Contacts of the strand formed by residues 229 - 235 (chain A) in PDB entry 1CPJ
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 GLY 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ILE* 3.7 9.7 - - - +
219A ASN* 3.1 36.1 + - - +
222A ASN 3.2 21.5 - - - -
223A ALA* 3.3 0.8 + - - -
225A TRP* 2.6 29.8 + - - -
227A ASP 3.2 0.2 - - - -
228A ASN* 1.3 72.7 - - - +
230A PHE* 1.3 59.2 + - - +
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Residues in contact with PHE 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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8A ARG* 3.3 30.7 - - - -
18A ALA* 3.6 28.0 - - - -
20A ILE* 3.9 16.6 - - + -
183A TYR* 3.8 0.3 - - - -
202A ARG* 4.0 7.2 - - - -
204A LEU* 4.0 15.0 - - + -
216A LEU* 4.8 13.5 - - + -
217A VAL 3.3 18.6 - - - +
218A ALA* 3.7 24.5 - - + -
225A TRP* 3.8 2.1 - - - -
227A ASP* 3.0 40.1 + - + +
228A ASN* 3.2 15.9 - - + -
229A GLY* 1.3 79.2 - - - +
231A PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 231 (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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174A PHE* 3.9 27.4 - + - -
180A PHE* 3.9 22.0 - + - -
183A TYR* 3.3 28.5 - - + -
188A TYR* 5.1 2.5 - - + -
201A ILE* 4.2 5.8 - - + -
216A LEU* 3.8 5.6 - - - +
217A VAL* 2.8 69.6 + - + -
219A ASN* 4.0 15.3 - - + -
225A TRP* 3.8 20.2 - + + -
227A ASP* 4.9 1.1 - - - -
230A PHE* 1.3 77.7 - - - +
232A LYS* 1.3 76.2 + - - +
233A ILE* 4.0 20.4 - - + -
242A ILE* 6.1 0.4 - - + -
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Residues in contact with LYS 232 (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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183A TYR* 3.2 7.1 + - - -
185A SER* 5.5 0.4 - - - -
186A GLY 3.4 31.9 + - - +
187A VAL* 4.1 2.7 - - + -
188A TYR* 3.1 27.9 + - - +
209A GLU* 3.3 26.8 + - - +
214A TYR* 3.6 46.2 - - + -
215A TRP 3.1 5.2 - - - +
216A LEU* 4.7 12.0 - - + +
227A ASP* 3.6 22.8 + - - +
231A PHE* 1.3 84.0 - - - +
233A ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 233 (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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174A PHE* 3.9 30.5 - - + -
187A VAL* 4.0 0.4 - - - -
188A TYR* 3.6 30.1 - - + +
214A TYR* 3.1 5.8 - - - -
215A TRP* 2.8 46.1 + - + -
217A VAL* 3.9 16.2 - - + -
231A PHE* 4.0 9.6 - - + -
232A LYS* 1.3 76.0 - - - +
234A LEU* 1.3 76.6 + - - +
239A HIS* 4.3 12.6 - - - +
240A CYS* 4.8 0.9 - - + -
242A ILE* 3.9 28.7 - - + -
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Residues in contact with LEU 234 (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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187A VAL* 3.6 6.1 - - + +
188A TYR 3.1 12.3 + - - +
189A LYS* 3.6 28.3 - - + +
212A VAL* 4.6 14.4 - - + -
213A PRO* 3.6 16.8 - - + +
215A TRP* 3.8 0.9 - - - -
233A ILE* 1.3 73.8 - - - +
235A ARG* 1.3 77.3 + - - +
237A GLU* 3.2 40.4 - - + +
239A HIS* 3.2 32.7 - - + +
242A ILE* 3.8 22.2 - - - +
243A GLU* 4.1 0.3 - - - +
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Residues in contact with ARG 235 (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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3A GLU* 4.6 1.4 + - - +
157A GLU* 3.0 25.7 + - - +
161A MET* 3.9 10.6 - - - +
206A TRP* 4.0 17.0 - - - -
207A GLY 2.8 35.6 + - - +
208A ILE* 3.6 21.0 - - - +
213A PRO* 3.1 29.7 + - - +
214A TYR* 3.1 34.1 + - - +
215A TRP* 3.4 47.8 - - + +
234A LEU* 1.3 86.1 - - - +
236A GLY* 1.3 61.0 + - - +
237A GLU* 3.6 2.5 - - - +
243A GLU* 3.8 0.2 - - - -
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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