Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 2ZB8
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 VAL 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A THR* 4.0 6.1 - - + +
159A VAL* 3.6 33.7 - - + -
217A LEU* 4.8 3.8 - - + -
221A CYS* 4.1 12.8 - - + -
224A GLY* 1.3 77.8 - - - +
226A ASP* 1.3 64.8 + - - +
227A VAL 3.5 27.1 - - - +
228A TYR 4.5 0.2 - - - +
240A VAL* 4.6 7.0 - - + +
243A GLN* 3.1 24.7 + - + +
244A MET* 3.4 20.8 - - + +
245A ASN* 2.9 25.0 + - - +
248A SER* 3.7 3.5 - - - -
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Residues in contact with ASP 226 (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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155A ASN 4.4 1.7 - - - +
156A LYS* 3.2 35.8 - - + +
157A THR* 2.8 34.0 + - - +
223A ALA 5.1 1.2 - - - +
224A GLY 5.0 0.3 - - - +
225A VAL* 1.3 75.4 - - - +
227A VAL* 1.3 66.7 + - + +
244A MET* 4.5 0.2 - - - -
245A ASN* 2.8 31.0 + - - +
248A SER* 3.2 10.1 - - - -
249A HIS* 3.1 24.4 + - - +
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Residues in contact with VAL 227 (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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148A GLY* 3.9 24.0 - - - +
150A ILE* 4.3 14.6 - - + -
156A LYS* 4.6 8.3 - - + +
157A THR 3.0 5.2 + - - +
158A MET* 3.1 23.0 - - + +
159A VAL 2.8 32.1 + - - +
180A CYS* 4.8 3.6 - - - -
225A VAL* 3.5 5.3 - - - +
226A ASP* 1.3 93.5 - - + +
228A TYR* 1.3 60.8 + - - +
229A PHE 4.0 0.2 - - - -
244A MET* 4.5 0.2 - - - -
249A HIS 3.4 9.4 - - - +
251A ILE* 3.5 31.0 - - + -
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Residues in contact with TYR 228 (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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159A VAL* 3.4 11.9 - - + +
161A SER* 2.9 42.7 + - - -
225A VAL* 4.7 0.4 - - + -
227A VAL* 1.3 74.9 - - - +
229A PHE* 1.3 64.0 + - - +
230A ASP* 3.2 20.2 + - + -
232A VAL* 4.2 0.3 - - - +
236A ILE* 3.9 3.5 - - - +
237A SER* 2.8 47.6 + - - -
240A VAL* 3.5 34.5 - - + -
241A ILE* 4.5 4.9 - - + -
244A MET* 3.8 22.9 - - + +
249A HIS 3.0 7.5 + - - -
250A ILE* 3.4 17.8 - - + +
251A ILE 2.7 31.6 + - - -
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Residues in contact with PHE 229 (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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139A THR 4.4 3.4 - - - -
140A SER* 3.7 44.0 - - - -
144A ILE* 3.9 6.3 - - + -
158A MET* 4.8 6.2 - - - +
159A VAL 2.8 12.6 + - - +
160A VAL* 3.5 15.1 - - + -
161A SER 3.0 25.8 + - - -
167A CYS* 4.3 1.6 - - + -
171A ALA* 3.7 22.2 - - + -
227A VAL 4.0 1.0 - - - -
228A TYR* 1.3 71.1 - - - +
230A ASP* 1.3 57.8 + - - +
231A ASN* 3.5 33.8 + - - -
251A ILE* 3.8 39.0 - - + +
253A CYS* 3.6 24.0 - - + -
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Residues in contact with ASP 230 (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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161A SER* 3.1 6.8 + - - -
228A TYR* 3.3 19.1 + - + -
229A PHE* 1.3 70.3 - - - +
231A ASN* 1.3 60.2 + - - +
232A VAL 3.0 3.8 + - - -
233A GLY* 2.9 19.9 + - - -
237A SER* 2.5 29.3 + - - -
241A ILE* 5.7 0.9 - - - +
250A ILE* 4.1 9.4 - - + +
251A ILE 2.9 16.1 + - - +
252A LEU* 4.2 6.1 - - + +
253A CYS* 3.0 12.4 + - - +
254A GLY 2.9 20.3 + - - +
255A GLN* 2.7 24.1 + - - +
284A ARG* 5.4 2.4 + - - -
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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