Contacts of the helix formed by residues 275 - 291 (chain B) in PDB entry 2PO5
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 PRO 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ARG* 3.5 29.8 - - - +
194B TYR* 3.5 30.1 - - + +
196B CYS* 4.2 5.6 - - - -
226B ARG* 4.1 16.6 - - - +
273B GLY 3.3 7.6 - - - +
274B ASP* 1.3 88.3 - - - +
276B TYR* 1.3 64.9 + - - +
277B PRO* 3.5 0.9 - - - -
278B GLN* 3.3 11.9 + - + +
279B GLU* 3.2 26.0 + - + +
398B GLN* 5.1 4.3 - - - +
403B CYS* 4.2 5.8 - - - -
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLN* 3.8 29.4 - - + -
194B TYR 3.1 14.4 + - - +
195B SER* 3.9 11.7 - - - -
198B THR* 5.9 2.7 - - + -
262B ALA* 3.6 6.9 - - - +
263B CYS* 2.9 48.2 + - + +
265B LEU* 3.4 28.7 - - + -
274B ASP* 2.9 20.1 + - - +
275B PRO* 1.3 75.4 - - - +
277B PRO* 1.3 69.6 - - + +
279B GLU* 3.0 5.7 + - - +
280B VAL* 2.9 44.4 + - + +
301B TRP* 3.8 15.0 - + - -
311B LEU* 6.2 0.2 - - + -
336B ALA* 3.6 8.8 - - + +
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Residues in contact with PRO 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 4.8 0.4 - - - -
265B LEU* 4.4 2.7 - - + -
270B VAL* 4.4 21.8 - - + -
274B ASP* 3.3 18.6 - - + +
275B PRO 3.6 0.9 - - - -
276B TYR* 1.3 99.5 - - + +
278B GLN* 1.3 61.2 + - - +
280B VAL* 3.4 1.7 + - - +
281B SER* 2.9 30.8 + - - -
301B TRP* 3.9 16.0 - - + -
311B LEU* 4.1 27.1 - - + -
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Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 3.1 44.8 + - - +
284A VAL* 4.1 5.1 - - + +
285A GLN* 3.1 29.3 + - - +
297A TYR* 3.2 28.5 + - + -
299A LEU* 4.0 27.1 - - + +
275B PRO* 3.3 11.7 + - + +
276B TYR 3.3 0.8 - - - -
277B PRO* 1.3 80.2 - - - +
279B GLU* 1.3 72.3 + - - +
281B SER* 3.4 3.8 - - - -
282B ALA 3.1 16.1 + - - -
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN* 5.0 0.9 - - - +
297A TYR* 4.9 5.4 + - - +
192B PRO 4.0 1.4 - - - +
193B GLN* 3.4 15.1 - - + +
194B TYR* 2.7 34.3 + - - +
226B ARG* 2.8 46.1 + - - +
228B PRO* 3.9 16.1 - - + +
275B PRO* 3.2 17.0 + - + +
276B TYR 3.0 7.2 + - - +
278B GLN* 1.3 86.7 - - - +
280B VAL* 1.3 66.6 + - - +
282B ALA* 3.0 17.4 + - - +
283B THR* 3.0 15.6 + - - -
398B GLN* 4.8 4.2 - - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLN* 3.6 19.7 - - + +
262B ALA* 3.7 23.3 - - + -
276B TYR* 2.9 59.6 + - + +
277B PRO 3.8 3.6 - - - +
279B GLU* 1.3 75.2 - - - +
281B SER* 1.3 63.4 + - - +
283B THR* 3.0 5.2 + - - -
284B VAL* 3.0 20.6 + - - +
299B LEU* 3.9 15.9 - - + -
301B TRP* 4.1 5.8 - - + -
335B ILE* 3.7 17.5 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PRO 4.6 0.7 + - - -
278A GLN* 3.1 32.7 + - - -
281A SER* 3.2 31.4 + - - -
282A ALA 5.3 0.7 - - - -
277B PRO 2.9 19.3 + - - -
278B GLN 3.4 0.7 - - - -
280B VAL* 1.3 77.7 - - - +
282B ALA* 1.3 61.2 + - - +
284B VAL* 3.3 1.1 + - - +
285B GLN* 3.0 20.1 + - - +
299B LEU* 3.6 21.2 - - - +
301B TRP* 5.0 1.9 - - - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 4.9 0.4 - - - -
282A ALA* 5.1 4.0 - - - +
285A GLN* 3.4 48.1 - - + +
228B PRO* 5.0 1.1 - - + -
229B THR* 3.9 9.4 - - + -
278B GLN* 3.1 11.0 + - - +
279B GLU* 3.0 11.2 + - - +
281B SER* 1.3 73.6 - - - +
283B THR* 1.3 65.2 + - - +
285B GLN* 3.3 7.6 + - - +
286B LYS* 3.1 26.3 + - - +
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLN* 2.9 26.1 + - - +
228B PRO 2.7 28.8 + - - +
233B LEU* 4.7 2.2 - - + -
234B ILE* 3.7 15.5 - - + -
237B PHE* 4.2 9.4 - - + -
279B GLU 3.0 10.0 + - - -
280B VAL 3.0 8.2 + - - -
282B ALA* 1.3 76.6 - - - +
284B VAL* 1.3 63.7 + - - +
286B LYS* 3.2 3.5 + - - +
287B VAL* 3.0 22.2 + - - +
335B ILE* 3.7 26.5 - - + -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 4.0 9.0 - - + +
