Contacts of the strand formed by residues 235 - 242 (chain B) in PDB entry 1JS6
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 ILE 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 4.6 12.8 - - + -
167B LEU* 3.9 26.9 - - + -
179B VAL* 4.9 4.5 - - + +
182B LYS* 2.5 41.6 + - + +
183B LEU* 3.4 22.2 - - + +
184B VAL* 3.0 19.9 + - - -
233B GLY 4.3 3.1 - - - +
234B LEU* 1.3 80.3 - - - +
236B PRO* 1.3 73.8 - - + +
237B PHE 3.5 0.5 + - - -
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Residues in contact with PRO 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 5.3 1.2 - - - +
184B VAL* 3.4 9.8 - - + +
186B TYR* 3.7 23.8 - - + +
226B LEU* 3.8 30.3 - - + +
229B ASP* 4.7 2.0 - - + -
230B LYS* 4.0 25.4 - - + +
234B LEU* 3.6 9.0 - - + +
235B ILE* 1.3 95.3 - - + +
237B PHE* 1.3 61.2 + - - +
264B GLU* 6.0 0.4 - - - +
265B ASP 5.4 1.2 - - - +
266B ILE* 3.8 17.6 - - + +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 3.9 12.8 - - + -
159B ALA* 3.9 9.7 - - + +
160B ARG* 3.5 37.5 - - - -
163B VAL* 4.2 23.8 - - + -
183B LEU* 3.6 22.9 - - + -
184B VAL 3.0 40.5 + - - -
185B ALA* 3.9 4.5 - - + -
186B TYR* 5.1 0.2 - - - -
204B VAL* 3.8 35.2 - - + -
235B ILE 4.1 2.7 - - - +
236B PRO* 1.3 76.3 - - - +
238B PHE* 1.3 74.7 + - + +
265B ASP 5.5 0.9 - - - -
266B ILE* 3.5 14.2 - - - +
267B TRP* 3.0 26.5 + - - +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 4.0 8.5 - - + -
155B ALA* 3.9 4.9 - - + -
156B LEU* 3.6 53.6 - - + -
159B ALA* 3.8 11.4 - - + -
184B VAL 3.9 0.2 + - - -
185B ALA* 3.2 11.8 - - + -
186B TYR* 2.8 25.7 + - - -
195B VAL* 5.6 2.9 - - + -
237B PHE* 1.3 101.8 - - + +
239B VAL* 1.3 67.4 + - - +
240B VAL* 3.4 24.2 - - + -
266B ILE* 3.6 0.6 - - - +
267B TRP* 3.5 36.3 - + - -
269B HIS* 3.6 25.4 - + + -
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 3.4 25.4 - - + +
217B MET* 4.7 12.3 - - + -
222B LEU* 4.4 11.7 - - + -
238B PHE* 1.3 81.6 - - - +
240B VAL* 1.3 70.9 + - - +
257B VAL* 4.3 10.1 - - + -
261B CYS* 3.9 20.2 - - - -
266B ILE* 3.7 22.4 - - + -
267B TRP 3.0 6.6 + - - +
268B LEU* 3.4 15.7 - - + +
269B HIS* 2.8 29.1 + - - +
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Residues in contact with VAL 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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152B THR* 4.4 3.8 - - + -
186B TYR 2.9 11.6 + - - +
187B ALA* 3.6 24.7 - - + +
188B SER 4.2 1.9 + - - -
195B VAL* 4.1 31.4 - - + -
217B MET* 4.1 8.7 - - - +
238B PHE* 3.4 36.1 - - + -
239B VAL* 1.3 73.4 - - - +
241B ALA* 1.3 65.0 + - - +
242B THR* 4.1 6.9 + - - +
269B HIS* 3.2 16.4 - - + +
271B ASP* 3.9 27.8 - - + -
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Residues in contact with ALA 241 (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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217B MET* 5.2 1.6 - - - -
239B VAL* 3.9 1.1 + - + -
240B VAL* 1.3 74.8 - - - +
242B THR* 1.3 60.6 + - - +
243B LEU* 4.9 1.3 - - + -
252B ASP* 3.4 16.4 - - + +
254B LEU* 3.9 27.8 - - + -
257B VAL* 4.5 11.0 - - + -
268B LEU* 4.1 15.0 - - + -
269B HIS 2.9 7.1 + - - +
270B VAL* 3.4 6.3 - - + +
271B ASP* 2.9 24.4 + - - -
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Residues in contact with THR 242 (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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188B SER* 5.2 1.8 + - - -
191B ALA* 4.1 24.7 - - - +
192B HIS 4.9 0.8 + - - +
240B VAL* 4.4 9.7 + - - +
241B ALA* 1.3 73.6 - - - +
243B LEU* 1.3 66.2 + - - +
244B GLY 4.0 0.6 + - - -
245B THR* 3.7 41.1 - - + +
250B SER 4.3 0.5 - - - +
251B PHE* 3.8 1.7 - - - -
252B ASP* 2.6 43.0 + - - +
271B ASP* 3.4 15.1 + - - +
602B PLP 4.0 15.5 - - + -
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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