Contacts of the strand formed by residues 869 - 873 (chain B) in PDB entry 5M64
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 869 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827B PHE* 3.9 27.8 - - + -
828B GLY 3.9 14.4 - - - +
830B ASP* 4.6 6.8 + - - +
832B TRP* 3.4 27.4 - - + +
833B PRO* 5.3 1.4 - - - +
836B TRP* 5.0 5.5 - - - -
860B ALA* 5.6 0.4 - - - -
861B TYR 3.3 8.5 - - - -
862B PHE* 3.6 24.9 - - + -
868B LYS* 1.3 77.2 + - - +
870B LYS* 1.3 63.2 + - - +
871B ILE* 3.7 12.0 - - - +
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Residues in contact with LYS 870 (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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859B CYS 3.9 0.7 - - - +
860B ALA* 3.4 3.8 - - - -
861B TYR* 3.1 66.0 + - + +
863B ASP* 2.3 38.1 + - - +
865B THR* 6.3 0.2 - - - +
866B LEU* 4.8 6.9 - - - +
868B LYS* 3.3 38.4 + - - +
869B THR* 1.3 74.4 - - - +
871B ILE* 1.3 65.9 + - - +
872B LYS* 6.0 0.4 - - + -
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Residues in contact with ILE 871 (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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836B TRP* 4.0 33.0 - - + -
857B PRO* 3.6 37.2 - - + -
859B CYS 3.9 2.5 - - - +
860B ALA* 3.7 21.1 - - + -
869B THR* 3.7 13.0 - - - +
870B LYS* 1.3 85.0 - - - +
872B LYS* 1.3 68.4 + - - +
873B THR* 4.0 12.1 + - + +
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Residues in contact with LYS 872 (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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808B LYS 5.4 1.6 + - - -
809B VAL* 3.9 32.0 - - + +
810B ASP 5.1 8.1 - - - +
858B ILE* 3.2 8.1 + - - +
859B CYS* 3.0 40.0 + - + +
861B TYR* 3.5 35.4 - - + +
870B LYS* 6.0 0.2 - - + -
871B ILE* 1.3 74.0 - - - +
873B THR* 1.3 63.9 + - - +
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Residues in contact with THR 873 (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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807B GLU* 5.5 1.4 - - - +
855B GLY* 3.7 6.1 - - - -
856B ASP 2.6 41.7 + - - -
858B ILE* 4.0 5.8 - - - +
871B ILE* 4.2 12.6 - - + +
872B LYS* 1.3 78.4 + - - +
874B TYR* 1.3 71.0 + - - +
875B HIS* 3.4 39.2 + - + +
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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