Contacts of the strand formed by residues 228 - 233 (chain B) in PDB entry 4LXZ
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 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU* 4.3 6.3 - - + +
193B TYR* 3.8 22.2 - - + +
200B THR* 3.5 15.9 - - - +
218B ASP 3.8 6.1 - - - +
219B ILE* 3.3 42.4 + - - +
220B GLY* 3.7 6.5 - - - +
226B TYR 4.5 2.4 - - - -
227B TYR* 1.3 78.7 - - - +
229B VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 5.0 0.7 + - - +
199B MET* 4.1 24.2 - - + -
200B THR* 2.7 17.0 + - - +
201B VAL* 3.4 23.1 - - + -
202B SER 2.9 25.6 + - - -
219B ILE* 6.2 0.4 - - - -
226B TYR 4.6 6.3 - - - +
228B ALA* 1.3 78.1 - - - +
230B ASN* 1.3 69.5 + - - +
231B PHE* 5.3 0.4 - - + +
249B ILE* 4.8 6.3 - - + -
253B VAL* 5.0 2.2 - - + -
371B LEU* 4.0 33.4 - - + +
374B ASN* 6.3 2.9 - - + -
375B LEU* 4.3 17.9 - - + -
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Residues in contact with ASN 230 (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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184B HIS* 2.9 28.5 + - - -
189B GLU* 2.8 23.6 + - - +
202B SER* 3.4 5.2 - - - -
204B HIS* 3.3 4.1 - - + -
214B GLY* 3.6 17.7 - - - +
215B ASP 3.5 20.4 + - - +
216B LEU* 3.8 7.7 + - - -
218B ASP* 3.0 30.1 + - - +
228B ALA 4.5 0.2 + - - -
229B VAL* 1.3 80.4 - - - +
231B PHE* 1.3 59.9 + - - +
232B PRO* 3.4 9.6 - - - +
371B LEU* 3.6 20.6 - - - +
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Residues in contact with PHE 231 (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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201B VAL* 6.4 0.2 - - + -
202B SER 2.8 10.0 + - - +
203B PHE* 3.6 27.0 - + + -
204B HIS* 3.2 24.0 + - - -
229B VAL* 5.3 0.6 - - + +
230B ASN* 1.3 71.5 - - - +
232B PRO* 1.3 78.9 - - - +
233B MET* 3.6 12.9 + - + +
245B ILE* 3.6 24.5 - - + -
249B ILE* 4.4 4.3 - - + -
363B TYR* 4.7 0.4 - + - -
364B MET* 3.6 51.8 - - + -
367B ILE* 3.7 22.9 - - + -
368B LYS* 3.9 15.9 - - + -
371B LEU* 3.5 21.3 - - + -
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Residues in contact with PRO 232 (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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204B HIS* 3.5 8.7 - - - +
206B TYR* 3.4 33.9 - - + -
214B GLY 4.3 3.1 - - - +
216B LEU* 3.9 28.7 - - + +
230B ASN 3.4 12.6 - - - +
231B PHE* 1.3 91.4 - - - +
233B MET* 1.3 55.4 + - - +
234B ARG* 4.6 3.1 - - - +
363B TYR* 2.6 33.1 + - - +
367B ILE* 4.1 17.4 - - + +
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Residues in contact with MET 233 (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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203B PHE* 3.9 20.6 - - + -
204B HIS 2.7 15.9 + - - +
205B LYS* 3.2 8.2 - - - +
206B TYR 3.2 24.8 + - - +
231B PHE* 3.8 14.6 - - + +
232B PRO* 1.3 78.9 - - - +
234B ARG* 1.3 66.2 + - - +
237B ILE* 3.7 22.7 - - + -
242B TYR* 3.7 34.5 - - + -
245B ILE* 3.6 30.7 - - + -
279B PHE* 3.7 23.3 - - + -
359B ASN* 3.7 8.3 - - - +
363B TYR* 4.2 0.2 - - - -
364B MET* 4.2 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
------------------------------------------------------------
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