Contacts of the helix formed by residues 288 - 302 (chain B) in PDB entry 4PS1
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 THR 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B LYS* 5.9 1.8 - - + -
287B CYS* 1.3 77.2 - - - +
289B VAL* 1.3 65.2 + - - +
290B GLU* 3.6 9.9 + - - +
291B GLN* 2.9 35.5 + - - +
292B ILE* 2.9 22.1 + - - +
325B GLY* 4.0 1.3 - - - -
326B THR* 3.9 10.5 - - - +
327B ASP* 3.5 33.2 - - + +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR* 1.3 72.9 - - - +
290B GLU* 1.3 65.9 + - - +
292B ILE* 3.2 9.9 + - + +
293B TYR* 3.0 50.8 + - + -
325B GLY* 3.5 12.8 - - - +
327B ASP* 3.2 5.0 + - - +
329B GLN* 3.1 48.9 - - + +
330B GLU 3.9 17.5 - - - +
331B ALA* 4.1 9.2 - - + +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLU* 5.5 2.6 - - - +
288B THR* 3.3 9.6 + - - +
289B VAL* 1.3 80.9 - - - +
291B GLN* 1.3 57.9 + - + +
293B TYR* 3.3 9.5 + - - +
294B GLU* 3.0 54.7 + - + +
327B ASP* 5.0 2.1 + - - +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASP* 4.3 15.2 + - - -
285B ASP 5.3 2.0 + - - -
286B ASP 3.4 9.3 + - - +
287B CYS* 3.4 18.4 - - + +
288B THR* 2.9 47.8 + - - +
290B GLU* 1.3 74.8 - - + +
292B ILE* 1.3 67.1 + - - +
294B GLU* 3.2 17.9 + - - +
295B ILE* 2.9 33.4 + - + +
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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
----------------------------------------------------------
239B ILE* 4.0 29.2 - - + -
241B ASN* 4.3 5.4 - - - +
287B CYS* 3.6 22.0 - - + +
288B THR 2.9 18.9 + - - +
289B VAL* 3.5 14.1 - - + +
291B GLN* 1.3 77.7 - - - +
293B TYR* 1.3 63.5 + - + +
295B ILE* 3.3 7.5 + - - +
296B LEU* 3.0 30.4 + - + +
314B ILE* 5.4 2.9 - - + -
323B ILE* 3.6 27.6 - - + -
325B GLY* 4.5 2.9 - - - -
331B ALA* 5.4 1.6 - - + -
336B LEU* 3.9 30.7 - - + -
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 3.0 41.3 + - + -
290B GLU* 3.8 8.3 - - - +
292B ILE* 1.3 75.8 - - + +
294B GLU* 1.3 58.6 + - + +
296B LEU* 3.4 6.3 + - + +
297B LYS* 2.9 32.1 + - - +
330B GLU 4.7 0.9 + - - -
331B ALA* 3.7 6.6 - - + +
332B PRO* 3.6 25.6 - - - +
335B GLU* 3.6 24.7 - - + +
336B LEU* 3.5 28.3 - - + -
339B GLN* 5.5 6.5 - - + -
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE 4.5 4.2 - - - +
283A PRO* 3.5 45.3 - - + +
290B GLU* 3.0 40.6 + - + +
291B GLN* 3.2 25.5 + - - +
293B TYR* 1.3 77.7 - - + +
295B ILE* 1.3 63.0 - - + +
297B LYS* 3.5 6.1 + - - +
298B ILE* 3.2 23.2 + - - +
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Residues in contact with ILE 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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285A ASP* 6.1 0.7 - - - +
237B LEU* 3.9 24.0 - - + -
239B ILE* 3.9 12.1 - - + -
284B HIS* 3.6 53.8 - - + +
287B CYS* 3.7 17.5 - - - -
291B GLN* 2.9 24.0 + - + +
292B ILE* 3.6 4.5 - - - +
294B GLU* 1.3 75.4 - - + +
296B LEU* 1.3 67.5 + - + +
298B ILE* 3.3 11.3 + - - +
299B TYR* 3.2 26.0 + - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.8 24.9 - - + -
239B ILE* 5.6 2.9 - - + -
292B ILE* 3.0 25.2 + - + +
293B TYR* 4.0 5.6 - - + +
295B ILE* 1.3 80.0 - - + +
