Contacts of the strand formed by residues 800 - 806 (chain A) in PDB entry 4EJX
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 800 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709A TYR* 3.5 49.1 - - + +
711A GLY 2.6 17.6 + - - +
712A GLU* 3.4 19.7 + - + +
713A ARG 2.8 27.0 + - - +
799A ASP* 1.3 73.0 - - - +
801A VAL* 1.3 61.1 + - - +
802A LYS* 3.4 26.7 + - + +
839A VAL* 4.9 19.3 - - + -
840A TRP 3.8 6.5 - - - +
841A LYS* 5.3 0.2 - - + -
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Residues in contact with VAL 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A ARG* 4.0 16.6 - - - -
715A TYR* 4.3 14.6 - - + -
793A LEU* 5.3 4.9 - - + -
794A HIS 4.6 1.8 - - - +
795A ALA* 3.6 34.1 - - + -
799A ASP* 4.5 2.0 - - + -
800A LYS* 1.3 69.7 - - - +
802A LYS* 1.3 64.0 + - - +
803A ILE* 3.7 27.9 + - + -
840A TRP* 2.9 55.1 + - + +
842A ILE* 4.1 10.1 - - + -
878A LEU* 5.4 2.9 - - + -
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Residues in contact with LYS 802 (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 GLU 6.0 0.4 - - - -
713A ARG 2.8 21.2 + - - +
714A THR* 3.2 24.6 - - + +
715A TYR* 2.5 37.1 + - - +
800A LYS* 4.5 28.0 - - + +
801A VAL* 1.3 73.8 - - - +
803A ILE* 1.3 57.8 + - - +
804A ILE* 3.9 12.4 - - + +
837A THR* 4.8 15.3 - - + +
838A TYR 4.5 2.5 - - - -
839A VAL* 5.6 11.9 - - + -
840A TRP 5.4 0.2 - - - +
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Residues in contact with ILE 803 (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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715A TYR* 3.5 13.5 - - + -
717A ILE* 3.6 25.8 - - + -
793A LEU* 3.8 25.1 - - + -
801A VAL* 3.8 21.8 - - + -
802A LYS* 1.3 74.1 - - - +
804A ILE* 1.3 61.2 + - - +
805A PHE* 3.2 12.3 + - + +
815A ILE* 3.8 27.4 - - + -
837A THR* 3.6 3.0 - - - +
838A TYR* 3.2 33.7 + - + +
840A TRP* 3.8 32.3 - - + +
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Residues in contact with ILE 804 (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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714A THR* 3.5 32.8 - - + -
715A TYR 2.8 11.6 + - - +
716A TYR* 3.5 31.5 - - + +
717A ILE 4.0 1.5 - - - +
771A SER* 5.6 4.0 - - - -
773A PHE* 3.0 28.1 - - + -
802A LYS* 4.4 9.2 - - + +
803A ILE* 1.3 69.6 - - - +
805A PHE* 1.3 58.1 + - - +
835A THR* 4.3 17.0 - - + -
836A LEU 3.8 6.1 - - - +
837A THR* 3.7 28.5 - - + +
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Residues in contact with PHE 805 (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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717A ILE* 3.2 24.5 - - + -
718A ALA* 3.8 2.7 - - - -
719A ALA* 3.4 32.5 - - + -
765A TYR* 3.9 23.8 - + - -
803A ILE* 3.2 5.8 + - + -
804A ILE* 1.3 75.3 - - - +
806A LYS* 1.3 80.2 + - - +
807A ASN* 4.2 6.3 - - + -
813A TYR* 4.4 8.3 - - + -
814A SER* 4.5 0.4 - - - -
815A ILE* 3.8 26.5 - - + -
830A THR* 3.4 27.3 - - - +
835A THR* 3.3 21.5 - - - +
836A LEU 3.2 16.7 + - - +
838A TYR* 3.7 26.5 - + + -
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Residues in contact with LYS 806 (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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717A ILE 3.0 7.8 + - - +
718A ALA* 3.2 25.2 - - + +
719A ALA 3.2 5.0 + - - -
773A PHE* 3.8 32.5 - - + +
805A PHE* 1.3 83.6 - - - +
807A ASN* 1.3 60.9 + - - +
808A MET* 3.4 53.4 - - + +
830A THR* 6.1 0.2 - - - -
833A GLY* 3.8 31.3 - - - -
834A GLU 3.5 12.6 - - - +
835A THR* 4.4 9.9 - - - +
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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