Contacts of the helix formed by residues 281 - 297 (chain B) in PDB entry 4PKO
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B GLY* 1.3 71.6 - - - -
282B GLY* 1.3 69.8 + - - +
283B ASP* 3.8 28.0 - - + -
284B ARG* 3.2 15.0 + - + +
285B ARG* 2.4 36.8 + - - +
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Residues in contact with GLY 282 (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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252B GLU* 6.0 0.4 - - - -
280B GLY 4.0 0.6 + - - -
281B PHE* 1.3 82.6 - - - +
283B ASP* 1.3 58.6 + - - +
285B ARG* 4.4 11.2 - - - +
286B LYS* 2.5 57.7 + - - +
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Residues in contact with ASP 283 (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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281B PHE* 3.6 20.7 - - + -
282B GLY* 1.3 73.7 - - - +
284B ARG* 1.3 78.1 + - + +
286B LYS* 4.7 5.1 - - - +
287B ALA* 3.4 19.4 + - - +
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Residues in contact with ARG 284 (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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280B GLY* 5.8 0.9 - - - -
281B PHE* 3.2 18.2 + - + +
282B GLY 3.1 0.2 - - - -
283B ASP* 1.3 94.8 + - + +
285B ARG* 1.3 62.3 + - - +
287B ALA* 3.3 5.4 + - - +
288B MET* 3.0 41.4 + - + +
357B THR* 5.8 2.0 - - - +
360B TYR 5.5 0.4 + - - -
361B ASP* 3.5 30.1 + - - +
364B LYS* 4.3 38.4 - - + +
368B ARG* 4.6 16.5 + - - +
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Residues in contact with ARG 285 (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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223B ALA 3.3 16.0 + - - +
224B ASP* 4.6 1.8 + - - +
250B ILE 5.3 0.2 + - - -
251B ALA* 4.5 0.8 - - - +
252B GLU* 2.7 44.5 + - - +
278B ALA* 3.0 37.9 - - + +
279B PRO* 4.2 5.4 - - + -
280B GLY 3.4 31.8 + - - +
281B PHE 2.4 29.6 + - - +
282B GLY* 4.5 7.3 - - - -
284B ARG* 1.3 70.2 - - - +
286B LYS* 1.3 75.1 + - - +
288B MET* 2.8 14.3 + - - +
289B LEU* 2.6 69.3 + - + +
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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
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224B ASP* 3.5 30.5 + - - +
252B GLU* 5.9 0.7 - - - -
282B GLY* 2.5 35.3 + - - +
283B ASP* 4.7 4.0 - - - +
285B ARG* 1.3 91.3 - - - +
287B ALA* 1.3 61.0 + - - +
289B LEU* 3.3 22.7 + - + +
290B GLN* 3.6 11.8 + - - +
304B GLU* 3.2 34.1 + - - +
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Residues in contact with ALA 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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283B ASP 3.4 20.1 + - - +
284B ARG 3.3 6.2 + - - +
285B ARG 3.1 0.2 - - - -
286B LYS* 1.3 78.8 - - - +
288B MET* 1.3 59.6 + - - +
289B LEU 3.2 0.4 - - - -
290B GLN* 3.5 17.5 - - - +
291B ASP* 2.9 24.6 - - - +
345B ARG* 3.7 3.0 + - - +
368B ARG* 4.0 27.7 - - - +
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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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193B MET* 5.1 8.9 - - + +
195B PHE* 6.0 2.9 - - + -
279B PRO* 4.5 21.8 - - + -
280B GLY* 5.1 5.6 - - - +
284B ARG* 3.0 26.0 + - + +
285B ARG* 2.8 17.0 + - + +
287B ALA* 1.3 74.8 - - - +
289B LEU* 1.3 61.6 + - + +
291B ASP* 3.2 10.7 - - + +
292B ILE* 3.2 31.0 + - + +
364B LYS 5.3 3.4 - - - +
367B GLU* 5.3 5.6 - - - +
368B ARG* 3.6 39.9 - - + +
371B LYS* 5.0 15.0 - - - -
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Residues in contact with LEU 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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221B LEU 6.0 0.2 - - - +
222B LEU* 2.9 44.3 - - + +
223B ALA 4.5 8.3 - - - +
224B ASP* 4.7 6.3 - - - +
250B ILE* 4.7 13.0 - - + +
278B ALA* 4.6 7.9 - - + -
279B PRO* 5.3 2.0 - - + -
285B ARG* 2.6 62.8 + - + +
286B LYS* 3.5 21.5 - - + +
287B ALA 3.2 0.6 - - - -
288B MET* 1.3 73.7 - - + +
290B GLN* 1.3 62.5 + - - +
291B ASP 3.0 4.3 - - - -
292B ILE* 3.0 22.5 + - + +
293B ALA 3.1 3.8 + - - -
