Contacts of the helix formed by residues 142 - 146 (chain B) in PDB entry 3ZUT
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 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 4.7 12.8 + - + +
139B ARG 5.9 1.3 - - - +
140B ASP 5.5 2.0 - - - +
141B LEU* 1.3 70.0 - - - +
143B LEU* 1.3 64.9 + - - +
144B GLU* 3.1 17.7 - - + +
145B ASN* 3.2 27.4 + - + +
146B THR* 3.8 4.9 + - - +
158B ILE* 4.7 3.5 - - - +
159B CYS* 3.3 43.4 + - + +
161B PHE 4.4 3.5 - - - +
162B GLY* 3.2 36.2 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.1 10.3 - - + +
128B VAL* 3.7 33.0 - - + -
141B LEU* 3.0 22.5 + - + +
142B LYS* 1.3 76.3 - - - +
144B GLU* 1.3 62.0 + - - +
145B ASN 3.2 1.1 + - - -
146B THR* 3.6 15.8 + - - +
158B ILE* 3.8 29.8 - - + -
199B ASP* 3.7 45.8 - - + +
202B SER* 3.5 18.2 - - - +
203B CYS* 4.4 4.3 - - - -
206B THR* 3.6 16.5 + - - -
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 5.9 1.6 - - - +
141B LEU 3.7 4.9 - - - +
142B LYS* 3.2 28.4 - - + +
143B LEU* 1.3 81.5 + - - +
145B ASN* 1.3 66.0 + - + +
146B THR 3.9 0.4 - - - -
178B GLY* 6.0 7.9 - - - -
182B TYR* 3.3 58.4 + - + +
202B SER* 4.3 4.5 + - - -
215B TYR* 4.7 5.7 + - - -
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Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 2.2 37.4 + - - +
101B GLU* 2.4 35.7 + - - +
103B PHE* 4.7 8.7 - - - +
142B LYS* 3.2 17.3 + - + +
143B LEU 3.2 0.8 - - - -
144B GLU* 1.3 89.2 + - + +
146B THR* 1.3 67.0 + - - +
147B LEU* 3.4 11.4 - - - +
159B CYS* 5.7 2.3 + - - +
176B THR* 4.1 9.4 + - - +
177B VAL 6.0 2.2 - - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 3.7 1.7 - - - +
102B LEU* 3.0 47.5 + - - +
103B PHE 4.6 0.3 + - - -
124B LEU* 4.1 20.6 - - + -
142B LYS 4.0 9.6 - - - +
143B LEU* 3.6 23.9 + - - +
144B GLU 3.9 0.8 - - - -
145B ASN* 1.3 77.4 + - - +
147B LEU* 1.3 64.9 + - - +
156B LEU* 3.6 14.4 - - - +
157B LYS 3.7 8.5 - - - -
158B ILE* 4.2 15.0 - - + +
159B CYS 5.7 0.2 - - - +
206B THR* 5.0 3.1 - - + +
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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