Contacts of the strand formed by residues 243 - 253 (chain B) in PDB entry 1PO3
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 LYS 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B THR* 6.0 1.3 - - + -
119B THR* 6.5 0.4 - - + -
142B ASP* 3.4 36.6 + - - +
230B GLU 3.7 1.4 - - - +
231B GLY* 3.5 3.3 - - - -
232B GLN* 3.1 57.9 + - + +
242B PRO* 1.3 71.0 - - - +
244B GLU* 1.3 61.5 + - - +
245B THR* 4.6 11.0 - - + -
267B THR* 4.9 8.1 - - + -
268B ARG 3.9 0.7 - - - -
269B GLY* 3.9 5.8 - - - -
270B SER* 3.5 28.0 + - - +
271B ASP* 3.5 39.0 + - + +
276B SER 4.7 1.2 + - - -
278B THR* 4.1 8.2 + - - -
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Residues in contact with GLU 244 (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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229B VAL* 4.1 11.3 - - + +
230B GLU 3.3 8.5 - - - +
231B GLY* 4.5 4.0 - - - -
242B PRO* 3.9 4.6 - - + +
243B LYS* 1.3 72.9 - - - +
245B THR* 1.3 71.5 + - - +
246B HIS* 2.6 41.4 + - - -
267B THR* 3.5 1.6 - - - +
268B ARG* 2.7 61.8 + - + +
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Residues in contact with THR 245 (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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118B THR* 2.8 41.1 + - + +
119B THR* 5.5 2.9 - - + -
142B ASP* 6.1 0.2 - - - +
229B VAL* 3.3 5.2 - - - +
230B GLU* 3.1 33.5 + - - +
232B GLN* 4.9 2.0 - - - +
243B LYS* 4.6 11.4 - - + -
244B GLU* 1.3 85.7 + - - +
246B HIS* 1.3 68.3 + - - +
266B GLY 3.3 10.3 - - - -
267B THR* 3.8 17.7 - - + +
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Residues in contact with HIS 246 (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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228B GLY 3.4 14.6 - - - +
229B VAL* 3.9 9.6 - - + +
244B GLU* 2.6 41.2 + - - -
245B THR* 1.3 77.5 + - - +
247B ASN* 1.3 64.1 + - - +
248B LEU* 6.3 0.2 - - + -
264B TYR* 3.3 37.2 + + - -
265B SER* 3.4 7.4 + - - -
266B GLY* 2.9 41.0 + - - +
268B ARG* 4.2 15.0 + - + -
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Residues in contact with ASN 247 (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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109B ARG* 4.3 19.7 + - - +
187B GLY* 4.1 26.0 + - - +
188B ASN* 4.9 0.2 - - - +
226B GLU* 4.9 5.3 - - - +
227B ALA* 2.7 41.7 - - - +
228B GLY* 2.7 38.5 + - - +
246B HIS* 1.3 82.0 - - - +
248B LEU* 1.3 57.9 + - - +
249B MET 5.1 0.6 - - - +
264B TYR 3.6 10.1 - - - +
265B SER* 4.4 0.4 - - - +
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Residues in contact with LEU 248 (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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188B ASN* 5.0 0.3 - - - +
225B ILE* 4.4 12.3 - - + -
226B GLU 3.3 16.8 - - - +
227B ALA* 3.8 11.0 - - + -
246B HIS* 6.3 0.4 - - + -
247B ASN* 1.3 76.6 - - - +
249B MET* 1.3 59.6 + - - +
250B VAL* 4.3 13.7 - - + -
262B LEU* 3.6 14.3 - - + +
263B LEU* 4.4 0.9 - - - +
264B TYR* 3.1 50.1 + - + +
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Residues in contact with MET 249 (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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224B GLY 4.8 0.9 - - - -
225B ILE* 3.3 4.2 - - - +
226B GLU* 3.0 41.3 + - - +
247B ASN* 5.1 1.2 - - - +
248B LEU* 1.3 74.0 - - - +
250B VAL* 1.3 70.6 + - - +
262B LEU 3.5 6.1 - - - -
263B LEU* 4.9 8.5 - - - -
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Residues in contact with VAL 250 (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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220B PRO* 6.0 0.2 - - - +
223B PHE* 3.1 26.0 - - + -
224B GLY 4.1 1.3 - - - -
225B ILE* 3.8 22.4 - - + -
248B LEU* 4.3 17.9 - - + -
249B MET* 1.3 85.0 - - - +
251B GLY* 1.3 55.3 + - - +
261B ALA* 3.1 3.1 - - - +
262B LEU* 2.5 50.1 + - + +
263B LEU* 5.6 0.4 - - - +
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Residues in contact with GLY 251 (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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220B PRO* 2.3 45.1 - - - +
223B PHE* 2.6 24.0 - - - -
224B GLY 3.8 1.8 + - - -
250B VAL* 1.3 75.0 - - - +
252B GLY* 1.3 49.7 + - - -
260B THR 2.9 15.9 - - - -
261B ALA* 3.3 10.3 - - - +
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Residues in contact with GLY 252 (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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219B ILE* 3.2 7.1 - - - +
220B PRO 3.3 4.3 - - - -
223B PHE* 3.2 27.2 - - - -
251B GLY* 1.3 74.2 - - - -
253B THR* 1.3 68.2 + - - -
254B ALA 4.2 0.2 - - - -
258B PHE 5.1 0.2 - - - -
259B GLY* 3.1 18.1 - - - -
260B THR 3.0 5.7 + - - -
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Residues in contact with THR 253 (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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219B ILE* 4.1 7.1 - - - +
220B PRO 2.5 24.6 + - - -
221B GLN* 3.1 23.7 + - - +
222B ASP* 4.9 3.1 - - - -
223B PHE 4.2 3.2 - - - +
252B GLY* 1.3 76.1 + - - -
254B ALA* 1.3 76.0 + - - +
255B ASP* 3.8 0.7 + - - +
257B GLY* 4.4 10.3 - - - +
258B PHE 4.4 1.1 - - - -
259B GLY* 3.8 17.2 - - - +
288B LYS* 5.6 1.3 - - + +
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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