300B VAL* 5.1 5.8 - - + -
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Residues in contact with GLN 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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286B LYS 3.6 8.6 + - - +
287B ALA* 3.5 15.5 - - - +
289B LEU* 1.3 78.8 - - - +
291B ASP* 1.3 52.0 + - - +
293B ALA* 3.9 0.6 - - - +
294B THR* 2.8 41.3 + - + +
300B VAL* 3.6 23.2 - - + +
345B ARG* 2.9 50.1 + - - +
348B GLN* 5.0 0.2 + - - -
203C TYR* 5.3 10.7 - - - -
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Residues in contact with ASP 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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193B MET* 6.0 1.1 - - + -
287B ALA 2.9 16.8 - - - +
288B MET* 3.2 12.4 - - + +
289B LEU 3.0 0.2 - - - -
290B GLN* 1.3 78.2 - - - +
292B ILE* 1.3 58.6 + - + +
294B THR* 3.2 6.1 + - - -
295B LEU* 3.0 29.3 + - - +
345B ARG* 2.6 37.4 + - - +
349B ILE* 5.5 0.5 - - - +
368B ARG* 3.0 32.9 - - + +
372B LEU* 3.5 35.4 - - + +
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Residues in contact with ILE 292 (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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193B MET* 3.8 29.8 - - + -
195B PHE* 4.2 21.8 - - + -
220B ILE* 4.0 21.5 - - + -
222B LEU* 5.4 1.3 - - + -
250B ILE* 4.5 12.1 - - + -
279B PRO* 5.6 6.1 - - + -
288B MET* 3.2 19.5 - - + +
289B LEU* 3.0 17.7 + - + +
291B ASP* 1.3 72.9 - - + +
293B ALA* 1.3 63.6 + - - +
295B LEU* 3.4 8.8 + - + +
296B THR* 2.9 29.0 + - + +
332B ILE* 4.0 24.0 - - + -
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Residues in contact with ALA 293 (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 ILE* 4.8 2.9 - - - -
222B LEU* 3.7 16.9 - - + +
289B LEU 3.1 5.4 + - - +
290B GLN 4.0 2.7 - - - +
292B ILE* 1.3 78.9 - - - +
294B THR* 1.3 53.0 + - + +
296B THR* 3.4 3.9 + - - -
297B GLY 2.7 12.6 + - - -
298B GLY* 2.3 53.8 + - - +
300B VAL* 3.6 30.1 - - + -
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Residues in contact with THR 294 (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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290B GLN* 2.8 24.8 + - + +
291B ASP* 3.2 8.1 + - - -
293B ALA* 1.3 74.9 - - + +
295B LEU* 1.3 65.2 + - - +
297B GLY* 3.4 9.4 + - - +
298B GLY 4.4 6.1 - - - +
300B VAL* 6.3 0.2 - - + -
337B GLY* 3.7 4.9 - - - -
341B ALA* 3.4 35.3 + - + +
342B ILE* 4.4 3.6 - - - +
345B ARG* 3.6 28.1 - - + +
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Residues in contact with LEU 295 (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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193B MET* 3.8 33.4 - - + -
291B ASP 3.0 18.0 + - - +
292B ILE* 3.5 9.9 - - + +
293B ALA 3.2 0.2 - - - -
294B THR* 1.3 78.8 + - - +
296B THR* 1.3 67.1 + - + +
332B ILE* 4.6 9.2 - - + -
335B GLY* 3.6 25.2 - - - +
336B VAL 3.4 3.5 + - - -
337B GLY* 3.0 21.1 + - - -
342B ILE* 4.0 28.3 - - + +
371B LYS 4.6 0.2 - - - +
372B LEU* 4.3 28.7 - - + +
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Residues in contact with THR 296 (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 ILE* 3.6 28.5 - - + +
292B ILE 2.9 17.5 + - - +
293B ALA* 3.4 4.0 + - - -
295B LEU* 1.3 90.3 - - + +
297B GLY* 1.3 56.7 + - - +
298B GLY 3.9 0.2 + - - -
318B GLY* 3.2 15.4 - - - -
319B GLN* 3.0 47.5 + - - +
320B ALA* 4.4 6.3 - - + -
332B ILE* 4.3 13.0 - - + -
335B GLY* 4.6 0.2 - - - -
336B VAL* 3.9 8.6 - - - +
337B GLY 4.0 4.3 - - - -
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Residues in contact with GLY 297 (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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293B ALA 2.7 7.8 + - - -
294B THR* 3.4 10.6 + - - -
295B LEU 3.3 3.6 - - - -
296B THR* 1.3 79.9 - - - +
298B GLY* 1.3 58.5 + - - -
299B THR* 5.2 0.5 + - - -
315B GLU 4.0 9.2 - - - +
317B LEU 4.2 2.1 - - - +
318B GLY* 4.2 1.6 - - - -
319B GLN* 5.5 0.4 - - - +
336B VAL* 5.0 1.1 - - - -
337B GLY* 4.0 10.3 - - - +
341B ALA* 5.9 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