Contacts of the strand formed by residues 232 - 240 (chain B) in PDB entry 3HVJ
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 PHE 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B THR* 3.7 21.1 - - + -
198B GLU* 3.6 11.4 - - - -
203B LEU* 4.5 3.4 - - + -
209B LEU* 3.8 24.7 - - + -
225B TYR* 3.5 26.2 - + - -
226B VAL* 3.4 39.6 - - + +
227B ARG 5.0 1.7 - - - +
229B SER* 3.3 19.5 + - - +
230B SER* 3.2 2.7 - - - +
231B SER* 1.3 90.4 - - - +
233B GLU* 1.3 65.8 + - - +
234B CYS* 4.0 5.8 + - - -
253B ALA* 3.9 16.4 - - + -
254B ILE 3.4 2.7 - - - +
255B TYR* 3.7 35.4 - + + -
256B GLN* 4.3 0.7 - - - -
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Residues in contact with GLU 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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230B SER 5.0 3.6 - - - +
232B PHE* 1.3 74.9 - - - +
234B CYS* 1.3 60.5 + - - +
235B THR* 5.1 1.3 + - - -
252B LYS* 3.7 1.6 - - - +
253B ALA* 3.6 0.7 - - - -
254B ILE* 2.9 42.5 + - + +
256B GLN* 3.5 35.2 - - + +
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Residues in contact with CYS 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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226B VAL* 3.2 54.1 - - - -
227B ARG* 3.8 11.7 - - + -
232B PHE* 4.0 4.2 + - - -
233B GLU* 1.3 76.7 + - - +
235B THR* 1.3 66.4 + - - +
251B GLU* 3.4 16.8 - - - +
252B LYS 3.1 4.3 - - - +
253B ALA* 3.9 10.1 - - - -
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Residues in contact with THR 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 GLU 5.1 0.9 + - - -
234B CYS* 1.3 76.4 + - - +
236B HIS* 1.3 68.6 + - - +
237B TYR* 3.7 33.2 + - + +
250B LEU 4.0 0.3 - - - +
251B GLU* 3.5 6.9 - - - -
252B LYS* 2.7 56.1 + - - +
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Residues in contact with HIS 236 (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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214B VAL* 3.7 23.1 - - + -
215B ILE* 3.8 24.6 - - + +
227B ARG* 3.7 13.0 + - - +
235B THR* 1.3 83.0 - - - +
237B TYR* 1.3 71.6 + - - +
238B SER* 4.1 16.8 + - - -
248B ASP 5.3 0.2 + - - -
249B GLY* 4.0 7.5 - - - -
250B LEU 3.4 9.6 + - - -
251B GLU* 2.9 24.0 + - - +
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Residues in contact with TYR 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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98A ARG* 6.3 0.9 - - - -
92B ILE* 3.6 45.1 - - + +
96B VAL* 4.8 8.4 - - + +
99B GLU* 5.3 0.7 + - - -
210B LEU* 4.9 1.3 - - + -
235B THR* 3.7 23.8 - - + +
236B HIS* 1.3 76.3 - - - +
238B SER* 1.3 61.6 - - - +
239B SER 3.7 0.2 + - - -
249B GLY* 3.0 5.2 - - - -
250B LEU* 2.8 48.6 + - + +
252B LYS* 3.1 54.7 + - + -
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Residues in contact with SER 238 (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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92B ILE* 4.4 4.3 - - - +
236B HIS* 4.1 19.0 + - - -
237B TYR* 1.3 70.4 - - - +
239B SER* 1.3 66.4 + - - +
247B VAL* 4.0 18.7 - - - +
248B ASP 4.0 3.3 + - - -
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Residues in contact with SER 239 (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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88B ALA* 3.6 23.2 + - - +
89B LYS* 3.5 25.5 - - - +
92B ILE* 3.8 14.3 - - - +
237B TYR 3.7 2.2 + - - -
238B SER* 1.3 78.0 + - - +
240B TYR* 1.3 87.8 + - - +
247B VAL* 3.7 8.5 - - - +
248B ASP 2.7 26.2 + - - +
249B GLY* 4.8 0.2 - - - -
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Residues in contact with TYR 240 (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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66A GLN* 2.9 33.8 + - + +
70A GLU* 2.5 34.2 + - - +
91A GLN* 5.8 2.2 - - - -
85B VAL 5.1 0.2 - - - +
88B ALA* 4.7 17.6 - - + +
89B LYS* 3.4 22.2 + - - +
239B SER* 1.3 96.9 + - - +
241B LEU* 1.3 66.1 + - - +
242B GLU* 3.5 0.7 + - - -
244B MET 3.5 16.4 - - - +
245B LYS* 3.6 59.1 + - + -
246B VAL 3.4 5.4 - - - +
247B VAL* 4.5 8.1 - - + -
248B ASP* 3.7 6.5 + - - +
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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