Contacts of the strand formed by residues 233 - 238 (chain B) in PDB entry 4B5G
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 ALA 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B MET* 3.6 28.3 - - + -
195B LEU* 3.9 21.7 - - + +
229B LEU 3.5 3.4 + - - -
230B ALA 3.2 16.3 + - - +
231B ALA 4.5 3.6 - - - +
232B LYS* 1.3 78.9 - - - +
234B VAL* 1.3 60.8 + - - +
252B VAL* 4.7 0.7 - - + -
253B GLU 3.3 14.6 - - - +
254B TYR* 4.0 8.3 - - + -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 4.3 14.2 + - - -
47A ASP* 5.0 0.3 - - - +
1B MET* 6.1 1.6 - - - -
195B LEU* 4.9 5.0 - - - +
196B TYR* 5.0 0.3 + - - -
232B LYS 3.4 15.9 - - - +
233B ALA* 1.3 74.8 - - - +
235B SER* 1.3 71.1 + - - +
253B GLU* 3.1 29.2 + - + -
254B TYR 4.7 0.4 - - - +
255B ASP* 3.8 23.1 - - + +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 4.2 15.7 - - - -
195B LEU* 3.9 7.5 - - - +
196B TYR* 3.6 12.1 - - - -
233B ALA 3.8 0.6 - - - -
234B VAL* 1.3 88.1 - - - +
236B ALA* 1.3 63.8 + - - +
237B HIS* 5.4 1.3 + - - -
252B VAL* 3.6 4.7 - - - +
253B GLU* 2.6 49.5 + - - +
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Residues in contact with ALA 236 (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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46A ALA* 3.9 4.9 - - - +
192B TRP* 3.3 28.2 - - + -
195B LEU* 3.6 18.6 - - + -
196B TYR* 3.1 18.2 + - + -
235B SER* 1.3 79.6 - - - +
237B HIS* 1.3 66.6 + - - +
251B VAL 3.1 13.5 - - - +
252B VAL* 3.7 14.8 - - + -
253B GLU* 3.9 2.2 - - - -
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Residues in contact with HIS 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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46A ALA* 5.4 4.7 - - + +
23B TYR* 5.4 0.2 + - - -
192B TRP* 3.5 9.4 - - - -
235B SER* 5.4 1.0 + - - -
236B ALA* 1.3 79.2 + - - +
238B VAL* 1.3 65.7 + - - +
239B TYR* 3.8 24.7 + + + -
250B LEU* 3.8 1.6 - - - +
251B VAL* 2.9 66.0 + - + +
253B GLU* 3.9 15.3 + - - -
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TRP* 4.2 18.6 - - + -
201B GLY* 4.0 16.2 - - - +
202B TYR 3.4 26.7 - - - +
203B THR* 4.2 12.1 - - + -
237B HIS* 1.3 79.1 - - - +
239B TYR* 1.3 61.4 + - - +
240B LYS* 3.3 21.4 + - + +
248B ALA* 3.6 26.5 - - + -
249B PRO 3.5 6.7 - - - +
250B LEU* 4.2 9.9 - - + -
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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
------------------------------------------------------------
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