Contacts of the strand formed by residues 722 - 726 (chain A) in PDB entry 1WBD
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 722 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A PRO* 4.0 16.4 - - + -
577A GLY* 3.4 37.2 - - - +
578A ILE* 4.3 12.8 - - + -
603A LEU* 4.3 15.0 - - + -
604A SER 3.5 31.9 - - - +
605A PRO* 4.7 1.8 - - + -
608A ARG* 3.2 18.4 - - + +
650A ILE* 6.2 4.0 - - + -
686A GLU 4.9 2.0 - - - +
687A TYR 6.2 0.4 - - - -
688A SER 3.1 13.7 + - - +
689A LEU* 3.3 12.4 - - + +
690A VAL* 2.8 25.1 + - - +
720A LYS 5.1 1.6 - - - +
721A ALA* 1.3 71.3 - - - +
723A THR* 1.3 59.7 + - - +
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Residues in contact with THR 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A LEU* 4.7 1.2 - - - +
608A ARG 2.9 7.4 + - - +
609A MET* 3.2 37.5 - - + +
610A LEU 3.1 22.9 + - - -
690A VAL* 3.2 22.5 - - + +
692A MET* 4.3 0.9 - - + -
715A LEU* 3.9 25.2 - - + +
721A ALA 3.7 8.8 + - - -
722A LEU* 1.3 76.6 + - - +
724A LEU* 1.3 76.0 + - - +
725A PHE* 4.1 10.3 - - + -
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Residues in contact with LEU 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LEU* 4.1 6.1 - - + -
603A LEU* 4.1 18.4 - - + -
610A LEU* 3.7 34.1 - - + -
612A ILE* 3.8 16.2 - - + -
623A TYR* 4.5 5.2 - - + +
624A MET* 3.7 30.3 - - + +
627A THR* 3.7 28.5 - - + +
689A LEU* 4.9 2.0 - - + +
690A VAL 2.9 8.1 + - - +
691A LEU* 3.5 17.3 - - + +
692A MET 3.0 27.0 + - - +
722A LEU 4.3 0.2 - - - -
723A THR* 1.3 78.8 - - - +
725A PHE* 1.3 59.5 + - - +
726A ALA 3.9 1.1 - - - -
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Residues in contact with PHE 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 4.6 3.8 - - + -
610A LEU 2.9 16.5 + - - +
611A ILE* 3.5 21.8 - - + -
612A ILE* 3.0 20.4 + - - +
692A MET* 3.6 33.7 - - + -
695A ILE* 4.0 25.8 - - + -
708A ALA* 3.7 22.4 - - + -
711A CYS 5.0 0.2 - - - -
712A ALA* 4.0 24.5 - - + -
715A LEU* 4.6 1.8 - - + -
723A THR* 4.1 13.2 - - + -
724A LEU* 1.3 70.5 - - - +
726A ALA* 1.3 68.0 + - - +
727A THR* 3.5 16.2 + - + -
732A LEU* 4.1 22.0 - - + -
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Residues in contact with ALA 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A ILE* 3.4 16.3 - - + +
620A LYS* 4.3 20.6 - - + -
624A MET* 3.8 17.8 - - + -
692A MET 3.0 7.4 + - - +
693A ASP* 3.4 23.6 - - - +
694A GLU* 2.9 28.3 + - + -
724A LEU 3.9 1.2 - - - -
725A PHE* 1.3 77.8 - - - +
727A THR* 1.3 61.5 + - - +
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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