Contacts of the strand formed by residues 689 - 693 (chain B) in PDB entry 1WBB
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 LEU 689 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ILE* 3.9 23.1 - - + -
603B LEU* 4.7 5.4 - - + -
627B THR* 4.2 15.0 - - + +
628B ALA* 4.0 30.7 - - + +
631B ALA* 4.0 19.5 - - + -
650B ILE* 4.4 11.2 - - + -
652B ARG 3.1 11.9 + - - +
653B ILE* 3.5 12.9 - - + -
654B PHE* 2.9 28.1 + - - +
687B TYR 4.1 0.2 + - - -
688B SER* 1.3 73.7 - - - +
690B VAL* 1.3 63.0 + - - +
691B LEU* 4.3 14.8 - - + -
722B LEU* 3.5 13.9 - - + +
723B THR* 5.5 0.4 - - - -
724B LEU* 5.7 0.4 - - + -
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Residues in contact with VAL 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B PHE* 3.5 24.9 - - + -
680B ILE* 3.8 26.5 - - + -
684B ALA* 4.3 4.5 - - + -
688B SER* 4.5 1.1 - - - -
689B LEU* 1.3 77.8 - - - +
691B LEU* 1.3 67.7 + - - +
692B MET* 3.6 25.4 - - + -
715B LEU* 4.2 11.2 - - + -
721B ALA* 4.0 23.1 - - + -
722B LEU 3.0 6.1 + - - -
723B THR* 3.2 12.7 - - + +
724B LEU 2.9 24.8 + - - -
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Residues in contact with LEU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B MET* 3.2 36.1 - - + +
625B ARG* 4.7 1.3 - - - +
627B THR* 4.4 2.2 - - - -
628B ALA* 3.5 25.8 - - + -
653B ILE* 5.1 0.2 - - + -
654B PHE 2.9 9.1 + - - +
655B THR* 3.5 18.2 - - + -
656B ARG* 2.8 28.6 + - - +
657B VAL* 3.7 14.6 - - + +
680B ILE* 5.2 0.2 - - - +
689B LEU* 4.3 18.8 - - + -
690B VAL* 1.3 80.0 - - - +
692B MET* 1.3 62.7 + - - +
724B LEU* 3.6 36.3 - - + -
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Residues in contact with MET 692 (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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624B MET* 3.4 4.9 - - - +
656B ARG* 4.0 5.8 - - + -
677B THR* 4.3 13.0 - - + +
680B ILE* 4.2 20.4 - - - -
681B LEU* 6.1 0.4 - - - -
690B VAL* 3.6 23.6 - - + -
691B LEU* 1.3 77.1 - - - +
693B ASP* 1.3 58.8 + - - +
694B GLU 3.6 0.9 - - - +
695B ILE* 3.5 45.3 - - + -
711B CYS* 4.7 2.7 - - + -
715B LEU* 4.1 10.1 - - + -
723B THR* 4.8 0.9 - - + -
724B LEU 2.9 11.0 + - - +
725B PHE* 3.6 31.9 - - + -
726B ALA* 2.9 34.4 + - - +
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Residues in contact with ASP 693 (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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616B ASN* 2.9 28.5 + - - -
621B SER* 3.5 15.2 + - - -
624B MET* 4.1 7.7 - - + +
656B ARG* 3.1 33.9 + - - +
657B VAL* 3.7 15.5 - - + -
658B GLY 3.6 24.9 + - - +
673B GLU* 4.0 1.7 - - - +
692B MET* 1.3 71.0 - - - +
694B GLU* 1.3 73.7 + - - +
695B ILE* 3.5 2.6 + - - +
726B ALA* 4.2 0.4 - - - -
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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