Contacts of the strand formed by residues 432 - 436 (chain A) in PDB entry 5MWB
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 LYS 432 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ASN* 4.7 0.7 - - - +
427A CYS* 4.0 1.3 - - - -
430A ALA 3.7 2.2 + - - +
431A GLY* 1.3 71.1 - - - -
433A CYS* 1.3 71.0 + - - +
434A VAL* 3.5 10.1 + - + +
442A CYS* 3.5 2.6 - - - -
443A GLU* 2.9 67.3 + - + +
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Residues in contact with CYS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A CYS* 2.0 60.7 - - + +
425A ASN* 3.7 18.2 + - - +
426A PRO* 3.5 20.6 - - + -
427A CYS* 3.6 4.3 - - - -
431A GLY 3.6 3.6 + - - -
432A LYS* 1.3 78.9 - - - +
434A VAL* 1.3 61.5 + - - +
440A PHE* 3.8 16.8 - - - -
441A HIS 3.5 3.8 - - - -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A CYS* 3.6 2.7 - - - -
432A LYS* 3.8 17.5 - - + +
433A CYS* 1.3 78.3 - - - +
435A ASN* 1.3 69.1 + - - +
436A THR* 3.5 2.2 + - + -
441A HIS* 2.6 55.5 + - + +
443A GLU* 3.4 30.7 - - + +
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Residues in contact with ASN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ASP* 3.2 17.8 + - - -
417A ASP* 3.3 42.6 + - - +
418A GLU* 3.0 9.7 + - - +
419A CYS* 3.3 12.0 - - + -
433A CYS 4.3 0.2 + - - -
434A VAL* 1.3 81.0 - - - +
436A THR* 1.3 63.6 + - - +
440A PHE* 4.3 2.0 - - - -
606A CA 2.4 27.4 - - - -
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Residues in contact with THR 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ASP* 3.1 4.2 - - - +
434A VAL* 3.5 13.9 + - + +
435A ASN* 1.3 83.0 + - - +
437A ASP* 1.3 61.7 + - - +
439A ALA* 2.7 31.5 + - - +
440A PHE* 3.2 2.5 + - - -
441A HIS* 4.0 18.2 - - + +
606A CA 2.4 31.0 - - - -
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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