Contacts of the strand formed by residues 353 - 358 (chain B) in PDB entry 5DX1
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 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B HIS* 3.3 4.9 - - - -
294B LEU* 2.9 57.1 + - + +
351B LYS 4.7 0.4 - - - +
352B SER* 1.3 75.3 - - - +
354B LYS* 1.3 64.4 + - - +
372B ILE* 4.3 4.7 - - + -
373B PRO 3.9 19.3 - - - +
374B PHE* 4.0 11.7 - - + -
375B LYS 4.6 7.9 - - - +
376B PHE* 3.2 28.3 - - + -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 3.7 26.3 + - + +
292B VAL 3.2 9.9 - - - +
293B HIS* 3.6 29.4 - - + +
352B SER 5.3 0.9 - - - +
353B VAL* 1.3 82.8 - - - +
355B TYR* 1.3 62.8 + - - +
356B THR* 4.0 16.1 + - - +
372B ILE* 5.5 0.5 - - - +
403B TRP* 6.2 0.6 - - - -
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Residues in contact with TYR 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 4.5 8.7 - + - -
290B GLY 4.0 0.5 - - - +
291B ASP* 3.4 1.7 - - - -
292B VAL* 2.8 37.5 + - + +
294B LEU* 5.0 0.6 - - + +
353B VAL 4.4 0.2 + - - -
354B LYS* 1.3 75.4 - - - +
356B THR* 1.3 77.0 + - - +
357B VAL* 4.0 18.3 - - + +
366B ASP 4.9 5.9 + - - -
367B LEU* 5.9 1.7 - - + +
370B ILE* 3.7 31.7 - - + +
371B GLU 3.6 19.5 + - - -
372B ILE* 3.8 39.0 - - + -
373B PRO* 5.6 1.1 - - + -
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 4.6 14.4 - - + -
290B GLY 3.4 5.8 - - - +
291B ASP* 2.6 25.0 + - - +
354B LYS* 4.0 13.9 - - - +
355B TYR* 1.3 89.6 - - - +
357B VAL* 1.3 75.5 + - - +
358B ASN* 4.1 4.6 + - + +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 5.1 4.5 - - + -
264B PHE* 4.2 22.9 - - + -
269B LEU* 5.3 0.7 - - + -
273B LEU* 5.3 0.4 - - + -
289B ILE* 3.4 4.9 - - - +
290B GLY* 2.8 39.6 + - - +
292B VAL* 6.2 0.2 - - + -
355B TYR* 4.0 19.7 - - + +
356B THR* 1.3 79.3 - - - +
358B ASN* 1.3 61.0 + - - +
359B PHE* 3.7 30.4 + - + -
362B ALA* 4.0 20.2 - - + -
367B LEU* 4.3 18.8 - - + -
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Residues in contact with ASN 358 (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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288B THR* 3.8 4.2 - - - +
289B ILE* 4.0 18.5 - - + +
356B THR* 4.1 5.5 + - + -
357B VAL* 1.3 72.3 - - - +
359B PHE* 1.3 54.9 + - - +
360B LEU* 3.0 26.0 + - - +
361B GLU* 3.1 38.6 + - + +
362B ALA* 2.8 37.7 + - - +
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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
------------------------------------------------------------
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