Contacts of the strand formed by residues 793 - 800 (chain A) in PDB entry 4Z96
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 ARG 793 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A ARG* 4.2 28.0 - - - +
780A LEU* 4.9 0.8 - - - +
786A TYR* 4.4 19.4 + - - -
789A ASP* 3.0 35.1 + - - +
790A LEU* 3.1 39.5 + - + +
791A TYR 4.5 2.8 - - - +
792A HIS* 1.3 79.5 - - - +
794A VAL* 1.3 64.5 + - - +
795A ASP* 4.7 9.6 - - - +
812A THR* 4.0 26.2 - - + +
813A LEU 3.7 5.2 - - - +
814A SER* 4.8 0.7 - - - +
815A ASN* 5.6 0.7 - - - -
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Residues in contact with VAL 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A HIS 3.9 0.4 - - - +
793A ARG* 1.3 77.5 - - - +
795A ASP* 1.3 64.3 + - - +
796A VAL* 3.8 18.0 + - + -
811A VAL 3.7 0.5 - - - +
812A THR* 3.7 0.3 - - - -
813A LEU* 2.8 39.7 + - - +
815A ASN* 3.5 36.6 - - - +
861A LEU* 3.6 20.6 - - + -
865A LEU* 3.9 13.9 - - + -
874A LYS* 4.2 20.4 - - + -
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Residues in contact with ASP 795 (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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793A ARG* 4.7 10.1 - - - +
794A VAL* 1.3 74.2 - - - +
796A VAL* 1.3 62.7 + - - +
797A ILE* 4.2 1.7 + - - +
810A VAL* 5.2 13.1 - - + +
811A VAL 3.3 5.8 - - - +
812A THR* 2.3 37.3 + - - +
874A LYS* 3.9 19.4 + - - +
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Residues in contact with VAL 796 (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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794A VAL* 3.8 20.8 + - + +
795A ASP* 1.3 77.2 - - - +
797A ILE* 1.3 69.8 + - - +
798A PHE* 3.4 34.1 - - + -
809A PHE 3.4 1.2 - - - +
810A VAL* 3.3 1.8 - - - -
811A VAL 2.7 40.8 + - - +
813A LEU* 4.4 3.4 - - + -
861A LEU* 4.3 15.7 - - + -
865A LEU* 3.9 17.9 - - + -
874A LYS* 3.6 10.5 - - + +
875A LYS* 4.4 0.9 - - - -
876A LEU* 4.0 20.4 - - + +
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Residues in contact with ILE 797 (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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795A ASP 5.2 1.6 - - - +
796A VAL* 1.3 71.2 - - - +
798A PHE* 1.3 61.1 + - - +
799A CYS* 3.7 22.9 + - - -
807A PRO 3.9 15.3 - - - +
808A GLY 4.4 0.2 - - - -
809A PHE 3.2 13.9 - - - +
810A VAL* 3.7 22.0 - - + -
873A PRO* 4.6 19.7 - - + -
874A LYS 2.7 22.1 + - - +
875A LYS* 3.1 10.8 - - + +
876A LEU 2.8 27.0 + - - +
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Residues in contact with PHE 798 (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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796A VAL* 3.4 29.2 - - + -
797A ILE* 1.3 71.0 - - - +
799A CYS* 1.3 60.5 + - - +
808A GLY* 3.2 17.3 - - - -
809A PHE* 2.9 34.5 + - + +
811A VAL* 3.6 24.7 - - + -
813A LEU* 3.7 23.8 - - + -
822A VAL* 4.1 6.3 - - + -
826A VAL* 3.5 28.9 - - + -
839A PHE* 3.6 28.0 - + - -
876A LEU* 3.1 33.9 - - + +
878A TYR* 3.7 14.7 - + + -
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Residues in contact with CYS 799 (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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797A ILE* 3.7 29.8 - - - -
798A PHE* 1.3 73.8 - - - +
800A ASP* 1.3 62.8 + - - +
806A ASP* 3.5 30.3 - - + +
807A PRO 4.4 1.6 - - - -
808A GLY* 4.0 2.7 - - - -
875A LYS* 4.8 8.5 - - - -
876A LEU 3.0 6.6 + - - -
877A TYR* 3.1 34.2 - - + -
878A TYR* 3.0 25.1 + - - -
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Residues in contact with ASP 800 (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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799A CYS* 1.3 72.0 - - - +
801A LYS* 1.3 58.3 + - - +
802A THR* 2.4 49.0 + - - +
803A ILE* 3.4 40.3 + - + +
804A PRO* 4.5 1.6 - - - +
806A ASP* 2.9 15.9 + - - +
877A TYR* 4.6 3.1 - - - -
878A TYR* 3.2 40.8 + - + +
879A GLN* 3.9 3.1 - - - -
880A GLN* 4.2 13.9 + - - +
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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