Contacts of the strand formed by residues 113 - 119 (chain C) in PDB entry 2ZNZ
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 ILE 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C LEU* 3.3 39.5 - - + +
110C TYR* 3.0 32.6 + - + +
111C PRO 3.6 2.7 - - - +
112C GLU* 1.3 74.3 - - - +
114C VAL* 1.3 58.6 + - - +
115C GLU 3.9 1.1 - - - +
116C VAL* 3.5 32.3 - - + -
127C VAL* 3.6 22.0 - - + -
128C LYS 3.5 3.6 - - - -
129C ILE* 3.9 19.3 - - + +
140C PHE* 5.8 0.4 - - + -
144C ILE* 4.2 11.0 - - + -
163D LYS* 2.7 34.3 + - + -
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Residues in contact with VAL 114 (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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111C PRO 4.2 5.6 - - - +
112C GLU 4.1 8.7 - - - +
113C ILE* 1.3 75.0 - - - +
115C GLU* 1.3 74.9 + - + +
128C LYS* 2.8 28.8 + - + +
130C ARG* 5.0 14.4 - - + +
163D LYS* 3.9 4.7 - - - +
164D GLU* 3.8 1.2 - - - -
165D THR* 3.1 54.5 + - + +
166D THR 5.2 0.9 - - - -
167D GLU 3.6 26.2 - - - +
168D LEU* 5.0 11.9 - - + -
169D PRO* 5.4 1.3 - - + -
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Residues in contact with GLU 115 (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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113C ILE 3.7 0.2 - - - -
114C VAL* 1.3 93.3 - - + +
116C VAL* 1.3 65.4 + - - +
117C TYR* 3.3 25.1 + - + +
126C VAL 4.3 1.6 - - - -
127C VAL* 3.2 6.9 - - - +
128C LYS* 2.9 69.8 + - + +
90D PHE* 4.4 2.4 - - - -
115D GLU* 3.9 1.7 - - - +
128D LYS* 2.7 30.8 + - - -
163D LYS 3.2 6.7 - - - +
164D GLU* 4.3 11.0 - - + +
165D THR 4.5 5.0 - - - +
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Residues in contact with VAL 116 (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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104C ALA* 4.5 10.3 - - + +
107C LEU* 4.2 29.2 - - + -
108C ALA* 4.3 7.2 - - - +
113C ILE* 3.5 22.9 - - + -
115C GLU* 1.3 79.4 - - - +
117C TYR* 1.3 68.5 + - - +
125C MET* 4.7 6.7 - - - -
126C VAL 3.5 2.9 - - - -
127C VAL* 4.4 6.5 - - + -
162D HIS* 2.9 52.4 + - + +
163D LYS* 2.8 24.1 + - + +
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Residues in contact with TYR 117 (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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115C GLU* 3.3 31.5 + - + -
116C VAL* 1.3 81.1 - - - +
118C GLU* 1.3 60.4 + - - +
119C THR* 4.3 7.0 - - + -
125C MET* 3.0 10.4 - - - +
126C VAL* 2.9 41.2 + - + +
128C LYS 6.0 0.2 - - - -
88D LEU* 3.5 20.9 - - + -
90D PHE* 3.5 26.0 - + - -
128D LYS* 3.1 19.4 + - - -
158D VAL* 3.7 24.2 - - + -
160D LYS 3.4 4.9 - - - +
161D THR* 3.5 27.6 - - + -
162D HIS* 4.7 0.9 - - - +
163D LYS 4.6 0.9 - - - -
164D GLU* 2.6 31.0 + - + +
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Residues in contact with GLU 118 (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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100C TYR* 3.8 35.0 - - + +
101C SER* 4.6 1.0 + - - -
117C TYR* 1.3 72.9 - - - +
119C THR* 1.3 53.6 + - - +
124C ASP 3.4 8.3 - - - +
125C MET* 4.0 16.6 - - + -
158D VAL* 3.4 5.4 - - - -
159D LEU* 2.6 42.6 + - + +
160D LYS* 2.8 39.6 + - - +
162D HIS* 2.7 35.1 + - + -
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Residues in contact with THR 119 (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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117C TYR* 4.3 3.1 - - + +
118C GLU* 1.3 79.5 - - - +
120C THR* 1.3 68.3 + - - +
121C GLY 4.9 0.2 - - - +
123C TYR 3.5 11.1 + - - +
124C ASP* 3.0 22.2 + - - +
125C MET 3.8 1.9 + - - -
126C VAL* 3.4 35.2 - - + +
90D PHE* 4.6 1.8 - - + -
156D MET* 3.6 18.9 - - + +
157D ILE 3.4 11.9 - - - +
158D VAL* 4.0 18.4 - - + -
159D LEU* 3.8 10.9 - - - +
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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