Contacts of the helix formed by residues 286 - 299 (chain B) in PDB entry 4U04
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 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B ARG* 4.7 5.0 + - - +
284B SER* 4.0 15.3 - - - +
285B VAL* 1.3 81.8 - - - +
287B ILE* 1.3 64.8 + - - +
288B SER* 3.4 12.9 + - - -
289B ASP* 2.8 48.5 + - - +
290B VAL* 3.6 6.9 + - - +
335B VAL* 4.4 6.5 - - - -
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Residues in contact with ILE 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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286B THR* 1.3 75.6 - - - +
288B SER* 1.4 70.2 + - - +
290B VAL* 3.1 10.7 + - + +
291B LEU* 3.1 32.9 + - + +
309B PHE* 4.1 22.9 - - + -
328B GLU* 4.5 4.7 - - + +
331B MET* 3.7 43.1 - - + +
332B GLN* 3.9 17.5 - - + +
335B VAL* 4.2 18.5 - - + +
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 3.2 11.8 + - - -
287B ILE* 1.4 85.4 - - - +
289B ASP* 1.4 57.2 + - - +
291B LEU* 3.5 11.6 + - - +
292B GLU* 2.9 38.5 + - - +
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TYR* 4.6 3.3 + - - -
278B LEU* 3.6 25.8 - - + +
281B ARG* 2.9 31.3 + - - -
285B VAL* 3.5 17.5 - - + +
286B THR* 2.8 38.3 + - - +
288B SER* 1.4 72.7 - - - +
290B VAL* 1.3 64.9 + - - +
292B GLU* 3.8 6.6 - - - +
293B ILE* 3.2 31.8 + - + +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.9 8.1 - - + -
286B THR 3.6 11.6 + - - +
287B ILE* 3.1 9.5 + - + +
289B ASP* 1.3 77.0 - - - +
291B LEU* 1.3 63.5 + - + +
293B ILE* 3.3 12.8 + - + +
294B HIS* 3.0 20.4 + - - +
309B PHE* 5.9 1.8 - - + -
331B MET* 5.0 10.5 - - + -
334B PHE* 5.3 2.0 - - + -
335B VAL* 4.6 15.9 - - + -
338B LEU* 5.5 0.4 - - + -
359B LEU* 4.8 16.8 - - + -
365B PHE* 4.1 24.5 - - + -
372B THR* 5.6 4.3 - - - -
376B LEU* 4.9 19.3 - - + -
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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
----------------------------------------------------------
287B ILE* 3.1 27.3 + - + +
288B SER* 3.8 9.0 - - - +
290B VAL* 1.3 76.8 - - + +
292B GLU* 1.3 53.1 + - - +
294B HIS* 3.4 4.2 + - - -
295B ARG* 2.8 35.1 + - - +
307B GLY* 3.6 29.0 - - - +
308B ARG* 4.4 2.2 - - - +
309B PHE* 3.9 30.5 - - + +
365B PHE* 3.7 26.0 - - + -
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 5.6 0.9 - - - +
308A ARG* 5.6 3.3 + - - -
273B TYR* 3.2 34.8 - - + +
288B SER* 2.9 25.5 + - - +
289B ASP 3.8 3.6 - - - +
291B LEU* 1.3 72.9 - - - +
293B ILE* 1.3 67.2 + - - +
295B ARG* 3.5 27.0 + - - +
296B ARG* 3.0 58.0 + - - +
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Residues in contact with ILE 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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270B ALA* 3.9 3.7 - - + +
273B TYR* 4.6 5.6 - - + -
274B ILE* 3.8 26.5 - - + -
278B LEU* 3.9 17.9 - - + -
289B ASP* 3.2 20.9 - - + +
290B VAL* 3.3 12.7 + - + +
292B GLU* 1.3 76.5 - - - +
294B HIS* 1.4 57.8 + - - +
296B ARG* 3.0 10.1 + - - +
297B VAL* 2.9 27.1 + - + +
372B THR* 4.5 11.7 - - - +
