Contacts of the strand formed by residues 233 - 237 (chain B) in PDB entry 5DO7
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 ILE 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 3.8 36.8 - - + +
35B SER 4.9 2.0 - - - +
36B LEU* 5.4 4.9 - - + -
134B ILE* 4.5 11.9 - - + -
147B CYS* 4.3 7.4 + - + +
148B VAL* 3.6 45.3 - - + -
149B ALA 3.9 5.2 + - - -
231B PRO* 3.4 25.2 - - - +
232B GLY* 1.3 82.8 - - - +
234B LEU* 1.3 75.5 + - - +
235B ILE* 4.3 10.5 - - + -
263B ARG* 5.9 0.2 - - - -
264B LEU* 3.4 33.0 - - + -
266B LEU* 5.5 0.7 - - + -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ALA* 3.5 30.3 - - + +
151B VAL* 4.9 4.5 - - + -
223B ILE* 4.9 4.7 - - + -
226B GLN* 4.8 6.3 - - + -
227B LEU* 3.9 20.2 - - + -
231B PRO* 4.2 3.6 - - + +
233B ILE* 1.3 80.5 - - - +
235B ILE* 1.3 64.9 + - - +
236B LEU* 4.2 26.7 - - + -
255B LEU* 5.1 1.3 - - + -
258B LEU* 3.5 33.0 - - + -
263B ARG* 5.5 4.0 - - + +
264B LEU 2.8 14.8 + - - +
265B VAL* 3.4 12.2 - - + +
266B LEU* 2.8 26.5 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.9 2.5 - - + -
115B LEU* 3.8 31.9 - - + +
118B ILE* 4.7 20.6 - - + -
119B THR* 4.7 10.3 - - - +
148B VAL* 3.7 25.6 - - + -
149B ALA 2.8 13.1 + - - +
150B HIS* 3.5 24.4 + - + +
151B VAL* 2.8 28.4 + - - +
233B ILE* 4.3 7.2 - - + -
234B LEU* 1.3 79.8 - - - +
236B LEU* 1.3 63.3 + - - +
266B LEU* 3.6 22.2 - - + -
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.6 6.3 - - - +
151B VAL* 3.3 39.3 - - + +
223B ILE* 4.4 11.0 - - + -
234B LEU* 4.2 17.3 - - + +
235B ILE* 1.3 76.5 - - - +
237B ASP* 1.3 60.0 + - - +
238B GLU 3.4 5.2 + - - -
239B PRO* 3.8 18.0 - - + +
255B LEU* 3.2 45.3 - - + -
265B VAL* 4.2 17.0 - - + -
266B LEU 2.8 13.4 + - - +
267B ILE* 3.5 7.1 - - + -
268B SER 3.5 18.0 + - - -
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Residues in contact with ASP 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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112B ALA* 3.4 26.8 - - - +
115B LEU* 3.6 17.8 - - + +
116B ASP* 3.3 22.9 - - - +
150B HIS* 4.1 5.8 + - - +
151B VAL* 2.8 17.8 + - - +
152B ARG* 3.9 19.2 + - - +
153B GLN* 3.1 29.5 + - + +
235B ILE 4.2 0.2 - - - -
236B LEU* 1.3 70.3 - - - +
238B GLU* 1.3 73.0 + - - +
239B PRO* 3.3 3.2 - - - +
268B SER* 3.4 11.3 + - - -
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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