Contacts of the helix formed by residues 287 - 300 (chain B) in PDB entry 2BEW
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 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLU* 4.8 3.8 + - + -
152B ALA* 3.7 14.0 - - + +
155B ALA* 3.5 32.1 - - + -
227B TRP* 4.0 19.3 - + + -
254B LEU* 3.9 11.9 - - + -
257B ILE* 3.1 39.0 - - + -
258B ILE* 4.3 4.5 - - + -
260B TRP* 3.6 23.1 - + - -
279B HIS* 3.4 5.1 + - - -
281B ALA* 6.0 0.2 - - - +
286B GLY* 1.3 69.4 - - - -
288B ALA* 1.3 65.1 + - - +
289B SER 3.0 0.4 - - - -
290B GLU* 3.0 34.6 + - + +
291B ILE* 3.2 37.2 + - + +
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Residues in contact with ALA 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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227B TRP* 4.3 0.2 - - - -
277B ILE* 3.5 33.4 - - + +
279B HIS* 3.1 25.5 + - + +
283B LEU 6.1 0.2 - - - +
287B PHE* 1.3 76.3 - - - +
289B SER* 1.3 57.9 + - - +
291B ILE* 3.3 2.6 + - - +
292B SER* 2.8 31.0 + - - -
309B ARG* 3.7 24.7 - - + -
311B CYS* 4.2 6.3 - - - -
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY* 4.3 9.5 - - - -
286B GLY 2.8 21.6 + - - -
288B ALA* 1.3 80.0 - - - +
290B GLU* 1.3 60.8 + - - +
292B SER* 4.0 2.0 - - - -
293B SER* 2.9 31.5 + - - -
309B ARG* 3.5 31.1 - - - +
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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
----------------------------------------------------------
260B TRP* 3.9 11.7 - - - +
286B GLY 5.4 0.2 - - - +
287B PHE* 3.0 31.3 + - + +
289B SER* 1.3 78.5 + - - +
291B ILE* 1.3 65.6 + - - +
293B SER* 4.3 3.9 - - - -
294B THR* 3.0 39.7 + - - -
1345B GOL 2.6 36.9 + - - +
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Residues in contact with ILE 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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225B VAL* 4.5 7.2 - - + -
227B TRP* 3.7 31.9 - - + -
254B LEU* 3.9 8.7 - - + -
260B TRP* 3.9 29.8 - - + -
265B ILE* 4.2 11.4 - - + -
275B LEU* 4.4 0.9 - - + -
277B ILE* 3.8 25.6 - - + -
287B PHE* 3.2 35.8 + - + +
288B ALA 3.9 4.0 - - - +
290B GLU* 1.3 76.2 - - - +
292B SER* 1.3 59.5 + - - +
294B THR* 3.3 1.2 + - - -
295B VAL* 2.9 41.4 + - + +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.7 8.9 - - - +
288B ALA 2.8 18.3 + - - -
289B SER* 4.0 6.1 - - - -
291B ILE* 1.3 78.7 - - - +
293B SER* 1.3 65.8 + - - +
295B VAL* 4.7 0.4 - - - -
296B GLN* 3.0 22.1 + - - +
307B ILE* 3.5 38.0 + - - +
309B ARG* 4.5 10.8 + - - +
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 2.9 18.1 + - - -
290B GLU* 4.4 4.2 - - - -
292B SER* 1.3 78.0 + - - +
294B THR* 1.4 66.3 + - - +
296B GLN* 3.0 13.5 + - - +
297B GLU* 2.8 37.6 + - - +
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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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260B TRP* 3.6 22.2 - - + -
262B VAL* 3.7 23.1 - - + -
266B CYS* 5.0 0.4 - - - -
290B GLU* 3.0 29.3 + - - -
291B ILE 3.8 0.7 - - - -
293B SER* 1.4 75.7 - - - +
295B VAL* 1.3 64.4 + - - +
297B GLU* 3.1 14.3 + - - +
298B GLU* 3.0 29.4 + - + +
1345B GOL 2.8 31.7 + - - +
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Residues in contact with VAL 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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260B TRP* 4.8 4.0 - - + -
265B ILE* 3.8 28.3 - - + -
266B CYS* 4.3 17.0 - - - +
269B VAL* 3.8 26.9 - - + -
275B LEU* 3.8 23.3 - - + -
291B ILE* 2.9 22.6 + - + +
292B SER 3.9 2.7 - - - +
294B THR* 1.3 79.3 - - - +
296B GLN* 1.3 56.2 + - - +
299B CYS* 2.8 35.2 + - + +
303B LEU* 4.2 1.5 - - + +
307B ILE* 3.8 9.9 - - + -
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Residues in contact with GLN 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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292B SER* 3.0 14.4 + - - +
293B SER* 3.0 17.1 + - - +
295B VAL* 1.3 80.4 - - - +
297B GLU* 1.3 83.7 + - - +
300B PHE* 3.2 45.7 + - + +
303B LEU* 3.9 15.9 - - + -
307B ILE* 4.0 7.6 - - + +
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Residues in contact with GLU 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 SER* 2.8 25.7 + - - +
294B THR* 3.1 20.5 + - - +
296B GLN* 1.3 91.5 + - - +
298B GLU* 1.3 69.5 + - - +
300B PHE* 4.5 5.2 + - - +
1345B GOL 4.0 11.3 + - - -
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Residues in contact with GLU 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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377A LYS* 3.4 26.1 + - - -
262B VAL* 4.9 4.5 - - + -
266B CYS* 3.7 28.3 - - + -
270B ILE* 5.2 4.7 - - + +
294B THR* 3.0 26.2 + - + +
297B GLU* 1.3 87.6 - - - +
299B CYS* 1.3 62.0 + - - +
300B PHE 3.6 1.1 + - - -
302B ASN* 4.5 2.4 - - - +
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Residues in contact with CYS 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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266B CYS* 3.7 44.6 - - - -
269B VAL* 4.1 18.6 - - + -
270B ILE* 4.0 8.3 - - - -
295B VAL* 2.8 26.0 + - + +
298B GLU* 1.3 82.8 - - - +
300B PHE* 1.3 66.7 + - - +
301B LEU 3.2 3.1 - - - -
302B ASN* 2.9 28.3 + - + +
303B LEU* 3.2 14.1 + - + +
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Residues in contact with PHE 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 GLN* 3.2 40.7 + - + +
297B GLU 4.7 4.5 - - - +
298B GLU 3.6 2.0 + - - -
299B CYS* 1.3 77.4 - - - +
301B LEU* 1.3 83.0 + - + +
302B ASN 3.2 0.5 + - - -
303B LEU* 3.5 20.2 + - + +
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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
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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