Contacts of the strand formed by residues 426 - 430 (chain B) in PDB entry 3OPY
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 426 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ARG 3.3 17.1 + - - -
369B ALA* 3.5 12.4 - - - +
370B PHE* 2.7 33.6 + - - +
393B ASP* 3.2 27.1 - - - +
415B VAL* 4.0 18.4 - - + +
418B HIS* 4.9 0.2 - - + -
419B ARG* 3.4 34.9 + - + +
423B LYS* 4.3 5.6 - - + +
424B ARG 3.6 3.2 + - - -
425B LYS* 1.4 71.6 - - - +
427B ILE* 1.4 58.5 + - - +
428B VAL* 5.3 3.5 - - - +
451B LEU* 5.6 0.6 - - - +
457B LEU* 4.3 5.5 - - - +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 4.0 15.5 - - + -
359B ILE* 3.8 19.7 - - + -
360B ASP* 3.7 20.9 - - - +
370B PHE* 3.4 26.9 - - + +
372B VAL* 3.9 24.9 - - + -
390B THR 5.7 2.2 - - - +
391B SER 5.9 0.2 - - - +
392B ALA* 3.7 20.4 - - + +
393B ASP* 3.0 38.2 + - - +
394B TYR 3.6 1.7 + - - -
423B LYS* 5.0 3.6 - - - +
425B LYS* 3.9 13.9 - - + +
426B THR* 1.4 78.5 - - - +
428B VAL* 1.3 62.3 + - - +
429B ILE* 4.3 5.8 - - + -
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Residues in contact with VAL 428 (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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369B ALA* 6.1 0.9 - - + -
370B PHE 2.9 11.0 + - - +
371B ILE* 3.3 5.9 - - + +
372B VAL* 2.9 25.3 + - - +
394B TYR* 3.3 15.0 - - + +
396B LEU* 3.8 15.7 - - + -
411B MET* 3.7 26.2 - - + -
415B VAL* 4.2 24.2 - - + -
426B THR* 5.3 3.6 - - - -
427B ILE* 1.3 76.8 - - - +
429B ILE* 1.3 63.2 + - - +
430B VAL* 4.2 2.7 - - + -
447B VAL* 3.8 12.1 - - + -
451B LEU* 4.3 21.5 - - + -
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Residues in contact with ILE 429 (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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356B ILE* 3.8 28.9 - - + -
372B VAL* 3.5 9.2 - - + -
374B VAL* 3.8 27.4 - - + -
383B GLY* 4.0 22.7 - - - +
386B ALA* 4.0 2.9 - - + -
387B GLY* 3.5 29.2 - - - +
390B THR* 4.3 0.2 - - - +
392B ALA* 3.6 23.1 - - + -
394B TYR 3.1 7.5 + - - -
395B ILE* 3.5 8.5 - - + -
396B LEU* 2.8 34.0 + - - +
397B ILE* 5.9 0.4 - - + -
427B ILE* 4.5 3.1 - - + -
428B VAL* 1.3 74.6 - - - +
430B VAL* 1.3 61.2 + - - +
431B ALA 4.0 0.6 + - - +
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Residues in contact with VAL 430 (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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371B ILE* 3.7 21.3 - - + -
372B VAL 3.0 9.7 + - - +
373B GLU* 3.6 4.4 - - + +
374B VAL 2.8 30.5 + - - -
396B LEU* 3.8 21.8 - - + -
428B VAL* 4.2 1.3 - - + -
429B ILE* 1.3 76.8 - - - +
431B ALA* 1.3 69.3 + - - +
434B ALA* 3.8 13.7 - - + -
442B ILE 4.2 9.6 - - - +
443B SER 4.6 6.3 - - - +
444B CYS* 4.1 20.4 - - - +
447B VAL* 3.9 17.0 - - + -
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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