Contacts of the strand formed by residues 374 - 377 (chain H) in PDB entry 1OAK
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 374 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373H VAL* 1.3 75.3 + - - +
375H VAL* 1.3 61.5 + - - +
376H THR* 4.2 19.7 - - + -
419H ASN 2.9 6.9 - - - +
421H ALA* 2.8 48.0 + - + +
423H PRO* 5.5 4.8 - - - +
428H LYS* 5.3 0.9 - - - -
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Residues in contact with VAL 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H CYS* 5.1 1.6 - - + -
365H VAL* 4.4 2.7 - - + -
373H VAL* 4.0 4.7 - - + +
374H THR* 1.3 78.3 - - - +
376H THR* 1.3 71.6 + - - +
377H TRP* 4.3 6.4 - - + +
386H VAL* 5.5 1.6 - - - +
388H THR* 4.2 23.2 + - + +
400H LEU* 4.0 30.1 - - + -
402H SER* 3.5 28.3 - - - +
418H CYS* 4.9 5.6 - - + -
419H ASN 3.1 7.2 - - - +
420H VAL* 4.1 21.5 - - + -
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Residues in contact with THR 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374H THR* 4.2 18.4 - - + -
375H VAL* 1.3 81.2 - - - +
377H TRP* 1.3 67.0 + - - +
379H SER* 4.0 5.5 - - - -
380H GLY* 3.9 17.5 - - - +
418H CYS* 3.3 5.2 - - - +
419H ASN* 2.6 61.3 + - - +
428H LYS* 5.4 1.0 + - - -
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Residues in contact with TRP 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H LEU* 4.5 0.2 - - + -
362H GLY* 3.3 33.7 - - - -
363H CYS* 3.8 4.9 - - + -
375H VAL* 4.3 2.3 - - + +
376H THR* 1.3 81.4 - - - +
378H ASN* 1.3 74.8 + - - +
379H SER 3.2 0.4 - - - -
380H GLY 3.1 7.3 + - - +
382H LEU* 3.2 38.0 + - + +
386H VAL* 3.5 29.4 - - + +
402H SER* 2.7 44.4 + - - -
403H SER 4.2 0.6 + - - -
404H VAL* 3.7 29.1 - - + +
416H VAL* 3.7 8.7 - - + -
417H THR 3.1 11.0 - - - -
418H CYS* 3.4 30.1 - - + -
433H ILE* 3.8 22.9 - - + -
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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
------------------------------------------------------------
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