Contacts of the strand formed by residues 874 - 880 (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 LYS 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794A VAL* 4.2 15.3 - - + -
795A ASP 3.9 18.9 + - - +
796A VAL* 3.6 14.6 - - + -
797A ILE* 2.7 38.3 + - - +
865A LEU* 4.6 22.3 + - + +
868A PHE* 3.8 26.8 + - + +
869A LYS 4.0 14.6 + - - -
870A PRO* 4.3 15.9 + - - +
872A GLN 3.9 13.7 - - - +
873A PRO* 1.3 71.9 - - + +
875A LYS* 1.3 55.0 + - - +
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Residues in contact with LYS 875 (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* 4.4 0.8 - - - +
797A ILE* 3.1 24.2 - - + +
799A CYS* 4.8 8.7 - - - -
842A SER* 3.7 5.7 + - - -
865A LEU* 5.2 0.4 - - - +
868A PHE* 3.6 25.7 - - + -
873A PRO 4.9 2.9 - - - +
874A LYS* 1.3 76.0 - - - +
876A LEU* 1.3 70.2 + - - +
877A TYR* 5.3 12.1 - - + +
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Residues in contact with LEU 876 (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* 4.0 8.0 - - + +
797A ILE 2.8 9.3 + - - -
798A PHE* 3.1 39.1 - - + +
799A CYS 3.0 21.5 + - - -
822A VAL* 5.3 3.1 - - + -
839A PHE* 5.4 5.6 - - + -
840A PHE 4.3 8.7 - - - +
841A LYS* 5.7 0.4 - - - -
842A SER* 3.5 30.3 - - - +
861A LEU* 4.1 19.3 - - + -
864A LEU* 4.1 30.1 - - + +
865A LEU* 4.0 15.5 - - + -
875A LYS* 1.3 76.8 - - - +
877A TYR* 1.3 67.2 + - - +
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Residues in contact with TYR 877 (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* 3.1 42.1 - - + +
800A ASP 5.2 1.3 - - - -
801A LYS* 4.1 16.4 - - + -
839A PHE* 3.7 5.4 - - - -
840A PHE* 2.9 35.9 + - + +
841A LYS 5.8 0.4 - - - -
842A SER* 5.7 5.1 - - - -
847A ASP* 4.2 10.6 + - - +
848A GLY* 3.7 15.6 + - - -
849A PRO* 3.4 55.8 - - + +
875A LYS* 5.3 11.8 - - + +
876A LEU* 1.3 78.4 - - - +
878A TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 878 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798A PHE* 3.7 22.2 - - + -
799A CYS 3.0 19.6 + - - -
800A ASP* 3.2 47.7 + - + +
801A LYS 2.8 24.6 + - - -
806A ASP* 4.9 1.7 + - - -
809A PHE* 3.6 22.1 - + - -
826A VAL* 5.3 1.8 - - + -
830A LEU* 3.7 31.5 - - + +
837A LEU* 4.4 7.0 - - + -
838A GLN 3.3 13.9 - - - +
839A PHE* 3.9 22.2 - + + -
840A PHE* 3.9 5.8 - - - -
877A TYR* 1.3 75.8 - - - +
879A GLN* 1.3 71.3 + - - +
880A GLN* 4.2 9.6 + - + +
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Residues in contact with GLN 879 (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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800A ASP* 3.9 4.5 - - - -
801A LYS* 5.0 1.3 - - + +
802A THR* 3.8 29.9 - - + +
837A LEU* 3.7 4.5 - - - -
838A GLN* 2.5 69.0 + - + +
840A PHE* 3.5 21.4 - - + -
878A TYR* 1.3 86.0 - - - +
880A GLN* 1.3 64.1 + - - +
881A LEU* 4.2 11.1 - - + +
888A PHE* 4.0 10.7 - - - -
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Residues in contact with GLN 880 (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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800A ASP* 4.2 10.1 + - - +
802A THR* 5.4 1.2 + - - +
830A LEU* 3.4 31.5 + - - +
832A THR* 3.2 33.4 + - - +
836A LEU* 3.8 5.1 - - - +
837A LEU* 3.5 11.8 - - + +
878A TYR* 4.2 12.2 + - + +
879A GLN* 1.3 81.0 + - - +
881A LEU* 1.3 67.0 + - - +
882A LYS 4.2 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