Contacts of the strand formed by residues 883 - 887 (chain B) in PDB entry 5YWB
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 883 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B VAL* 5.3 3.1 - - + -
703B ILE* 4.2 26.2 - - + +
704B PRO 4.3 5.6 - - - +
705B ARG* 3.3 27.1 - - - +
706B GLY 3.4 3.1 + - - +
707B GLN 4.3 7.0 - - - +
849B ASN* 3.0 16.7 + - - +
850B VAL* 3.8 25.1 - - + +
851B VAL* 2.9 30.5 + - - +
882B ARG* 1.3 72.9 - - - +
884B VAL* 1.3 65.7 + - - +
885B VAL* 4.7 0.4 - - + -
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Residues in contact with VAL 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B ILE* 5.5 0.2 - - - +
707B GLN 3.3 12.0 + - - +
708B LEU* 3.7 27.4 - - + -
709B THR* 3.3 22.5 + - - -
851B VAL* 3.6 21.3 - - + +
853B LEU* 4.9 3.1 - - + -
873B ILE* 4.8 4.3 - - + +
877B LEU* 3.7 35.9 - - + -
878B ARG* 6.3 0.2 - - - -
882B ARG 4.0 8.5 + - - +
883B THR* 1.3 78.0 - - - +
885B VAL* 1.3 68.5 + - - +
886B LEU* 4.0 19.5 - - + -
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Residues in contact with VAL 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B ILE* 4.5 28.0 - - + -
709B THR* 3.9 15.5 - - + +
711B ILE* 4.0 27.8 - - + -
723B LEU* 4.2 4.8 - - + +
850B VAL* 4.3 14.8 - - + -
851B VAL 2.9 7.7 + - - -
852B PHE* 3.3 39.5 - - + +
853B LEU 2.9 24.3 + - - +
883B THR* 4.7 0.7 - - + -
884B VAL* 1.3 77.0 - - - +
886B LEU* 1.3 60.8 + - - +
887B VAL* 4.2 0.6 + - - -
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Residues in contact with LEU 886 (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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708B LEU* 4.5 1.1 - - + +
709B THR 3.2 17.7 + - - +
710B MET* 3.4 35.7 - - + +
711B ILE 3.5 1.2 + - - -
853B LEU* 3.6 28.0 - - + -
856B PRO* 3.7 8.7 - - + -
857B PHE* 3.4 26.2 - - + -
869B MET* 5.7 0.4 - - + -
873B ILE* 3.5 41.5 - - + -
884B VAL* 4.0 12.9 + - + -
885B VAL* 1.3 74.1 - - - +
887B VAL* 1.3 63.7 + - - +
888B THR* 3.5 16.9 + - + -
893B TYR* 5.2 0.4 - - + -
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Residues in contact with VAL 887 (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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711B ILE* 3.6 46.9 - - + +
719B LYS* 3.6 42.4 - - + +
723B LEU* 3.7 22.7 - - + -
853B LEU 3.0 11.3 + - - +
854B ASP* 4.7 9.4 - - - +
855B ASP* 2.8 32.9 + - - +
886B LEU* 1.3 78.0 - - - +
888B THR* 1.3 60.8 + - - +
2501B ADP 5.4 0.2 - - - +
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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