297B LYS* 1.3 50.3 + - - +
299B TYR* 3.2 1.5 + - - -
300B GLN* 2.8 35.4 + - - +
312B CYS* 4.1 15.7 - - - -
314B ILE* 5.7 1.1 - - + -
336B LEU* 3.7 54.3 - - + +
339B GLN* 4.6 11.4 - - + -
340B PHE* 3.5 25.3 - - + -
355B PHE* 4.9 3.1 - - + -
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Residues in contact with LYS 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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282A LYS* 6.4 0.4 - - - +
293B TYR 2.9 18.9 + - - +
294B GLU* 3.7 8.1 - - - +
296B LEU* 1.3 73.0 - - - +
298B ILE* 1.3 65.9 + - - +
300B GLN* 2.6 35.0 + - - +
301B LEU* 3.0 50.1 + - + +
339B GLN* 4.9 12.8 + - - +
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Residues in contact with ILE 298 (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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284A HIS* 3.6 37.5 - - + +
291A GLN* 4.1 11.0 - - - +
295A ILE* 4.1 14.8 - - + -
298A ILE* 3.9 28.3 - - + -
299A TYR* 5.7 1.8 - - + -
294B GLU 3.2 13.3 + - - +
295B ILE* 3.3 14.4 - - + +
297B LYS* 1.3 77.4 - - - +
299B TYR* 1.3 73.2 + - + +
301B LEU* 3.2 12.4 + - + -
302B MET* 3.0 43.4 + - + +
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Residues in contact with TYR 299 (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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291A GLN* 3.9 19.0 + - - -
235B TYR* 3.7 33.4 - + - -
237B LEU* 3.7 31.0 - - + -
282B LYS* 3.3 29.6 - - - +
284B HIS* 4.8 8.7 + - - -
295B ILE* 3.2 25.5 + - + +
296B LEU 3.9 5.4 - - - +
298B ILE* 1.3 94.2 - - + +
300B GLN* 1.3 62.0 + - - +
302B MET* 3.3 28.2 + - + +
304B HIS* 2.7 29.3 + + - -
310B PHE* 4.2 10.5 - + + -
340B PHE* 3.8 17.0 - - + -
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Residues in contact with GLN 300 (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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296B LEU 2.8 18.9 + - - +
297B LYS* 2.6 46.0 + - - +
299B TYR* 1.3 75.2 - - - +
301B LEU* 1.3 74.8 + - - +
302B MET 3.6 1.6 + - - +
339B GLN* 3.2 34.3 - - + +
340B PHE* 3.6 12.2 - - + -
344B LYS* 2.8 40.0 + - - +
345B CYS* 3.6 16.9 - - + -
346B PRO* 5.6 0.3 - - - +
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Residues in contact with LEU 301 (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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294A GLU* 4.7 0.5 - - - +
298A ILE* 3.8 38.9 - - + +
302A MET* 6.2 0.9 - - + -
297B LYS* 3.0 39.6 + - + +
298B ILE* 3.2 12.1 + - + +
300B GLN* 1.3 94.3 - - - +
302B MET* 1.3 66.3 + - - +
303B ASP 4.0 0.2 + - - -
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 3.5 35.9 - - + +
294A GLU* 3.4 28.7 - - + +
295A ILE* 5.8 0.4 - - + -
298A ILE* 4.8 0.7 - - + -
235B TYR* 3.5 29.2 - - + +
298B ILE* 3.0 35.4 + - + +
299B TYR* 3.6 38.8 - - + +
300B GLN 3.3 6.3 - - - +
301B LEU* 1.3 83.8 - - - +
303B ASP* 1.3 62.2 + - - +
304B HIS* 3.3 19.5 + - + +
345B CYS* 4.6 0.2 - - - -
347B SER* 3.6 5.0 + - - -
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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