Contacts of the strand formed by residues 113 - 119 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LYS* 2.6 35.3 + - + +
107D LEU* 3.7 39.9 - - + +
110D TYR* 3.2 25.6 + - + +
111D PRO 4.3 0.6 - - - +
112D GLU* 1.3 76.6 - - + +
114D VAL* 1.3 54.8 + - - +
115D GLU 3.6 10.5 - - - +
116D VAL* 3.5 31.2 - - + -
127D VAL* 3.7 18.8 - - + -
128D LYS 3.4 3.6 - - - +
129D ILE* 4.0 18.6 - - + -
140D PHE* 5.8 2.2 - - + -
144D ILE* 4.2 12.8 - - + -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LYS* 4.0 2.8 - - - +
164C GLU* 3.6 2.8 + - - -
165C THR* 2.8 50.3 + - + +
166C THR 5.4 0.7 - - - -
167C GLU 3.7 23.6 - - - +
168C LEU* 4.5 15.7 - - + -
169C PRO* 5.4 0.9 - - + -
111D PRO 4.1 7.4 - - - +
112D GLU 3.3 10.3 + - - +
113D ILE* 1.3 75.5 - - - +
115D GLU* 1.3 64.0 + - + +
128D LYS* 2.9 43.7 + - + +
130D ARG* 4.7 13.7 - - + +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 4.6 1.9 - - - -
115C GLU* 3.9 1.7 - - - +
128C LYS* 2.8 30.6 + - - -
163C LYS 3.3 6.5 - - - +
164C GLU* 4.2 11.1 - - + +
165C THR 4.5 6.2 - - - +
90D PHE* 4.8 0.2 - - - -
113D ILE* 3.5 3.8 - - - +
114D VAL* 1.3 92.2 - - + +
116D VAL* 1.3 67.9 + - - +
117D TYR* 3.2 25.4 + - + +
126D VAL 4.4 1.1 - - - -
127D VAL* 3.3 4.9 - - - -
128D LYS* 3.0 67.3 + - + +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C THR* 3.7 1.0 - - - -
162C HIS* 2.9 46.0 + - + +
163C LYS* 2.9 30.2 + - + +
104D ALA* 4.4 15.0 - - + +
107D LEU* 4.2 17.0 - - + -
108D ALA 4.1 15.7 - - - +
113D ILE* 3.5 21.1 - - + -
115D GLU* 1.3 81.5 - - - +
117D TYR* 1.3 65.8 + - - +
125D MET* 4.5 7.6 - - - -
126D VAL 3.6 3.8 - - - -
127D VAL* 4.5 4.9 - - + -
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Residues in contact with TYR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 3.5 21.3 - - + -
90C PHE* 3.5 27.1 - + - -
128C LYS* 3.1 20.2 + - - -
158C VAL* 3.8 24.2 - - + -
160C LYS 3.3 7.6 - - - +
161C THR* 3.5 27.1 - - + -
162C HIS* 4.8 0.9 - - - +
163C LYS 4.5 0.4 - - - -
164C GLU* 2.8 30.3 + - + +
115D GLU* 3.2 31.9 + - + -
116D VAL* 1.3 77.8 - - - +
118D GLU* 1.3 62.7 + - - +
119D THR* 4.3 5.4 - - + -
125D MET* 3.1 9.4 - - - +
126D VAL* 2.9 41.2 + - + +
128D LYS 6.0 0.4 - - - -
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C VAL* 3.5 2.4 - - - -
159C LEU* 2.8 35.2 + - + +
160C LYS* 2.8 30.6 + - + +
162C HIS* 2.7 36.6 + - + +
100D TYR* 3.6 35.9 - - - +
101D SER* 4.6 1.4 + - - -
117D TYR* 1.3 73.2 - - - +
119D THR* 1.3 62.4 + - - +
124D ASP 3.4 8.3 - - - +
125D MET* 3.9 16.2 - - + -
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 4.6 4.7 - - + -
156C MET* 3.4 23.4 - - + +
157C ILE 3.3 13.0 - - - +
158C VAL* 4.2 17.3 - - + -
159C LEU* 3.9 11.3 - - - +
117D TYR* 4.3 4.0 - - + +
118D GLU* 1.3 79.8 - - - +
120D THR* 1.3 67.8 + - - +
121D GLY 3.9 0.5 + - - +
123D TYR 3.7 8.3 + - - +
124D ASP* 3.0 26.0 + - - +
125D MET 3.8 1.6 + - - -
126D VAL* 3.6 28.4 - - + +
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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