Contacts of the helix formed by residues 143 - 150 (chain A) in PDB entry 1ZY3
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 TRP 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR* 4.9 17.8 - - + +
41A LEU* 4.8 23.3 - - + -
44A ALA* 5.9 2.9 - - + -
45A MET* 5.7 7.7 - - + +
95A LEU* 3.7 36.6 - - + -
99A PHE* 4.7 27.1 - + + -
129A LEU* 5.9 8.1 - - + -
137A ILE* 6.1 4.5 - - + -
141A GLY 3.2 1.4 + - - -
142A GLY* 1.3 81.4 - - - -
144A ALA* 1.3 61.8 + - - +
145A GLU 3.5 1.8 - - - -
146A PHE* 3.1 43.5 + + + +
147A THR* 2.9 29.4 + - - +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER 3.1 14.2 + - - +
141A GLY* 3.3 15.5 + - - +
143A TRP* 1.3 75.3 - - - +
145A GLU* 1.3 61.8 + - - +
147A THR* 2.8 24.8 + - - -
148A ALA* 4.1 2.4 + - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A SER 5.1 0.3 - - - -
140A SER* 2.6 45.1 + - - +
144A ALA* 1.3 76.7 - - - +
146A PHE* 1.3 68.2 + - + +
148A ALA* 3.0 19.4 + - - +
149A LEU* 3.1 36.1 + - + +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.7 37.9 - - + -
45A MET* 5.7 0.2 - - - -
48A ALA* 4.2 22.9 - - + -
92A TRP* 5.3 2.0 - - + -
95A LEU* 4.2 20.6 - - + -
96A VAL* 3.8 27.1 - - + -
142A GLY 5.2 0.4 - - - +
143A TRP* 3.2 48.8 - + + +
144A ALA 3.1 0.2 - - - -
145A GLU* 1.3 83.3 - - + +
147A THR* 1.3 56.3 + - - +
149A LEU* 2.9 36.2 + - + +
150A TYR* 3.1 31.3 + + + -
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Residues in contact with THR 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.9 30.3 - - + +
44A ALA* 5.7 1.1 - - + -
143A TRP* 2.9 12.2 + - - +
144A ALA* 2.8 17.2 + - - -
145A GLU 3.2 0.4 - - - -
146A PHE* 1.3 76.2 - - - +
148A ALA* 1.3 58.0 + - - +
150A TYR* 3.3 35.5 - - + +
151A GLY* 3.9 8.8 + - - -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA 4.1 1.1 + - - +
145A GLU* 3.0 14.1 + - - +
147A THR* 1.3 77.1 - - - +
149A LEU* 1.3 65.7 + - + +
150A TYR 3.5 0.4 - - - -
151A GLY* 3.7 10.3 + - - +
152A ASP 5.1 0.5 + - - -
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TRP* 3.7 48.5 - - + +
95A LEU* 5.8 2.7 - - + -
145A GLU* 3.1 37.3 + - + +
146A PHE* 2.9 32.7 + - + +
148A ALA* 1.3 82.2 - - + +
150A TYR* 1.3 57.5 + - - +
151A GLY 3.2 3.2 + - - -
152A ASP 4.6 0.5 + - - -
218B ARG* 3.5 24.7 + - - -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.4 22.0 + - - +
43A GLN* 3.9 12.7 - - + +
44A ALA* 3.6 21.4 + - + -
46A ARG* 5.2 4.5 - - - -
47A ALA* 3.5 33.0 - - + -
51A GLU* 3.9 20.3 - - + +
146A PHE* 3.1 42.9 + + + +
147A THR* 3.3 37.9 - - + +
149A LEU* 1.3 75.1 - - - +
151A GLY* 1.3 65.1 + - - +
152A ASP 3.4 9.7 - - - +
218B ARG* 4.7 2.7 - - - +
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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