Contacts of the strand formed by residues 228 - 232 (chain B) in PDB entry 4I6J
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 GLU 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B LYS 3.1 4.3 + - - +
202B LEU* 3.1 44.4 - - + +
203B LEU 3.1 23.0 + - - -
204B LYS* 3.5 11.2 + - - +
226B LEU* 3.5 4.9 - - - +
227B ARG* 1.3 87.4 + - - +
229B LEU* 1.3 62.7 + - - +
252B LEU* 5.0 2.0 - - - -
253B GLU* 4.5 8.4 - - - +
254B HIS* 2.9 50.0 + - + +
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Residues in contact with LEU 229 (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 LEU* 3.2 40.8 - - + +
204B LYS* 5.3 1.7 - - - +
205B MET* 4.9 1.1 - - + -
216B ILE* 4.8 5.6 - - + -
219B VAL* 5.9 0.2 - - + -
220B ALA* 6.1 0.9 - - + -
226B LEU* 4.4 18.8 - - + -
228B GLU* 1.3 78.2 - - - +
230B ALA* 1.3 63.3 + - - +
231B LEU* 3.5 34.3 - - + -
240B LEU* 4.6 8.7 - - + -
244B LEU* 4.1 20.6 - - + -
252B LEU* 5.3 3.8 - - + -
254B HIS* 3.1 6.6 + - - +
255B LEU* 3.5 24.1 - - + +
256B ARG* 2.8 25.7 + - - +
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Residues in contact with ALA 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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203B LEU 3.0 7.1 + - - -
204B LYS* 3.9 29.1 - - + +
205B MET* 3.1 26.0 + - - +
206B SER* 4.6 9.4 - - - +
229B LEU* 1.3 76.7 - - - +
231B LEU* 1.3 66.1 + - - +
254B HIS* 6.2 0.4 - - + -
256B ARG* 3.2 27.6 - - + -
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Residues in contact with LEU 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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205B MET* 4.1 12.8 - - + +
206B SER* 4.1 13.2 - - - +
216B ILE* 3.9 29.6 - - + -
229B LEU* 3.5 41.1 - - + -
230B ALA* 1.3 77.8 - - - +
232B ASN* 1.3 79.8 + - - +
235B LEU* 4.6 15.9 - - + +
236B LEU* 4.6 3.8 - - + +
240B LEU* 4.3 6.3 - - + -
255B LEU* 5.4 0.4 - - + -
256B ARG* 3.0 6.6 + - - +
257B ILE* 3.5 22.7 - - + -
258B ASP 3.1 20.4 + - - -
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Residues in contact with ASN 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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496A ARG* 5.7 0.6 - - - +
205B MET 4.8 0.4 + - - -
206B SER* 4.3 6.6 - - - +
207B SER* 4.6 17.2 - - - +
208B CYS 6.0 0.2 - - - +
231B LEU* 1.3 90.4 - - - +
233B TYR* 1.3 65.7 + - - +
234B HIS* 3.0 31.7 + - + +
235B LEU* 3.2 20.2 + - + +
258B ASP* 3.6 17.7 + - - +
260B VAL* 3.7 23.5 + - - +
262B GLU* 3.2 30.7 + - - +
269B PHE* 5.8 0.7 - - - -
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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