Contacts of the strand formed by residues 862 - 869 (chain A) in PDB entry 5J67
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 GLU 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807A ARG* 3.8 10.4 - - + -
808A VAL 3.3 3.4 - - - +
809A ARG* 2.7 58.4 + - + -
861A SER* 1.3 73.7 - - - +
863A LEU* 1.3 58.6 - - - +
864A THR* 3.7 20.3 + - - +
927A GLU 4.1 0.7 - - - +
928A GLU* 3.5 6.0 - - - +
929A LYS* 2.8 62.2 + - + +
954A LEU* 4.0 20.3 - - + +
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Residues in contact with LEU 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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806A TRP* 3.9 8.3 - - + +
807A ARG* 3.3 4.6 - - - +
808A VAL* 2.9 32.4 + - + +
810A SER* 5.6 0.2 + - - -
861A SER 4.3 0.2 - - - -
862A GLU* 1.3 71.2 - - - +
864A THR* 1.3 62.1 + - - +
865A CYS* 3.7 28.3 - - - -
926A CYS* 3.9 13.7 - - + -
927A GLU 4.0 6.7 - - - +
928A GLU* 3.9 16.8 - - + +
938A LEU 4.7 4.0 - - - +
939A CYS* 3.8 42.1 - - + +
941A ARG* 4.0 28.0 - - + +
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Residues in contact with THR 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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805A GLN* 3.8 35.2 - - + +
806A TRP 3.5 2.9 - - - +
807A ARG* 3.7 13.6 - - + +
862A GLU* 3.7 18.7 + - - +
863A LEU* 1.3 74.1 - - - +
865A CYS* 1.3 61.7 + - - +
866A ILE* 5.3 6.2 - - + +
925A ARG 4.1 0.7 - - - +
926A CYS* 3.5 0.7 - - - -
927A GLU* 2.9 41.0 + - - +
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Residues in contact with CYS 865 (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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805A GLN* 3.4 3.6 - - - +
806A TRP* 2.7 42.1 + - + +
863A LEU* 3.7 22.0 - - - -
864A THR* 1.3 74.2 - - - +
866A ILE* 1.3 69.6 + - - +
867A ILE 4.2 0.2 - - - -
901A ILE* 3.6 26.2 - - + -
924A ILE* 4.5 0.7 - - + -
925A ARG 3.5 3.6 - - - -
926A CYS* 2.1 48.0 - - - -
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Residues in contact with ILE 866 (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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803A VAL* 4.1 13.5 - - + -
804A GLN 3.6 4.9 - - - +
805A GLN* 4.4 20.0 - - + +
864A THR* 5.3 6.1 - - + -
865A CYS* 1.3 81.8 - - - +
867A ILE* 1.3 69.5 + - - +
868A HIS* 3.3 35.7 - - + +
924A ILE* 3.5 2.1 - - - -
925A ARG* 2.9 35.5 + - + +
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Residues in contact with ILE 867 (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 LEU* 4.6 12.6 - - + -
803A VAL* 3.3 6.2 - - - +
804A GLN* 2.8 40.5 + - - +
806A TRP* 5.0 2.5 - - + -
866A ILE* 1.3 76.2 - - - +
868A HIS* 1.3 60.5 + - - +
869A PHE* 3.3 30.8 + - + -
900A PHE* 4.3 16.2 - - + -
901A ILE* 4.0 35.9 - - + -
904A LEU* 3.7 26.7 - - + -
922A VAL* 3.9 13.5 - - + -
923A GLU 3.6 4.9 - - - +
924A ILE* 4.2 8.5 - - + +
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Residues in contact with HIS 868 (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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784A ASP* 3.7 13.5 + - - -
802A MET 3.6 5.2 - - - +
803A VAL* 3.3 19.3 - - + +
866A ILE* 3.3 37.5 + - + +
867A ILE* 1.3 70.9 - - - +
869A PHE* 1.3 63.5 + - - +
921A GLY 3.9 2.9 - - - +
922A VAL* 3.4 6.1 - - - -
923A GLU* 2.7 46.4 + - + +
925A ARG* 4.0 25.3 - - + +
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Residues in contact with PHE 869 (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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801A PRO* 3.8 5.2 - - - +
802A MET* 2.9 41.1 + - + +
804A GLN* 3.5 35.2 - - + -
867A ILE* 3.3 33.7 - - + -
868A HIS* 1.3 75.6 - - - +
870A PRO* 1.4 67.6 - - + +
871A SER 3.9 15.7 - - - +
874A VAL* 4.7 0.7 - - + -
875A GLN* 3.7 36.1 - - + +
878A LEU* 4.2 13.5 - - + -
900A PHE* 3.8 16.8 - + - -
904A LEU* 3.9 11.0 - - + -
921A GLY 5.0 0.7 - - - -
922A VAL* 4.1 15.9 - - + -
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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