Contacts of the strand formed by residues 258 - 265 (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 VAL 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B LYS* 6.4 0.2 - - - -
185B ARG* 4.9 2.2 - - - +
252B ARG* 5.6 0.4 - - - -
253B ASN* 3.0 36.2 + - - +
256B LYS* 2.8 30.8 + - + +
257B ASN* 1.3 80.4 - - - +
259B VAL* 1.3 62.5 + - - +
260B GLU* 3.4 13.6 + - + +
275B GLU* 3.7 39.5 - - + +
276B ALA 3.3 7.9 - - - +
277B GLU* 3.4 18.4 - - - +
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Residues in contact with VAL 259 (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* 3.4 34.1 - - + +
170B ILE* 3.9 19.3 - - + -
250B ALA* 4.3 7.9 - - + -
251B LYS 3.6 12.1 - - - +
252B ARG* 4.3 5.2 - - + +
258B VAL* 1.3 69.6 - - - +
260B GLU* 1.3 60.4 + - - +
261B ILE* 3.2 13.4 + - + +
275B GLU* 3.7 0.7 - - - -
276B ALA* 2.9 30.2 + - + +
277B GLU 3.8 12.6 - - - +
279B LEU* 3.7 36.3 - - + +
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Residues in contact with GLU 260 (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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249B SER 3.8 1.7 - - - +
250B ALA* 3.5 2.9 - - - -
251B LYS* 3.0 34.3 + - + +
253B ASN* 3.5 34.1 + - - +
258B VAL* 3.8 18.3 - - + +
259B VAL* 1.3 69.1 - - - +
261B ILE* 1.3 64.3 + - - +
262B VAL* 4.4 6.4 - - + +
274B LEU 3.7 7.9 - - - +
275B GLU* 4.7 10.2 - - + +
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Residues in contact with ILE 261 (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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187B THR* 3.8 20.9 - - + +
247B VAL* 3.9 30.7 - - + -
249B SER 3.5 7.9 - - - +
250B ALA* 4.2 3.8 - - + +
259B VAL* 3.2 29.6 + - + +
260B GLU* 1.3 75.0 - - - +
262B VAL* 1.3 63.7 + - - +
263B VAL* 4.0 9.9 - - + -
273B ASN* 3.6 1.0 - - - +
274B LEU* 2.8 41.8 + - + +
275B GLU* 3.8 12.1 - - - +
276B ALA* 3.7 23.8 - - + -
279B LEU* 3.8 22.7 - - + -
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Residues in contact with VAL 262 (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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247B VAL* 3.7 3.3 - - - +
248B ILE* 2.9 37.3 + - + -
249B SER* 2.8 34.0 + - - +
260B GLU* 4.4 6.3 - - + +
261B ILE* 1.3 78.9 - - - +
263B VAL* 1.3 60.1 + - - +
271B GLN* 3.5 43.3 - - + +
272B GLU 3.4 5.6 - - - +
273B ASN* 4.5 13.0 - - - +
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Residues in contact with VAL 263 (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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212B VAL* 4.3 7.6 - - + -
242B LYS* 4.4 8.1 - - - +
245B THR* 3.5 22.4 - - + -
246B LYS 3.4 6.1 - - - +
247B VAL* 3.8 24.2 - - + -
248B ILE* 4.2 2.0 - - - +
261B ILE* 4.0 10.5 - - + -
262B VAL* 1.3 78.0 - - - +
264B GLU* 1.3 63.6 + - - +
271B GLN* 3.4 7.8 - - - +
272B GLU* 3.0 48.0 + - + +
274B LEU* 4.3 26.9 - - + -
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Residues in contact with GLU 264 (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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245B THR* 3.3 4.4 - - - -
246B LYS* 3.0 54.1 + - + +
248B ILE* 3.8 27.7 - - + +
263B VAL* 1.3 77.4 - - - +
265B ASP* 1.3 64.8 + - - +
266B THR* 3.3 2.9 + - - -
269B ASN* 3.6 37.5 - - + +
270B LYS 4.1 15.7 - - - +
271B GLN* 4.7 3.5 + - + +
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Residues in contact with ASP 265 (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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243B LEU 3.5 8.3 - - - +
244B SER* 3.2 12.6 - - - +
245B THR* 3.2 19.2 + - - +
264B GLU* 1.3 71.7 - - - +
266B THR* 1.3 65.2 + - - +
267B LYS* 2.8 31.1 + - - +
268B THR 3.2 7.6 - - - +
269B ASN* 3.2 22.9 - - - -
270B LYS 4.0 9.9 + - - +
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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