Contacts of the strand formed by residues 784 - 790 (chain A) in PDB entry 4B87
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 784 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A THR* 5.3 7.0 - - + -
712A PHE* 3.8 28.9 - - + -
779A CYS 3.3 0.5 - - - +
780A ILE* 3.2 5.2 - - - -
781A VAL* 2.7 37.9 + - - +
782A ASN 3.7 11.2 - - - +
783A GLY* 1.3 84.9 - - - +
785A LYS* 1.3 71.3 + - - +
786A VAL* 3.5 4.2 + - + +
802A PHE* 5.1 0.9 - - + -
803A TYR 3.2 25.1 - - - +
804A LEU* 4.5 8.5 - - + -
805A PRO* 4.4 18.8 - - + -
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Residues in contact with LYS 785 (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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778A GLU* 3.4 40.4 - - + +
779A CYS 3.5 3.8 - - - +
780A ILE* 3.9 20.1 - - + +
783A GLY 4.2 0.8 + - - -
784A VAL* 1.3 75.2 - - - +
786A VAL* 1.3 63.7 + - - +
802A PHE* 3.8 0.2 - - - -
803A TYR* 3.0 61.1 + - + +
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Residues in contact with VAL 786 (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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712A PHE* 4.1 13.7 - - + -
729A PHE* 4.2 11.7 - - + -
773A LEU* 4.0 26.9 - - + -
777A THR 3.8 1.4 - - - +
778A GLU* 3.7 0.5 - - - -
779A CYS* 2.8 39.4 + - + +
781A VAL* 4.1 13.9 - - + -
784A VAL* 4.0 8.3 - - + +
785A LYS* 1.3 78.7 - - - +
787A VAL* 1.3 68.5 + - - +
788A LEU* 5.2 0.7 - - + -
800A ILE* 4.5 8.1 - - + -
801A LEU 3.2 8.1 - - - +
802A PHE* 3.7 27.4 - - + -
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Residues in contact with VAL 787 (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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776A ASP* 4.0 18.6 - - - -
777A THR 4.2 4.0 - - - +
778A GLU* 4.0 28.7 - - + +
785A LYS* 5.5 0.2 - - + -
786A VAL* 1.3 80.3 - - - +
788A LEU* 1.3 76.3 + - - +
789A LEU* 4.0 10.1 + - + +
799A MET 3.8 0.2 - - - +
800A ILE* 3.5 3.9 - - - -
801A LEU* 2.7 47.7 + - + +
803A TYR* 4.1 17.9 - - + -
826A LEU* 3.9 26.5 - - + -
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Residues in contact with LEU 788 (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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729A PHE* 5.0 7.0 - - + -
751A CYS* 3.7 26.5 - - - +
752A SER* 4.0 5.6 - - - +
773A LEU* 3.7 50.0 - - + +
774A PRO 4.3 6.6 + - - +
775A LEU* 3.4 15.9 - - + -
776A ASP* 2.8 31.3 + - - +
777A THR 4.9 1.2 + - - -
779A CYS* 6.3 0.4 - - - -
786A VAL* 5.2 0.9 - - + -
787A VAL* 1.3 76.8 - - - +
789A LEU* 1.3 61.6 + - - +
798A VAL* 4.0 24.0 - - + -
799A MET 3.3 1.1 - - - -
800A ILE* 4.0 23.1 - - + -
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Residues in contact with LEU 789 (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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775A LEU* 4.6 4.9 - - - -
776A ASP* 3.6 22.7 - - - +
787A VAL* 4.2 10.5 - - + +
788A LEU* 1.3 77.9 - - - +
790A ASP* 1.3 61.3 + - - +
798A VAL* 3.0 8.9 - - - -
799A MET* 2.7 53.4 + - + +
801A LEU* 4.5 13.0 - - + -
811A LEU* 4.2 17.0 - - + -
825A SER* 4.6 13.0 - - - +
826A LEU* 4.2 22.0 - - + -
827A LEU* 4.1 29.6 - - + -
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Residues in contact with ASP 790 (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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775A LEU* 4.2 24.9 - - + +
776A ASP* 5.5 1.2 + - - -
789A LEU* 1.3 73.8 - - - +
791A ALA* 1.3 61.9 + - - +
792A ASN* 2.6 32.9 + - - +
796A GLY 5.9 1.2 + - - -
797A ALA 4.0 8.5 - - - +
799A MET* 3.8 7.5 - - - +
822A MET* 3.5 15.8 - - - +
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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