Contacts of the strand formed by residues 143 - 153 (chain V) in PDB entry 1ZGL
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 LYS 143 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168U MET* 5.4 11.7 - - + -
173U PHE* 6.3 3.6 - - + -
137V GLU* 3.1 22.0 + - - +
138V ILE* 2.9 17.6 + - - +
141V THR* 2.9 18.7 - - - +
142V GLN* 1.3 80.4 - - - +
144V ALA* 1.3 61.5 - - - +
198V ARG* 6.3 1.6 - - + -
199V VAL 3.9 5.2 - - - +
200V SER* 4.3 2.9 - - - -
201V ALA 3.6 8.3 - - - +
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Residues in contact with ALA 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133V PRO* 3.8 10.1 - - + -
137V GLU* 3.4 1.3 - - - -
138V ILE* 3.1 23.8 - - + -
143V LYS* 1.3 72.7 - - - +
145V THR* 1.3 62.9 + - - +
198V ARG* 2.9 5.3 - - - +
199V VAL* 2.6 52.2 + - + +
200V SER 4.1 2.7 - - - +
201V ALA* 4.4 0.7 - - - -
204V TRP* 3.9 24.2 - - + -
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Residues in contact with THR 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140U LEU* 3.5 32.3 - - + +
132V GLU 3.9 0.5 - - - -
133V PRO* 3.0 29.8 - - - +
137V GLU* 2.7 33.8 + - - -
144V ALA* 1.3 73.5 - - - +
146V LEU* 1.3 77.2 + - - +
147V VAL* 4.5 2.7 - - + -
196V ARG* 4.2 16.2 - - + -
197V LEU 3.8 2.2 - - - -
198V ARG* 3.9 17.1 - - + +
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Residues in contact with LEU 146 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130V VAL* 4.8 8.1 - - + -
131V PHE 3.3 10.5 - - - +
132V GLU* 4.4 1.3 - - - -
133V PRO* 3.3 25.4 - - + -
144V ALA 4.7 3.1 - - - +
145V THR* 1.3 83.1 - - - +
147V VAL* 1.3 68.9 + - - +
162V TRP* 3.7 25.4 - - + -
196V ARG* 3.4 7.4 - - - +
197V LEU* 2.9 36.0 + - + +
199V VAL* 4.9 6.5 - - + -
204V TRP* 4.3 13.5 - - + -
211V PHE* 3.6 43.5 - - + -
242V ALA* 5.1 0.9 - - + -
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Residues in contact with VAL 147 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128U LEU* 5.7 4.9 - - + -
138U VAL* 4.5 11.0 - - + -
140U LEU* 4.9 10.5 - - + -
179U VAL* 4.3 32.3 - - + -
131V PHE* 2.9 53.2 + - + +
145V THR* 4.5 7.9 - - + -
146V LEU* 1.3 80.7 - - - +
148V CYS* 1.3 68.5 + - - +
149V LEU* 4.4 10.8 - - + -
162V TRP* 4.1 2.5 - - - -
194V SER* 5.3 2.5 - - - -
195V SER 3.7 5.4 - - - +
196V ARG* 3.9 13.7 - - + -
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Residues in contact with CYS 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128V VAL* 4.2 16.2 - - - -
129V ALA 3.5 6.1 - - - -
130V VAL* 4.4 2.2 - - - +
147V VAL* 1.3 74.6 - - - +
149V LEU* 1.3 78.0 + - - +
150V ALA 4.2 0.2 - - - -
160V LEU* 4.5 10.3 - - + -
162V TRP* 3.2 19.8 - - + +
194V SER* 3.6 0.7 - - - -
195V SER 3.1 27.6 + - - +
213V CYS* 2.0 50.0 - - + -
215V VAL* 4.7 2.0 - - - -
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Residues in contact with LEU 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138U VAL* 3.9 22.7 - - + -
181U TRP* 3.9 44.4 - - + -
127V GLU 2.8 20.8 - - - +
128V VAL* 4.3 0.9 - - - -
129V ALA* 2.9 26.5 + - + +
131V PHE* 4.1 16.4 - - + -
147V VAL* 4.4 9.9 - - + -
148V CYS* 1.3 85.6 - - - +
150V ALA* 1.3 61.0 + - - +
151V THR* 3.4 10.4 + - + -
193V LEU 3.7 11.4 - - - +
194V SER* 3.7 15.9 - - - -
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Residues in contact with ALA 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126V PRO* 4.3 4.7 - - + -
127V GLU 4.1 7.9 - - - -
128V VAL* 4.0 5.8 - - + +
148V CYS* 4.2 1.2 - - - -
149V LEU* 1.3 70.5 - - - +
151V THR* 1.3 59.7 + - - +
153V PHE* 3.0 24.7 - - + -
158V VAL* 6.0 1.3 - - + -
160V LEU* 4.7 6.2 - - + +
193V LEU* 3.2 26.7 + - + +
215V VAL* 3.7 36.6 - - + -
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Residues in contact with THR 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181U TRP* 4.4 16.6 - - + +
125V PRO 4.2 0.2 - - - +
126V PRO* 3.4 3.8 - - - +
127V GLU* 2.8 52.2 + - - +
149V LEU* 3.4 21.9 + - + -
150V ALA* 1.3 75.6 - - - +
152V GLY* 1.3 66.6 + - - +
153V PHE 3.3 3.5 + - - -
182V GLU* 4.1 2.5 - - - -
191V TYR 3.6 4.7 - - - -
192V SER* 3.4 23.1 - - - +
193V LEU 5.0 0.7 - - - +
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Residues in contact with GLY 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124V PHE* 3.6 2.6 - - - +
125V PRO 3.6 5.2 - - - +
127V GLU* 5.5 1.1 - - - -
151V THR* 1.3 76.4 - - - +
153V PHE* 1.3 56.2 + - - -
182V GLU* 3.0 30.0 + - - -
190V ARG* 2.8 38.7 + - - -
191V TYR 3.1 5.3 + - - -
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Residues in contact with PHE 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124V PHE 3.4 16.4 - - - +
126V PRO* 3.8 22.0 - - + -
150V ALA* 3.0 30.7 - - + -
151V THR 3.9 3.6 - - - -
152V GLY* 1.3 74.8 - - - +
154V TYR* 1.3 60.4 + - - +
155V PRO 3.7 9.9 - - - +
156V ASP* 4.2 21.3 - - - -
158V VAL* 3.3 47.3 - - + -
179V PRO* 5.0 3.4 - - + -
190V ARG* 3.8 1.3 - - - +
191V TYR* 2.8 69.3 + - + +
192V SER* 4.1 1.8 - - - -
193V LEU* 4.2 12.8 - - + -
217V PHE* 4.9 0.9 - + + -
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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