Contacts of the strand formed by residues 231 - 235 (chain B) in PDB entry 3HUU
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 GLN 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B HIS* 2.8 30.5 + - - -
202B SER 3.2 12.3 + - - +
203B VAL* 3.3 11.8 - - + -
204B ILE 2.9 20.1 + - - -
226B ILE* 4.4 0.4 - - - -
227B PRO* 3.6 19.5 + - + +
230B ILE* 1.3 80.0 - - - +
232B THR* 1.3 69.7 + - - +
291B SER 3.1 16.4 - - - +
292B THR* 3.1 9.0 - - - +
293B THR* 2.9 52.0 + - - +
295B ILE* 4.3 11.5 - - - +
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.2 1.1 - - - -
204B ILE* 3.2 11.9 - - + +
212B ASN* 4.5 4.7 - - - -
215B LEU* 4.0 14.4 - - + -
216B LEU* 4.0 5.1 - - + +
219B LEU* 3.8 28.7 - - + -
226B ILE* 4.1 11.3 - - + +
230B ILE* 4.9 0.9 - - + -
231B GLN* 1.3 83.9 - - - +
233B ALA* 1.3 61.8 + - - +
248B GLN* 2.6 34.2 + - - -
291B SER* 2.7 34.3 + - - -
292B THR* 3.5 7.7 - - - +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.3 25.1 - - + -
137B LEU* 4.5 13.5 - - + -
203B VAL* 5.0 0.7 - - + -
204B ILE 3.0 7.2 + - - +
205B ILE* 3.2 8.2 - - + -
206B THR* 3.0 24.6 + - - -
212B ASN* 4.0 2.5 - - - +
232B THR* 1.3 76.8 - - - +
234B THR* 1.3 63.0 + - - +
248B GLN* 4.6 1.3 - - - +
249B THR* 3.3 14.8 - - + +
292B THR* 4.3 13.0 - - + -
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.1 4.4 - - - +
206B THR* 2.8 33.6 + - - -
208B ASP 3.2 18.2 + - - -
209B VAL* 4.5 1.6 - - - -
212B ASN* 3.7 23.1 - - + +
233B ALA* 1.3 72.7 - - - +
235B PHE* 1.3 79.0 + - - +
241B THR* 4.0 15.3 - - + -
248B GLN* 4.5 2.9 - - + -
249B THR 3.1 6.8 + - - +
250B SER* 3.2 17.5 - - - -
251B VAL* 3.1 22.9 + - - +
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Residues in contact with PHE 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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129B ALA* 4.2 6.3 - - + -
130B ALA* 3.8 36.6 - - + -
133B LEU* 3.8 13.5 - - + -
147B PHE* 4.0 10.8 - + - -
160B ARG* 3.4 50.9 - - + +
205B ILE* 3.8 19.7 - - + -
206B THR 3.3 18.8 - - - -
207B SER* 3.6 11.0 - - - +
208B ASP* 4.4 0.8 - - - -
209B VAL* 3.6 18.2 + - - +
234B THR* 1.3 86.6 + - - +
236B ASN* 1.3 74.6 + - - +
250B SER* 4.6 0.2 - - - -
251B VAL* 3.9 28.5 - - + -
253B ILE* 5.2 1.8 - - + -
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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