Contacts of the strand formed by residues 225 - 235 (chain B) in PDB entry 1P4A
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 ASN 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B GLY* 3.3 23.8 + - - -
197B SER 2.8 6.3 + - - -
198B ASN* 3.1 27.1 + - - +
199B VAL* 2.8 32.4 + - - +
219B LEU* 4.6 1.6 - - - -
223B ASN 4.7 2.9 - - - +
224B ALA* 1.3 78.9 - - - +
226B VAL* 1.3 64.8 + - - +
227B ALA* 5.6 0.4 - - - -
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Residues in contact with VAL 226 (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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199B VAL 3.7 4.3 - - - +
201B ILE* 4.6 4.7 - - + -
216B ILE* 4.3 27.1 - - + -
219B LEU* 4.0 22.4 - - + -
224B ALA 5.6 0.4 - - - +
225B ASN* 1.3 72.8 - - - +
227B ALA* 1.3 61.4 + - - +
228B GLY* 3.9 9.4 - - - +
229B ILE* 3.7 34.8 - - + -
244B ASP* 4.1 13.5 - - - +
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Residues in contact with ALA 227 (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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129B ARG* 2.9 33.8 + - + +
130B GLU 3.5 25.4 - - - +
131B ILE* 3.9 14.8 - - + -
198B ASN* 4.0 6.1 - - + -
199B VAL 2.9 23.9 + - - +
200B LEU* 5.2 0.4 - - - -
225B ASN* 3.3 3.4 + - - -
226B VAL* 1.3 73.8 - - - +
228B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 228 (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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126B PHE* 4.0 3.8 - - - -
129B ARG* 3.8 13.0 - - - -
199B VAL 3.6 2.9 + - - +
200B LEU* 3.4 16.0 - - - +
201B ILE 2.9 23.2 + - - -
226B VAL* 3.3 6.4 - - - +
227B ALA* 1.3 80.7 - - - +
229B ILE* 1.3 69.0 + - - +
244B ASP* 6.0 0.2 - - - -
245B GLU* 5.3 2.0 - - - -
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Residues in contact with ILE 229 (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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126B PHE* 3.5 12.8 - - - -
200B LEU* 3.8 0.8 - - - +
201B ILE* 3.3 16.6 - - + +
212B ILE* 4.2 29.6 - - + -
216B ILE* 4.1 10.1 - - + -
226B VAL* 3.7 14.4 - - + -
228B GLY* 1.3 79.6 - - - +
230B GLY* 1.3 61.9 + - - +
231B VAL* 4.5 2.7 - - + -
243B VAL* 3.8 15.7 - - + -
244B ASP* 3.5 24.5 - - - +
245B GLU* 3.4 25.2 + - - +
246B TYR* 3.3 14.3 - - + +
247B MET 2.8 27.0 + - - -
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Residues in contact with GLY 230 (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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122B PHE* 3.7 21.8 - - - -
126B PHE* 4.3 4.0 - - - -
200B LEU* 4.3 0.2 - - - +
201B ILE 2.8 12.4 + - - +
202B ILE* 3.1 15.4 - - - +
203B ASP 2.9 24.4 + - - -
229B ILE* 1.3 74.9 - - - +
231B VAL* 1.3 62.9 + - - +
247B MET 3.4 6.3 - - - -
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Residues in contact with VAL 231 (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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122B PHE* 3.8 8.6 - - - -
203B ASP* 3.0 14.8 - - + +
204B ASP 4.6 0.2 - - - +
206B MET* 4.2 16.6 - - + +
212B ILE* 3.5 32.3 - - + -
229B ILE* 4.5 5.6 - - + -
230B GLY* 1.3 80.2 - - - +
232B LEU* 1.3 62.4 + - - +
233B VAL 3.7 27.1 - - - +
234B GLU* 4.1 7.0 - - + +
246B TYR* 5.0 1.8 - - + -
247B MET 2.9 9.7 + - - +
248B SER* 3.3 18.3 - - - -
249B LEU 3.2 17.0 + - - -
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Residues in contact with LEU 232 (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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87B LEU* 3.8 26.9 - - + -
91B LEU* 6.0 0.7 - - + -
105B LEU* 4.5 18.2 - - + -
108B ILE* 4.7 15.0 - - + -
109B LEU* 4.1 25.8 - - + -
118B VAL* 4.1 14.8 - - + -
122B PHE* 4.0 3.7 - - + -
144B LEU* 4.0 16.2 - - + -
203B ASP 3.1 8.3 + - - -
204B ASP 3.2 8.3 - - - +
231B VAL* 1.3 71.4 - - - +
233B VAL* 1.3 69.7 + - + +
249B LEU* 3.3 29.5 + - + +
250B LEU* 2.9 26.0 + - + +
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Residues in contact with VAL 233 (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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91B LEU* 3.8 28.3 - - + -
103B VAL* 5.8 4.7 - - + -
105B LEU* 4.5 11.4 - - + -
204B ASP 2.9 7.4 + - - +
205B PHE* 3.2 28.7 - - + -
206B MET 2.8 24.3 + - - -
231B VAL* 3.7 6.5 - - - +
232B LEU* 1.3 94.3 - - + +
234B GLU* 1.3 70.0 + - - +
250B LEU* 3.3 13.0 - - + +
251B THR 4.6 0.4 - - - -
252B LEU* 3.9 19.3 - - + +
264B ILE* 5.9 1.1 - - + -
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Residues in contact with GLU 234 (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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206B MET* 3.4 25.1 - - + +
231B VAL* 4.1 1.5 - - + +
233B VAL* 1.3 76.7 - - - +
235B ALA* 1.3 68.8 + - - +
236B GLU* 5.6 0.7 - - - -
237B GLY 5.7 0.7 + - - -
238B VAL* 5.1 1.6 + - - +
246B TYR* 2.6 31.3 + - - -
248B SER* 2.4 33.4 + - - +
250B LEU 2.9 16.3 + - - +
251B THR* 3.3 18.1 + - + +
252B LEU 2.8 23.8 + - - -
267B GLY 4.8 0.2 - - - -
268B ASN* 4.4 6.6 + - - +
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Residues in contact with ALA 235 (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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205B PHE* 4.0 13.0 - - + -
206B MET 2.9 11.0 + - - +
207B LYS* 3.8 35.2 - - + +
234B GLU* 1.3 83.4 - - - +
236B GLU* 1.3 68.2 + - - +
237B GLY 3.6 1.4 + - - -
238B VAL* 3.7 14.7 + - - +
252B LEU* 3.7 15.7 - - + +
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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