375B LEU* 3.6 33.9 - - + -
376B LEU* 5.4 17.9 - - + +
379B LEU* 5.5 6.1 - - + -
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Residues in contact with HIS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL 3.0 9.1 + - - +
291B LEU 3.7 6.3 - - - +
293B ILE* 1.4 72.9 - - - +
295B ARG* 1.4 65.4 + - - +
297B VAL* 4.2 4.7 - - + -
298B LEU* 3.0 49.6 + - + +
305B GLU 3.7 8.5 - - - -
306B ALA* 3.8 2.2 - - - -
307B GLY* 2.9 27.0 + - - -
365B PHE* 3.4 59.2 - + + +
366B ILE 5.7 0.2 - - - -
367B ASP 2.8 25.2 + - - -
368B GLY* 4.1 3.4 - - - -
372B THR* 3.8 16.8 - - - +
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Residues in contact with ARG 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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295A ARG* 3.6 18.7 - - - +
303A PRO* 3.3 27.4 + - - +
304A VAL* 2.8 35.3 + - - +
306A ALA 4.4 3.4 + - - -
308A ARG* 4.5 14.1 - - - +
291B LEU 2.8 20.5 + - - +
292B GLU* 3.7 30.9 + - - +
293B ILE 3.3 0.6 - - - -
294B HIS* 1.4 72.4 - - - +
296B ARG* 1.3 60.7 + - - +
299B GLY* 3.1 26.2 + - - -
306B ALA* 3.9 17.2 + - - +
307B GLY* 3.8 11.9 - - - +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PRO* 5.3 1.6 - - + -
304A VAL* 3.4 45.9 - - + +
266B GLY* 2.9 27.4 - - - +
269B ALA* 3.8 16.3 + - + +
270B ALA* 3.7 16.6 - - - +
273B TYR* 3.5 49.3 - - - +
292B GLU* 3.0 50.4 + - - +
293B ILE* 3.0 8.7 + - - +
295B ARG* 1.3 81.0 - - - +
297B VAL* 1.3 61.7 + - - +
298B LEU 3.4 0.4 + - - -
299B GLY* 4.0 0.7 + - - -
300B TYR* 4.0 11.7 - - + -
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Residues in contact with VAL 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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262B ASN 5.0 0.7 - - - +
263B GLU* 4.5 11.6 - - - +
266B GLY* 3.8 16.7 - - - -
267B MET* 4.1 7.6 - - - +
270B ALA* 3.6 5.4 - - + -
293B ILE* 2.9 23.9 + - + +
294B HIS* 3.3 8.5 + - + +
296B ARG* 1.3 76.2 - - - +
298B LEU* 1.4 60.8 + - - +
300B TYR 5.3 0.2 + - - -
301B VAL* 5.2 2.1 - - - +
368B GLY* 4.3 8.7 - - - +
371B ARG* 3.7 39.8 + - + +
372B THR* 4.2 13.2 - - - +
375B LEU* 3.5 31.2 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B HIS* 3.0 42.8 + - + +
297B VAL* 1.4 75.8 - - - +
299B GLY* 1.3 56.2 + - - +
300B TYR 3.3 2.7 - - - -
301B VAL* 2.9 31.1 + - + -
302B ASP* 2.7 49.2 + - + +
305B GLU* 4.6 7.9 - - + -
306B ALA* 3.8 14.8 - - + +
366B ILE* 5.9 1.1 - - + +
367B ASP* 3.7 35.9 - - + +
368B GLY* 4.6 1.6 - - - +
371B ARG* 4.2 15.5 - - - +
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Residues in contact with GLY 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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299A GLY 3.2 15.4 - - - +
303A PRO* 3.5 19.1 - - - -
295B ARG 3.1 24.7 + - - -
296B ARG 4.0 1.7 + - - -
297B VAL 3.7 1.0 - - - -
298B LEU* 1.3 74.7 - - - +
300B TYR* 1.3 59.6 + - - +
303B PRO* 3.3 18.8 - - - +
306B ALA* 3.4 12.4 - - - +
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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