Contacts of the strand formed by residues 850 - 854 (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 VAL 850 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B VAL* 4.4 18.8 - - + -
739B TRP* 5.8 7.2 - - + -
770B VAL* 3.3 29.8 - - + +
771B ALA 3.4 1.0 - - - +
848B THR* 3.4 14.9 + - - +
849B ASN* 1.3 87.5 - - + +
851B VAL* 1.3 62.3 + - - +
852B PHE* 4.2 23.3 - - + -
883B THR* 3.4 29.2 - - + +
885B VAL* 4.3 9.0 - - + -
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Residues in contact with VAL 851 (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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771B ALA* 3.4 15.0 - - + +
843B ALA* 4.1 11.4 - - + +
844B LEU* 5.8 0.2 - - - -
848B THR* 3.8 17.9 - - + -
849B ASN 4.8 0.2 - - - +
850B VAL* 1.3 79.2 - - - +
852B PHE* 1.3 61.2 + - - +
853B LEU* 4.1 18.4 + - + +
877B LEU* 4.0 15.0 - - + -
882B ARG* 3.9 14.4 - - + +
883B THR 2.9 18.4 + - - +
884B VAL* 3.6 21.8 - - + -
885B VAL* 2.9 27.5 + - - +
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Residues in contact with PHE 852 (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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679B VAL* 5.5 8.1 - - + -
703B ILE* 5.6 2.5 - - + -
723B LEU* 3.5 31.0 - - + -
726B THR* 3.9 32.8 - - + -
727B LEU* 3.8 20.0 - - + -
770B VAL* 3.5 31.2 - - + -
771B ALA 3.3 6.6 + - - -
772B TYR* 3.4 19.8 - + + -
773B ALA 3.0 25.8 + - - -
843B ALA* 5.2 0.2 - - - +
850B VAL* 4.2 16.8 - - + -
851B VAL* 1.3 74.3 - - - +
853B LEU* 1.3 64.5 + - - +
854B ASP 4.1 0.4 - - - -
885B VAL* 3.3 31.6 - - + -
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Residues in contact with LEU 853 (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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723B LEU* 4.5 2.0 - - - -
773B ALA* 4.0 11.7 - - + -
840B VAL* 4.3 16.8 - - + -
843B ALA* 5.3 8.7 - - + +
844B LEU* 6.5 0.4 - - + -
851B VAL* 4.1 28.9 - - + +
852B PHE* 1.3 79.9 - - - +
854B ASP* 1.3 59.0 + - - +
855B ASP 3.3 3.3 + - - -
856B PRO* 3.7 28.7 - - + +
873B ILE* 4.8 11.2 - - + -
877B LEU* 5.3 6.1 - - + -
884B VAL* 4.9 5.6 - - + -
885B VAL 2.9 10.2 + - - +
886B LEU* 3.6 26.6 - - + -
887B VAL* 3.0 28.2 + - - +
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Residues in contact with ASP 854 (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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720B SER* 3.0 38.2 + - - -
723B LEU* 3.7 20.4 - - + +
724B LEU* 5.5 0.2 - - - +
772B TYR* 3.6 14.8 + - + -
773B ALA 3.1 20.9 + - - +
774B SER* 3.7 5.6 + - - +
775B GLN* 3.3 41.8 + - - +
853B LEU* 1.3 68.6 - - - +
855B ASP* 1.3 72.9 + - - +
856B PRO* 4.3 1.4 - - - +
887B VAL* 4.4 9.9 - - - +
2501B ADP 5.1 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