Contacts of the strand formed by residues 258 - 269 (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 PHE 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B ALA* 3.2 25.0 + - + +
256B ASN* 3.1 20.0 + - - +
257B GLY* 1.3 76.1 - - - +
259B GLY* 1.3 69.2 + - - +
260B THR* 3.9 21.3 - - - -
287B SER* 4.7 9.4 - - - -
288B LYS 3.8 1.3 - - - -
289B TYR* 3.8 34.5 - + + -
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Residues in contact with GLY 259 (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 6.5 - - - -
252B GLY 3.1 15.7 - - - -
253B THR* 3.8 10.5 - - - +
257B GLY 3.8 1.4 + - - -
258B PHE* 1.3 79.7 - - - +
260B THR* 1.3 68.7 + - - -
287B SER* 3.4 1.7 - - - -
288B LYS* 3.0 36.7 + - - +
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Residues in contact with THR 260 (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* 3.3 5.8 - - - +
251B GLY* 2.9 19.8 - - - -
252B GLY 3.0 11.2 + - - -
258B PHE* 3.9 15.6 - - - -
259B GLY* 1.3 74.5 + - - -
261B ALA* 1.3 72.6 + - - +
285B LEU* 5.0 12.1 - - + -
286B LYS 3.0 10.8 - - - +
287B SER* 2.7 22.6 + - - +
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Residues in contact with ALA 261 (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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217B ARG 5.7 0.4 - - - +
218B ALA 5.4 0.9 - - - +
219B ILE* 3.3 24.0 - - + -
220B PRO* 4.1 5.4 - - + -
250B VAL 3.1 9.0 - - - +
251B GLY* 3.4 13.7 - - - +
260B THR* 1.3 82.1 - - - +
262B LEU* 1.3 64.2 + - - +
263B LEU* 3.9 9.4 - - + -
285B LEU* 3.6 8.1 - - - +
286B LYS* 2.6 36.9 + - + +
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Residues in contact with LEU 262 (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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248B LEU* 3.6 15.9 - - + +
249B MET* 3.5 7.4 - - - -
250B VAL* 2.5 41.9 + - + +
261B ALA* 1.3 72.8 - - - +
263B LEU* 1.3 63.1 + - - +
264B TYR* 3.8 26.0 - - + +
283B LEU* 3.3 28.5 - - + -
284B MET 3.7 4.9 - - - +
285B LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 263 (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* 3.6 28.0 + - + +
216B THR* 4.1 5.8 - - + -
217B ARG* 3.9 37.9 - - + +
248B LEU 5.2 0.2 - - - +
249B MET* 4.9 9.0 - - - -
250B VAL 5.6 0.2 - - - +
261B ALA* 3.9 7.7 + - + -
262B LEU* 1.3 78.5 - - - +
264B TYR* 1.3 57.3 + - - +
284B MET* 2.7 78.8 + - + +
286B LYS* 4.2 20.2 - - + -
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Residues in contact with TYR 264 (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* 3.1 12.1 + - - +
246B HIS* 3.3 35.1 + + - -
247B ASN* 3.6 1.6 - - - +
248B LEU* 3.1 53.8 + - + +
262B LEU* 3.7 19.9 + - + -
263B LEU* 1.3 73.7 - - - +
265B SER* 1.3 84.5 + - - +
266B GLY* 3.9 1.4 - - - -
268B ARG* 4.0 4.5 + - - -
281B ASP* 2.6 32.2 + - + -
282B ASP 3.4 17.3 - - - -
283B LEU* 4.1 13.7 - - + -
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Residues in contact with SER 265 (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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185B SER* 4.0 15.9 - - - -
187B GLY* 3.2 23.0 + - - -
188B ASN* 3.3 24.7 - - - -
246B HIS 3.4 11.8 + - - -
247B ASN* 4.4 0.4 - - - +
264B TYR* 1.3 85.8 - - - +
266B GLY* 1.3 61.5 + - - +
280B ILE* 5.0 0.8 - - - +
282B ASP* 2.8 30.8 + - - +
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Residues in contact with GLY 266 (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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245B THR* 3.3 3.3 - - - -
246B HIS* 2.9 50.0 + - - +
264B TYR* 3.9 4.5 - - - -
265B SER* 1.3 78.2 + - - +
267B THR* 1.3 69.4 + - - -
268B ARG* 4.4 0.2 - - - -
280B ILE* 3.0 12.6 - - - -
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Residues in contact with THR 267 (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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119B THR* 6.0 1.4 - - - +
142B ASP* 4.5 12.8 - - + +
243B LYS* 4.9 5.8 - - - -
244B GLU* 3.5 12.8 + - - +
245B THR* 3.8 14.7 - - + +
266B GLY* 1.3 78.8 + - - -
268B ARG* 1.3 78.5 + - - +
278B THR* 4.1 24.2 - - + -
279B ARG* 3.5 2.1 - - - -
280B ILE* 2.7 52.8 + - + +
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Residues in contact with ARG 268 (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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242B PRO 4.3 0.2 - - - +
243B LYS* 3.9 0.2 - - - -
244B GLU* 2.7 52.6 + - + +
246B HIS* 4.2 9.3 + - + -
264B TYR* 4.0 7.3 + - - -
267B THR* 1.3 94.2 + - - +
269B GLY* 1.3 59.2 + - - +
278B THR 3.3 5.4 - - - -
279B ARG* 3.8 23.8 - - - +
280B ILE 3.3 9.1 + - - -
281B ASP* 2.9 39.4 + - - -
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Residues in contact with GLY 269 (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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241B ASN* 6.0 0.7 - - - -
242B PRO 3.4 13.7 - - - -
243B LYS* 3.9 8.1 - - - -
268B ARG* 1.3 76.9 - - - +
270B SER* 1.3 65.0 + - - -
277B ALA* 3.3 1.1 - - - -
278B THR* 2.7 40.9 + - - +
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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