Contacts of the strand formed by residues 230 - 235 (chain E) in PDB entry 2ZUQ
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 230 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E ALA* 4.8 8.1 - - + -
138E PRO* 3.5 39.9 - - + +
140E VAL* 3.4 27.7 - - + +
219E CYS 3.4 3.1 - - - +
220E GLU* 3.3 19.4 - - - -
221E ALA* 3.5 15.6 + - + -
225E THR* 5.8 1.3 - - - +
228E SER 3.4 5.8 + - - +
229E PRO* 1.3 69.3 - - - +
231E VAL* 1.3 68.0 + - - +
232E LYS* 5.0 3.1 - - + -
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Residues in contact with VAL 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E THR* 3.3 22.7 - - + +
219E CYS 3.7 5.4 - - - -
220E GLU* 4.2 18.3 - - - +
229E PRO* 3.4 10.4 + - + +
230E ILE* 1.3 82.7 - - - +
232E LYS* 1.3 70.9 + - - +
233E SER* 4.4 6.3 - - - +
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Residues in contact with LYS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 3.9 30.3 - - + +
141E SER* 3.7 15.2 - - - +
142E ILE* 3.1 65.4 + - + +
143E PHE* 5.4 0.2 - - - -
218E THR* 4.2 0.7 - - - -
219E CYS 3.5 20.4 + - - +
230E ILE* 4.6 3.8 - - + +
231E VAL* 1.3 81.4 - - - +
233E SER* 1.3 59.8 + - - +
132F PRO* 6.0 1.8 - - - +
133F VAL* 3.5 25.8 - - + +
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Residues in contact with SER 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ILE* 4.2 3.8 - - - +
216E SER* 3.7 12.1 + - - -
217E TYR 2.5 23.2 + - - -
218E THR* 3.1 20.8 - - - +
231E VAL* 4.4 8.6 - - - +
232E LYS* 1.3 75.3 - - - +
234E PHE* 1.3 61.1 + - - +
235E ASN* 5.0 4.5 + - - -
133F VAL* 5.3 5.0 - - - +
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Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ILE* 3.8 26.7 - - + -
144E PRO* 3.2 48.2 - - + -
145E PRO* 4.3 1.3 - - + -
157E VAL* 3.6 22.0 - - + -
211E TYR* 3.5 15.7 - - - -
217E TYR* 2.7 74.7 + + + +
233E SER* 1.3 75.5 + - - +
235E ASN* 1.3 70.0 + - - +
236E ARG* 4.9 1.3 - - - -
239E CYS* 5.5 1.8 - - + -
133F VAL* 5.1 10.1 - - + -
134F CYS* 4.9 16.2 - - + +
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Residues in contact with ASN 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E ASN* 3.1 29.8 - - - +
216E SER* 3.6 19.5 + - - -
233E SER* 5.0 4.0 + - - -
234E PHE* 1.3 86.7 - - - +
236E ARG* 1.3 68.6 + - - +
237E ASN* 3.4 21.1 + - - +
134F CYS* 4.8 6.3 - - - +
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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