260B PHE* 3.7 34.0 - - + -
280B VAL 3.0 16.1 + - - +
281B SER* 3.5 8.3 - - - +
283B THR* 1.3 77.1 - - - +
285B GLN* 1.3 62.8 + - - +
287B VAL* 3.3 5.5 + - - +
288B MET* 2.9 24.0 + - + +
297B TYR* 3.7 30.3 - - + -
299B LEU* 3.8 33.0 - - + -
335B ILE* 4.1 9.2 - - + -
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 4.7 9.3 - - - +
229A THR* 4.2 10.2 + - + +
278A GLN* 2.9 27.5 + - - +
279A GLU* 4.8 4.0 - - - +
282A ALA* 3.4 27.9 - - + +
281B SER 3.0 13.5 + - - +
282B ALA* 3.6 9.0 - - - +
284B VAL* 1.3 77.8 - - - +
286B LYS* 1.3 58.0 + - + +
288B MET* 3.4 4.1 + - - +
289B GLU* 2.9 47.9 + - - +
293B TYR* 2.9 37.4 + - - -
297B TYR* 3.4 12.6 + - - -
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN* 6.0 0.9 - - + -
286A LYS* 6.4 2.2 - - - -
289A GLU* 4.9 14.1 + - - +
229B THR* 3.1 47.9 + - + -
231B HIS* 4.3 15.8 - - - +
234B ILE* 3.6 34.3 - - + +
282B ALA 3.1 16.2 + - - +
283B THR 3.7 2.0 - - - +
285B GLN* 1.3 76.5 - - + +
287B VAL* 1.3 63.6 + - - +
289B GLU* 3.3 12.5 + - - +
290B ARG* 3.1 18.5 + - - +
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Residues in contact with VAL 287 (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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234B ILE* 3.7 22.9 - - + -
237B PHE* 3.8 22.2 - - + -
238B ALA* 4.4 7.6 - - - +
241B ILE* 3.4 33.2 - - + -
260B PHE* 3.8 13.5 - - + -
283B THR 3.0 17.2 + - - +
284B VAL 3.6 6.7 - - - +
286B LYS* 1.3 76.3 - - - +
288B MET* 1.3 63.9 + - - +
290B ARG* 3.1 5.0 + - - +
291B LEU* 3.0 27.3 + - + +
335B ILE* 4.1 12.8 - - + -
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Residues in contact with MET 288 (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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258B ILE* 4.4 8.7 - - + -
260B PHE* 3.4 33.0 - - + -
284B VAL 2.9 20.3 + - - +
285B GLN* 3.8 4.7 - - - +
287B VAL* 1.3 77.3 - - - +
289B GLU* 1.3 61.3 + - - +
291B LEU* 3.3 16.4 + - + +
292B GLU 3.1 3.3 + - - -
293B TYR* 2.9 65.2 + - + -
294B CYS 4.5 2.5 - - - +
295B ASN 3.4 27.8 - - - +
297B TYR* 3.5 31.6 - - + -
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Residues in contact with GLU 289 (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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229A THR* 3.5 23.5 + - - +
286A LYS* 4.3 19.7 + - - +
285B GLN* 2.9 35.2 + - - +
286B LYS* 3.7 11.0 - - + +
287B VAL 3.2 0.2 - - - -
288B MET* 1.3 77.1 - - - +
290B ARG* 1.3 63.0 + - - +
292B GLU* 3.0 18.4 + - - +
293B TYR* 2.9 32.3 + - + +
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Residues in contact with ARG 290 (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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231B HIS 5.3 1.7 + - - -
234B ILE* 4.2 11.4 - - + -
235B GLN* 3.5 53.3 + - - +
238B ALA* 4.0 20.2 - - + +
239B ASP* 4.0 13.3 + - - -
242B LEU* 5.6 5.3 - - - +
286B LYS 3.1 13.6 + - - +
287B VAL 3.6 8.3 - - - +
289B GLU* 1.3 77.9 - - - +
291B LEU* 1.3 59.4 + - - +
292B GLU* 3.1 10.2 + - - +
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Residues in contact with LEU 291 (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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238B ALA* 3.7 19.5 - - + +
241B ILE* 3.7 39.5 - - + -
242B LEU* 3.4 43.5 - - + +
258B ILE* 4.7 4.3 - - + -
287B VAL* 3.0 22.1 + - + +
288B MET* 3.3 20.6 + - + +
289B GLU 3.2 0.2 - - - -
290B ARG* 1.3 75.1 - - - +
292B GLU* 1.3 70.4 + - - +
293B TYR 3.1 1.4 + - - +
294B CYS* 3.1 29.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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