Contacts of the strand formed by residues 375 - 381 (chain B) in PDB entry 2J0U
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 GLY 375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B GLY 3.5 4.1 + - - +
251B ILE* 3.3 15.6 - - - +
252B LYS* 2.9 25.4 + - - +
346B VAL 4.8 3.4 - - - -
347B SER 3.4 13.2 - - - -
349B ILE* 6.5 1.1 - - - -
373B ARG 4.5 0.7 - - - -
374B LYS* 1.3 78.6 - - - +
376B VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 376 (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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251B ILE* 4.5 0.6 - - - +
252B LYS* 3.3 18.8 - - + +
254B PHE* 4.2 15.3 - - + -
347B SER 2.9 15.1 + - - +
348B LEU* 3.3 19.8 - - + +
349B ILE* 2.7 36.4 + - - +
375B GLY* 1.3 78.9 - - - +
377B ALA* 1.3 64.1 + - - +
378B VAL* 4.6 4.7 - - + -
403B MET* 5.7 1.6 - - + -
407B VAL* 5.2 16.2 - - + +
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Residues in contact with ALA 377 (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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251B ILE* 4.1 7.3 - - + +
252B LYS 2.9 8.7 + - - +
253B GLN* 3.5 10.2 - - + -
254B PHE* 2.9 29.6 + - - +
349B ILE* 3.1 5.4 - - + +
365B ILE* 3.5 44.9 - - + -
376B VAL* 1.3 75.1 - - - +
378B VAL* 1.3 63.4 + - - +
379B ASN* 4.2 5.8 - - - +
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 3.5 5.2 - - + -
256B VAL* 4.8 2.5 - - + +
271B LEU* 6.4 1.6 - - + -
348B LEU* 4.4 13.9 - - + -
349B ILE 2.8 6.1 + - - -
350B ILE* 3.6 20.6 - - + -
351B ASN* 2.7 33.4 + - - +
376B VAL* 4.6 4.0 - - + -
377B ALA* 1.3 78.0 - - - +
379B ASN* 1.3 64.4 + - - +
380B PHE* 3.6 31.9 - - + -
403B MET* 3.2 39.7 - - + -
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Residues in contact with ASN 379 (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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254B PHE 2.9 25.4 + - - +
255B PHE* 3.2 10.3 - - + -
256B VAL 2.9 29.1 + - - -
351B ASN* 2.6 29.9 + - - +
354B LEU* 3.2 25.9 - - + +
361B TYR* 3.3 24.7 + - - -
377B ALA* 4.2 4.6 - - - +
378B VAL* 1.3 80.7 - - - +
380B PHE* 1.3 63.5 + - - +
381B VAL* 3.4 10.9 - - + +
389B LEU* 4.4 7.4 - - + -
400B ILE* 4.8 3.2 - - - +
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Residues in contact with PHE 380 (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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256B VAL* 4.3 17.3 - - + -
258B VAL* 4.0 13.7 - - + -
264B LYS* 3.9 15.9 - - + -
267B THR* 4.4 7.6 - - - -
268B LEU* 3.5 42.6 - - + -
271B LEU* 5.5 4.7 - - + -
282B ILE* 5.6 0.2 - - + -
350B ILE* 4.1 18.6 - - + -
351B ASN* 3.0 11.5 + - - +
352B TYR* 3.5 53.2 - + - +
353B ASP* 4.9 0.2 - - - -
354B LEU* 4.3 13.7 + - - +
378B VAL* 3.6 22.0 - - + -
379B ASN* 1.3 76.4 - - - +
381B VAL* 1.3 61.4 + - - +
382B LYS 4.1 0.9 + - - -
385B ASP* 5.6 1.0 - - - +
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Residues in contact with VAL 381 (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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255B PHE* 3.9 11.0 - - + -
256B VAL 3.5 5.7 + - - +
257B ALA* 4.4 2.1 - - - -
258B VAL* 3.4 31.6 + - - +
259B GLU* 3.8 2.6 - - - +
354B LEU* 3.8 12.3 - - + -
379B ASN* 3.4 20.9 - - + +
380B PHE* 1.3 77.3 - - - +
382B LYS* 1.3 65.5 + - - +
383B ASN 3.7 0.5 + - - -
385B ASP* 3.4 35.4 - - + +
386B ILE* 3.7 16.9 - - + +
389B LEU* 3.8 25.4 - - + -
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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