Contacts of the helix formed by residues 261 - 273 (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 ASP 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B SER 3.5 23.5 + - - +
212B GLN* 3.5 14.6 + - - +
213B ALA* 2.8 35.1 + - + +
254B LEU* 4.4 4.7 + - + +
256B THR 4.7 0.8 + - - -
259B PRO 4.1 0.6 + - - -
260B TRP* 1.3 74.5 - - - +
262B VAL* 1.3 66.5 + - - +
263B ASP* 3.6 8.8 + - - +
264B THR* 2.7 39.5 + - - -
265B ILE* 3.4 15.9 - - - +
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Residues in contact with VAL 262 (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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374A GLN* 3.8 39.9 - - + +
260B TRP* 3.0 46.4 + - + +
261B ASP* 1.3 69.9 - - - +
263B ASP* 1.3 67.8 + - - +
265B ILE* 3.3 2.9 + - - +
266B CYS* 3.0 34.7 + - - -
294B THR* 3.7 24.2 - - + -
298B GLU* 4.9 5.4 - - + -
1345B GOL 4.3 4.5 - - - -
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Residues in contact with ASP 263 (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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374A GLN* 4.6 7.6 + - - -
261B ASP* 3.2 8.3 + - - +
262B VAL* 1.3 84.6 - - - +
264B THR* 1.3 57.0 + - - +
266B CYS* 4.1 3.9 - - - +
267B LYS* 3.0 31.4 + - - +
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Residues in contact with THR 264 (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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212B GLN* 5.5 0.9 + - - -
213B ALA* 4.0 23.1 + - + +
215B VAL* 4.0 26.6 - - + +
252B ILE* 4.6 5.2 - - + -
261B ASP* 2.7 32.1 + - - -
262B VAL 3.3 0.2 - - - -
263B ASP* 1.3 79.2 - - - +
265B ILE* 1.3 62.5 + - - +
267B LYS* 3.6 8.2 + - + +
268B SER* 3.2 21.1 + - - -
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Residues in contact with ILE 265 (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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213B ALA* 4.2 11.2 - - + -
223B THR* 5.2 0.9 - - + -
225B VAL* 4.2 20.2 - - + -
252B ILE* 3.6 35.0 - - + -
254B LEU* 4.2 12.8 - - + -
260B TRP* 3.9 15.7 - - + -
261B ASP 3.4 13.0 - - - +
262B VAL 3.3 5.1 + - - +
264B THR* 1.3 77.7 - - - +
266B CYS* 1.3 62.0 + - - +
268B SER* 3.2 6.7 + - - -
269B VAL* 3.0 27.6 + - + +
275B LEU* 4.7 1.8 - - + -
291B ILE* 4.2 14.4 - - + -
295B VAL* 3.8 22.9 - - + -
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Residues in contact with CYS 266 (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 VAL* 3.0 36.7 + - - +
263B ASP* 4.1 4.0 - - - +
265B ILE* 1.3 75.3 - - - +
267B LYS* 1.3 59.3 + - - +
269B VAL* 3.2 1.5 + - - -
270B ILE* 2.8 42.2 + - + +
294B THR 4.8 0.2 - - - -
295B VAL* 4.3 16.8 - - - -
298B GLU* 3.7 28.7 - - + -
299B CYS* 3.7 19.4 - - - -
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Residues in contact with LYS 267 (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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263B ASP 3.0 19.5 + - - +
264B THR* 3.8 7.2 - - - +
265B ILE 3.3 0.2 - - - -
266B CYS* 1.3 75.9 - - - +
268B SER* 1.3 63.1 + - - +
270B ILE* 3.6 12.4 + - - +
271B LYS* 3.2 20.3 + - - +
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Residues in contact with SER 268 (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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215B VAL* 5.7 0.9 - - - -
223B THR* 2.7 28.7 + - - +
250B GLU* 2.6 32.7 + - - +
252B ILE* 3.7 14.6 - - - -
264B THR 3.2 10.5 + - - -
265B ILE 3.2 8.9 + - - -
267B LYS* 1.3 80.2 - - - +
269B VAL* 1.3 57.3 + - - +
271B LYS* 3.0 9.8 + - - +
272B THR* 2.8 27.4 + - - +
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Residues in contact with VAL 269 (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 THR* 3.9 14.6 - - + +
265B ILE* 3.0 17.5 + - + +
266B CYS 3.9 2.9 - - - +
268B SER* 1.3 73.3 - - - +
270B ILE* 1.3 61.5 + - - +
272B THR* 3.6 6.1 - - - -
273B GLY* 2.8 29.1 + - - -
274B ARG 4.5 7.0 - - - +
275B LEU* 3.9 28.9 - - + -
295B VAL* 3.8 22.7 - - + -
299B CYS* 4.1 10.3 - - + -
302B ASN* 4.3 2.8 - - + +
303B LEU* 3.8 28.7 - - + -
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Residues in contact with ILE 270 (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* 2.8 33.9 + - + +
267B LYS* 3.7 9.9 - - - +
269B VAL* 1.3 73.2 - - - +
271B LYS* 1.3 62.5 + - - +
273B GLY* 4.5 1.0 + - - -
298B GLU* 5.2 4.9 - - + +
299B CYS* 4.0 11.7 - - - -
302B ASN* 3.7 42.3 + - - +
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Residues in contact with LYS 271 (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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218B GLU* 4.8 10.9 + - - +
219B GLY 3.2 23.0 + - - +
220B SER* 4.2 13.1 - - - +
250B GLU* 2.8 34.7 + - - -
267B LYS 3.2 10.0 + - - +
268B SER* 3.0 6.7 + - - +
270B ILE* 1.3 84.1 - - - +
272B THR* 1.3 67.0 + - + +
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Residues in contact with THR 272 (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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219B GLY 3.8 21.8 - - - +
220B SER* 3.5 16.9 - - - +
221B ASP* 3.4 12.4 - - - +
222B VAL* 3.7 26.2 - - - +
223B THR* 2.7 29.2 + - - +
250B GLU* 4.5 1.1 - - + -
268B SER* 2.8 19.3 + - - +
269B VAL* 3.6 2.3 - - - -
271B LYS* 1.3 80.8 - - - +
273B GLY* 1.3 63.7 + - - +
274B ARG* 3.2 12.1 + - - +
304B GLU* 4.4 6.9 - - - +
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Residues in contact with GLY 273 (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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269B VAL 2.8 20.2 + - - -
270B ILE 4.5 0.8 + - - -
271B LYS 3.6 0.8 - - - -
272B THR* 1.3 70.9 - - - +
274B ARG* 1.3 65.7 + - - +
302B ASN* 3.3 22.4 - - - -
303B LEU* 3.6 11.0 - - - +
304B GLU* 2.8 34.2 + - - -
305B ALA 4.2 0.7 + - - -
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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