - +
110C HIS* 3.7 23.1 - - + +
111C ALA 4.5 1.3 - - - -
157C VAL* 3.3 6.8 - - - +
158C ILE* 2.5 48.7 + - + +
160C LYS* 3.6 28.9 - - + +
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Residues in contact with ARG 99 (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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98C LEU* 1.3 76.0 - - - +
100C GLU* 1.3 67.0 + - - +
102C ARG* 3.3 60.1 + - + +
108C GLU* 4.2 6.1 + - - +
109C ASP* 3.0 42.2 + - - +
110C HIS 5.6 1.2 - - - -
111C ALA* 4.4 8.5 - - + +
154C THR* 3.3 42.0 - - + +
156C CYS 3.4 15.9 - - - +
157C VAL* 4.5 1.1 - - - +
158C ILE* 4.2 1.5 - - - +
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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