Contacts of the strand formed by residues 245 - 253 (chain B) in PDB entry 1JEH
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 THR 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ILE* 5.8 1.0 - - - +
212B VAL* 3.5 17.1 - - + +
213B GLU 3.1 22.5 + - - -
214B PHE* 3.2 6.7 + - - -
242B LYS* 3.2 29.8 + - + +
243B LEU 3.1 14.0 + - - -
244B SER* 1.3 75.0 - - - +
246B LYS* 1.3 61.4 + - - +
263B VAL* 3.5 33.9 - - + -
264B GLU 3.3 12.6 - - - +
265B ASP* 3.2 15.3 + - + +
266B THR* 4.7 0.4 - - - -
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 5.7 3.1 - - + -
189B ILE* 6.1 1.1 - - - -
214B PHE* 4.1 31.2 - - + +
245B THR* 1.3 74.2 - - - +
247B VAL* 1.3 66.7 + - - +
248B ILE* 3.5 23.5 + - + +
263B VAL* 3.4 3.2 - - - +
264B GLU* 3.0 55.6 + - + +
266B THR* 4.3 9.5 - - + +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 3.2 44.0 - - + -
163B ILE* 4.3 10.1 - - + -
187B THR* 6.2 0.4 - - + -
189B ILE* 3.5 31.8 - - + +
212B VAL* 4.2 6.7 - - + +
245B THR 4.4 0.2 + - - -
246B LYS* 1.3 75.7 - - - +
248B ILE* 1.3 65.2 - - - +
249B SER 4.0 16.6 - - - +
250B ALA* 4.5 1.8 - - + -
261B ILE* 3.9 22.4 - - + -
262B VAL 3.7 2.5 - - - -
263B VAL* 3.8 20.6 - - + -
279B LEU* 6.0 1.8 - - + -
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Residues in contact with ILE 248 (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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160B PHE* 5.1 3.1 - - - -
161B PRO 5.4 2.9 - - - +
163B ILE* 5.1 2.1 - - - +
246B LYS* 3.7 28.5 - - + +
247B VAL* 1.3 76.7 - - - +
249B SER* 1.3 69.8 + - - +
262B VAL* 2.9 24.6 + - + +
263B VAL 4.2 3.8 - - - +
264B GLU* 3.8 33.4 - - + +
271B GLN* 5.7 3.8 - - + +
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLY 5.8 0.9 - - - -
163B ILE* 4.6 3.6 - - - -
247B VAL* 3.7 4.2 - - - -
248B ILE* 1.3 86.1 - - - +
250B ALA* 1.3 60.9 + - - +
251B LYS* 6.3 1.3 - - - -
260B GLU 3.8 1.7 - - - +
261B ILE* 3.5 1.6 - - - +
262B VAL* 2.8 54.1 + - - +
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Residues in contact with ALA 250 (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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162B GLY 4.1 7.4 + - - +
163B ILE* 3.7 32.1 - - + +
164B GLU 5.1 0.5 + - - -
170B ILE* 4.4 3.0 - - - +
247B VAL* 4.5 2.2 - - + -
249B SER* 1.3 78.3 - - - +
251B LYS* 1.3 71.2 + - - +
259B VAL* 4.3 4.5 - - + -
260B GLU 3.5 6.5 - - - -
261B ILE* 4.3 14.1 - - + -
279B LEU* 3.7 28.0 - - + -
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Residues in contact with LYS 251 (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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162B GLY 4.1 15.3 + - - +
164B GLU* 5.0 16.4 - - + +
170B ILE* 4.7 0.9 - - - -
249B SER* 6.3 1.8 - - - -
250B ALA* 1.3 80.9 - - - +
252B ARG* 1.3 69.4 + - - +
253B ASN 3.5 1.0 + - - -
258B VAL 3.8 0.2 - - - +
259B VAL* 4.3 3.7 - - - +
260B GLU* 3.0 40.9 + - + +
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Residues in contact with ARG 252 (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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166B ASP* 3.0 30.1 + - - +
168B GLU* 3.0 33.1 + - - +
169B LYS* 3.4 35.2 - - + +
170B ILE* 4.0 22.1 - - + +
251B LYS* 1.3 78.9 - - - +
253B ASN* 1.3 67.0 + - - +
254B ASP* 3.0 37.5 + - - +
258B VAL 4.2 2.9 - - - -
259B VAL* 4.3 7.0 - - + +
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Residues in contact with ASN 253 (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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169B LYS* 5.9 0.3 - - - +
252B ARG* 1.3 77.5 + - - +
254B ASP* 1.3 71.7 + - - +
255B ASP* 3.0 36.6 + - - +
256B LYS* 2.9 17.8 + - - +
257B ASN* 3.3 4.0 - - - -
258B VAL* 3.0 33.0 + - + +
260B GLU* 3.5 30.7 + - - +
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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