Contacts of the strand formed by residues 202 - 206 (chain A) in PDB entry 4PBZ
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.0 25.8 - - + -
195A SER 3.2 16.6 - - - +
196A ALA* 4.8 0.7 - - - -
200A HIS 5.7 0.2 - - - +
201A THR* 1.3 77.6 - - - +
203A CYS* 1.3 61.7 + - - +
222A ILE* 3.4 4.7 - - - +
223A PHE* 2.8 43.8 + - + +
226A HIS* 4.3 8.7 - - + -
230A VAL* 4.0 15.5 - - + -
233A VAL* 4.2 8.5 - - + -
243A PHE* 4.1 13.9 - - + -
245A SER* 3.4 35.4 - - - +
255A TRP* 3.8 17.5 - - + +
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Residues in contact with CYS 203 (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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175A GLY* 3.7 32.3 - - - -
176A HIS* 3.5 23.3 - - - +
194A LEU* 3.3 5.7 - - - +
195A SER 3.0 30.2 + - - -
201A THR* 4.2 3.1 - - - -
202A ILE* 1.3 77.0 - - - +
204A LEU* 1.3 60.9 + - - +
205A TRP* 3.2 29.7 - - + -
219A ALA* 4.3 2.2 - - + -
221A THR 3.6 3.8 - - - +
222A ILE* 3.9 18.2 - - - -
223A PHE* 5.3 0.2 - - - -
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Residues in contact with LEU 204 (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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192A HIS* 4.2 15.0 - - + -
193A LEU 3.2 11.7 - - - +
194A LEU* 3.9 9.0 - - + -
202A ILE 4.2 0.2 + - - -
203A CYS* 1.3 74.7 - - - +
205A TRP* 1.3 85.8 + - - +
219A ALA* 3.5 7.8 - - - +
220A LYS* 2.9 40.7 + - + +
221A THR* 3.1 36.7 + - - +
223A PHE* 4.2 8.7 - - + -
235A TRP* 3.9 24.9 - - + -
257A THR* 4.9 17.0 - - + -
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Residues in contact with TRP 205 (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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149A VAL* 3.9 23.6 - - + -
173A LEU* 3.4 48.3 - - + +
174A ARG 2.9 34.8 + - - +
175A GLY 4.5 0.4 - - - -
176A HIS* 3.9 6.1 - + - -
191A GLY 4.0 0.2 - - - -
192A HIS* 3.3 1.7 - - - -
193A LEU* 2.9 48.5 + - + +
194A LEU 4.7 0.2 - - - -
195A SER* 3.4 26.0 - - - -
203A CYS* 3.2 30.5 - - + -
204A LEU* 1.3 84.1 - - - +
206A ASP* 1.3 58.3 + - - +
207A ILE* 3.8 10.3 - - + -
217A VAL* 4.1 9.9 - - + -
218A ASP 3.7 11.6 - - - -
219A ALA* 3.5 20.0 - - + +
220A LYS* 4.5 3.4 - - - +
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Residues in contact with ASP 206 (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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191A GLY 3.5 4.5 - - - +
192A HIS* 3.3 32.9 + - + +
205A TRP* 1.3 73.1 - - - +
207A ILE* 1.3 59.0 + - - +
208A SER* 2.7 45.2 + - - -
209A ALA* 3.3 23.0 + - + +
217A VAL* 5.0 9.2 - - - +
220A LYS* 4.5 24.7 + - + +
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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