Contacts of the strand formed by residues 236 - 243 (chain B) in PDB entry 3BEQ
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 SER 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B CYS* 3.3 2.4 - - - +
233B VAL 2.8 30.7 + - - +
234B ASN 3.4 4.0 + - - -
235B GLY* 1.3 79.6 - - - +
237B CYS* 1.3 62.8 + - - +
238B PHE* 3.7 25.1 - - - -
256B LYS* 3.4 19.8 + - - -
257B ILE 3.4 9.6 - - - -
258B GLU* 3.4 18.8 + - - +
308B GLN* 5.5 2.7 + - - -
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Residues in contact with CYS 237 (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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183B CYS* 3.7 16.8 - - - -
185B ASP* 3.7 18.6 - - - -
190B LEU* 4.0 18.8 - - + -
207B TYR* 6.3 0.9 - - - -
231B ALA 3.2 5.4 - - - +
232B CYS* 2.1 45.1 - - - -
235B GLY 5.3 0.2 - - - -
236B SER* 1.3 74.6 - - - +
238B PHE* 1.3 63.9 + - - +
255B LEU 3.8 0.2 - - - +
256B LYS* 3.6 2.9 - - - -
257B ILE* 2.8 41.1 + - + +
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Residues in contact with PHE 238 (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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226B GLN* 4.0 0.7 - - - +
230B CYS* 3.2 7.2 - - - +
231B ALA* 2.7 40.7 + - - +
233B VAL* 4.3 17.7 - - + -
236B SER* 3.7 32.5 - - - -
237B CYS* 1.3 76.7 - - - +
239B THR* 1.3 62.1 - - - +
255B LEU 3.2 11.7 - - - +
256B LYS* 3.6 23.3 - - + -
257B ILE* 5.5 0.9 - - - -
280B CYS* 5.1 3.4 - - - +
287B VAL* 3.9 17.7 - - + -
305B PHE* 3.6 33.4 - + + -
306B ASP 4.3 2.2 - - - -
308B GLN* 3.9 31.4 - - + -
310B LEU* 3.7 19.5 - - + -
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Residues in contact with THR 239 (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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181B SER* 4.2 3.3 + - - -
192B ILE* 3.9 23.1 - - + -
225B THR* 3.2 19.0 + - - +
226B GLN* 2.6 26.0 + - - +
230B CYS* 4.1 7.0 - - - -
238B PHE* 1.3 75.8 - - - +
240B ILE* 1.3 72.5 + - - +
241B MET* 4.6 2.7 - - + -
254B ILE* 3.4 6.6 - - - +
255B LEU* 3.0 54.0 + - + -
257B ILE* 4.1 4.7 - - + -
280B CYS* 5.2 1.8 - - - -
305B PHE* 5.5 0.7 - - - -
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Residues in contact with ILE 240 (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 THR* 2.9 24.6 + - - -
226B GLN* 4.1 4.9 + - - +
239B THR* 1.3 86.3 + - - +
241B MET* 1.3 72.4 + - - +
242B THR* 4.7 5.8 - - - +
252B TYR* 4.9 8.3 - - + -
253B LYS 3.3 9.9 - - - +
254B ILE* 3.7 31.6 - - + -
268B LEU* 5.4 3.1 - - + -
275B TYR* 5.0 4.3 - - + -
278B CYS* 3.9 28.3 - - + -
280B CYS* 4.0 4.0 - - - -
289B CYS* 3.9 21.3 - - - -
303B VAL* 4.1 17.0 - - + -
305B PHE* 4.1 6.1 - - + -
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Residues in contact with MET 241 (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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192B ILE* 3.7 31.0 - - + -
194B ILE* 4.5 5.8 - - + -
203B ALA* 3.7 14.4 - - + -
215B ILE* 3.9 12.6 - - + -
218B TRP* 3.9 10.4 - - + -
223B LEU* 4.0 31.9 - - + -
224B ARG 3.3 9.2 - - - +
225B THR* 3.8 10.3 - - - +
239B THR* 4.6 5.8 - - + -
240B ILE* 1.3 79.6 - - - +
242B THR* 1.3 64.4 + - - +
252B TYR* 3.4 3.1 - - - -
253B LYS* 2.9 34.4 + - + +
255B LEU* 3.7 33.6 - - + +
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Residues in contact with THR 242 (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 TRP* 4.3 1.6 - - - -
223B LEU* 3.4 4.3 - - - +
224B ARG* 2.9 68.1 + - - +
240B ILE* 4.7 3.8 - - - +
241B MET* 1.3 76.4 + - - +
243B ASP* 1.3 63.6 + - - +
250B ALA* 3.9 6.7 - - + -
251B SER 3.3 11.4 - - - +
252B TYR* 3.7 15.5 - - + -
275B TYR* 2.7 33.4 + - - +
276B GLU* 4.3 5.1 - - + -
277B GLU 5.4 0.2 + - - -
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Residues in contact with ASP 243 (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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217B SER* 2.6 26.4 + - - -
218B TRP* 2.9 33.8 + - + -
219B ARG* 2.8 26.5 + - + +
221B ASN 2.9 37.3 + - - +
222B ILE 4.4 0.4 - - - -
223B LEU* 4.1 7.4 - - + -
224B ARG* 4.2 0.9 - - - +
242B THR* 1.3 76.4 - - - +
244B GLY* 1.3 59.9 + - - +
250B ALA* 4.3 1.6 - - - -
251B SER* 3.0 34.1 + - - +
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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