Contacts of the strand formed by residues 758 - 760 (chain A) in PDB entry 5MJA
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 CYS 758 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A ASN* 2.9 28.6 + - - +
705A LEU* 4.1 12.8 - - - -
724A MET* 3.6 37.1 + - - +
727A GLY* 4.3 4.7 - - - -
728A ILE* 3.7 15.0 - - + -
750A ILE* 3.7 15.5 - - + -
751A LEU 3.3 3.8 - - - -
752A VAL* 4.0 22.0 - - - -
756A LEU 3.4 8.6 + - - -
757A VAL* 1.3 71.4 - - - +
759A LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A ARG* 3.0 29.5 + - - +
679A ASN* 3.3 5.6 - - - +
680A ILE 4.4 3.3 + - - +
681A ILE* 3.9 18.6 - - + +
682A ARG* 4.4 1.0 - - - +
698A GLU* 2.8 41.7 + - - +
700A MET* 3.5 28.7 - - + -
728A ILE* 5.9 0.4 - - - -
750A ILE* 3.5 7.3 - - - +
751A LEU* 2.8 32.3 + - - +
753A ASN* 4.5 5.2 - - - +
757A VAL* 3.8 15.3 - - + -
758A CYS* 1.3 78.1 - - - +
760A VAL* 1.3 65.1 + - - +
761A SER* 3.5 1.9 + - - -
902B SO4 2.8 26.7 + - - -
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Residues in contact with VAL 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ASN 2.8 19.6 + - - +
680A ILE* 3.9 12.3 - - + -
681A ILE* 3.1 25.1 + - - +
728A ILE* 4.2 21.0 - - + +
731A GLY 4.4 1.1 - - - -
732A MET* 3.9 32.8 - - + -
735A LEU* 4.4 1.3 - - + -
742A HIS* 3.5 32.8 - - + +
745A LEU* 4.7 7.0 - - + -
749A ASN 4.2 3.8 - - - +
750A ILE* 4.5 3.6 - - + -
759A LYS* 1.3 69.4 - - - +
761A SER* 1.3 61.8 + - - +
763A PHE* 3.4 15.3 - - + -
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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