Contacts of the strand formed by residues 228 - 235 (chain B) in PDB entry 1Q8Z
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 LEU 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B ILE* 4.7 12.6 - - + -
206B LEU* 3.9 35.2 - - + +
207B GLN* 4.8 8.5 - - + +
210B ASN* 3.3 25.3 + - - +
226B LEU 3.9 0.8 + - - -
227B LYS* 1.3 74.0 - - - +
229B LEU* 1.3 63.6 + - - +
230B ASP* 3.3 26.5 - - - +
231B HIS* 4.3 20.0 - - + +
244B MET* 3.5 30.1 - - + -
245B VAL 3.5 8.3 - - - +
246B PHE* 3.9 13.4 - - + -
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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
----------------------------------------------------------
158B TYR* 5.9 0.4 - - - +
180B ASN* 6.3 1.1 - - - +
184B VAL* 4.4 15.3 - - + -
227B LYS* 4.2 14.1 - - + +
228B LEU* 1.3 79.3 - - - +
230B ASP* 1.3 65.6 + - + +
245B VAL* 2.7 18.4 + - + +
246B PHE* 3.8 5.2 - - - +
247B GLU* 3.6 42.8 - - + +
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Residues in contact with ASP 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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154B LYS* 2.8 35.2 + - - +
157B ARG* 4.0 3.9 + - - +
158B TYR* 2.8 28.8 + - - +
228B LEU* 3.3 10.9 - - - +
229B LEU* 1.3 85.9 - - + +
231B HIS* 1.3 96.8 + - - +
232B PHE* 4.7 1.8 - - - -
245B VAL* 2.9 33.7 + - + -
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Residues in contact with HIS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LYS* 5.0 1.4 + - - -
200B GLU* 5.1 4.5 + - - -
203B ILE* 3.7 37.4 - - + +
207B GLN* 3.7 24.4 + - - -
228B LEU* 4.3 14.4 - - + +
230B ASP* 1.3 92.3 + - - +
232B PHE* 1.3 73.0 + - - +
242B VAL* 5.4 2.5 - - + -
243B VAL 3.1 15.0 - - - +
244B MET* 4.5 2.7 - - + -
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Residues in contact with PHE 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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153B TYR* 3.6 30.7 - + + -
154B LYS* 3.4 50.9 - - + -
158B TYR* 3.9 20.2 - + - -
186B MET* 4.6 1.3 - - - -
230B ASP* 4.5 1.8 - - - -
231B HIS* 1.3 88.0 - - - +
233B ASN* 1.3 78.8 + - - +
234B HIS* 4.3 1.8 - - + -
242B VAL* 3.8 3.3 - - - +
243B VAL* 2.9 57.5 + - + +
245B VAL* 4.0 8.5 - - + -
802B SO4 3.7 7.2 - - - -
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Residues in contact with ASN 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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200B GLU* 5.3 0.3 - - - +
232B PHE* 1.3 81.5 - - - +
234B HIS* 1.3 60.3 + - - +
235B LYS 4.1 0.8 + - - -
240B VAL* 4.0 21.6 - - + +
241B HIS 3.6 1.1 - - - -
242B VAL* 3.8 26.0 - - - +
802B SO4 3.2 15.8 + - - -
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Residues in contact with HIS 234 (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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145B HIS* 3.3 25.0 + + - -
151B GLU* 2.8 30.3 + - - +
152B PRO 3.9 5.7 + - - -
153B TYR* 3.4 32.6 - + + -
188B ILE* 5.6 0.4 - - - +
232B PHE* 4.3 1.3 - - + -
233B ASN* 1.3 74.7 - - - +
235B LYS* 1.3 73.4 + - - +
236B GLY 3.6 1.0 + - - -
239B GLY 3.9 0.2 - - - +
240B VAL* 4.5 1.3 - - - -
241B HIS* 2.8 43.2 + - + +
243B VAL* 3.8 16.5 - - + +
802B SO4 3.0 35.2 + - - +
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Residues in contact with LYS 235 (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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233B ASN 4.1 1.4 - - - -
234B HIS* 1.3 90.0 + - - +
236B GLY* 1.3 59.9 + - - +
239B GLY 3.8 4.3 - - - +
240B VAL* 4.4 15.4 - - + +
802B SO4 3.3 30.9 + - - +
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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
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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