Contacts of the strand formed by residues 858 - 864 (chain A) in PDB entry 5E3H
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 858 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847A HIS* 3.8 16.4 - - + +
849A LYS* 3.3 21.5 - - + +
850A PRO* 3.5 22.3 - - - +
851A LYS 3.2 16.9 + - - +
853A PHE* 3.9 19.3 - - + -
857A GLU* 1.3 72.8 - - - +
859A ARG* 1.3 65.1 + - - +
875A ILE* 5.5 1.3 - - + -
877A VAL* 4.1 9.4 - - + -
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Residues in contact with ARG 859 (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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846A PRO* 3.7 16.5 - - - +
847A HIS* 3.7 14.8 + - - +
850A PRO* 5.4 11.9 - - - +
857A GLU* 3.4 28.0 + - - +
858A LYS* 1.3 82.0 - - - +
860A ALA* 1.3 65.7 + - + +
876A HIS* 3.5 17.7 + - + +
877A VAL* 4.5 4.5 - - - -
878A LYS* 3.6 41.1 - - - +
883A GLU* 5.3 1.1 - - - +
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Residues in contact with ALA 860 (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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844A SER* 4.1 18.8 - - - +
845A ARG 3.2 22.4 - - - +
846A PRO* 4.0 3.6 - - + -
847A HIS* 3.5 8.9 + - - -
859A ARG* 1.3 82.0 - - + +
861A LYS* 1.3 60.8 + - - +
875A ILE* 3.6 6.1 - - - +
876A HIS* 2.8 36.4 + - + +
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Residues in contact with LYS 861 (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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844A SER* 3.3 2.3 - - - -
845A ARG 2.8 30.0 + - - +
847A HIS* 3.7 22.7 + - + +
860A ALA* 1.3 73.5 - - - +
862A ILE* 1.3 60.8 + - - +
863A PHE* 3.2 27.9 - - + -
872A ASP* 4.4 7.2 - - - +
874A GLY 3.9 7.0 - - - +
875A ILE* 4.3 6.1 - - + +
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Residues in contact with ILE 862 (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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838A PHE* 5.3 1.6 - - + -
842A PHE* 3.5 39.0 - - + -
843A VAL 3.5 3.8 - - - -
844A SER* 4.5 1.1 - - - +
861A LYS* 1.3 73.1 - - - +
863A PHE* 1.3 69.0 + - - +
872A ASP* 3.7 8.1 - - - +
873A TRP* 3.4 33.9 + - + -
874A GLY* 2.7 22.3 + - - +
875A ILE 3.1 35.9 - - - +
876A HIS* 3.7 11.2 - - + +
885A PRO* 3.4 26.9 - - + -
886A VAL 4.1 4.5 - - - +
887A ILE* 5.2 4.7 - - + -
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Residues in contact with PHE 863 (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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842A PHE* 3.2 7.0 - - - +
843A VAL* 2.7 48.3 + - + +
844A SER* 4.6 1.6 - - - -
845A ARG* 4.1 35.2 - - + -
861A LYS* 3.2 46.7 - - + -
862A ILE* 1.3 76.6 - - - +
864A CYS* 1.3 61.9 + - - +
870A SER* 3.6 28.0 - - - +
871A HIS 3.4 5.4 - - - +
872A ASP* 4.1 19.3 - - + -
873A TRP* 4.7 2.0 - - - +
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Residues in contact with CYS 864 (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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813A CYS* 3.8 0.4 - - - -
815A ALA* 4.9 2.5 - - - -
841A CYS 4.2 1.1 - - - -
843A VAL* 4.1 7.0 - - - +
863A PHE* 1.3 74.5 - - - +
865A ALA* 1.3 64.9 + - - +
866A ARG* 3.5 22.0 - - - +
869A CYS* 3.7 1.1 - - - -
870A SER* 3.6 19.2 + - - +
871A HIS 3.0 22.4 + - - +
873A TRP* 3.5 32.3 - - - +
1001A ZN 2.3 37.2 - - - -
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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