Contacts of the strand formed by residues 233 - 238 (chain B) in PDB entry 2B92
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 LYS 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE* 3.4 17.9 - - + +
199B ASP* 4.7 3.8 - - - +
202B LEU* 4.2 15.0 - - + -
203B THR* 6.2 5.6 - - + -
206B LEU* 4.2 20.9 - - + -
226B ILE* 4.2 5.8 - - + -
227B ARG* 3.6 39.6 + - - +
230B PHE* 3.0 25.7 + - + +
231B PRO 3.0 12.3 + - - -
232B LYS* 1.3 79.8 - - - +
234B LYS* 1.3 65.6 + - - +
272B TYR* 4.6 3.1 + - - -
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE 2.9 9.1 + - - +
179B VAL* 3.3 8.5 - - + -
180B TRP 2.9 22.9 + - - -
199B ASP* 3.0 31.5 + - - +
202B LEU* 3.5 10.3 - - - +
233B LYS* 1.3 76.7 - - - +
235B CYS* 1.3 65.1 + - - +
236B PHE* 3.5 34.3 - - + -
272B TYR* 3.3 43.8 - - + +
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Residues in contact with CYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 4.9 4.9 - - - -
180B TRP* 3.3 22.7 - - - +
182B LEU* 4.2 24.5 - - - -
198B PRO* 3.3 45.4 - - - +
199B ASP* 2.9 11.2 + - - +
201B TYR* 5.0 1.1 - - - -
202B LEU* 4.0 16.4 - - + -
234B LYS* 1.3 80.2 - - - +
236B PHE* 1.3 79.1 + - - +
237B VAL* 5.5 0.4 - - - -
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.7 19.3 - - + -
180B TRP 2.9 9.2 + - - +
181B THR* 3.5 1.9 - - + -
182B LEU* 2.8 28.4 + - - +
198B PRO* 4.6 2.7 - - + -
234B LYS* 3.5 34.3 - - + -
235B CYS* 1.3 79.9 - - - +
237B VAL* 1.3 63.4 + - - +
238B PHE* 3.7 22.1 - - + -
265B GLN 5.0 3.6 - - - -
268B ASP* 4.0 21.1 - - + -
269B PHE* 3.8 25.8 - + + -
272B TYR* 3.7 35.4 - + + -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.6 13.5 - - + -
185B PHE* 3.9 42.4 - - + -
189B LEU* 4.2 17.3 - - + -
198B PRO* 4.3 22.1 - - + +
201B TYR* 6.0 0.2 - - + -
236B PHE* 1.3 76.1 - - - +
238B PHE* 1.3 78.6 + - - +
239B ASP* 5.7 0.7 - - - +
265B GLN* 3.6 28.6 - - + +
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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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54B LEU* 4.4 16.4 - - + -
181B THR* 3.8 17.7 - - + -
182B LEU 3.0 18.2 + - - +
183B ARG* 3.8 24.5 - - - +
184B ASP 3.0 24.1 + - - -
185B PHE* 3.0 7.3 + - - +
236B PHE* 3.7 24.9 - - + -
237B VAL* 1.3 88.5 - - - +
239B ASP* 1.3 61.5 + - - +
262B PHE* 4.4 19.5 - + + -
265B GLN* 3.2 38.1 - - + -
266B VAL* 4.0 11.4 - - + -
269B PHE* 3.9 25.6 - + + -
593B GDP 5.9 0.4 - - - +
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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