Contacts of the strand formed by residues 893 - 903 (chain A) in PDB entry 3IJE
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 893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783A ARG* 3.3 8.3 - - - +
784A ASN* 2.9 26.7 + - - +
889A LEU* 3.8 13.8 - - + +
890A ASP* 3.1 35.5 + - + +
891A ARG 3.9 5.8 - - - +
892A GLY* 1.3 86.6 - - - +
894A SER* 1.3 63.4 + - - +
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Residues in contact with SER 894 (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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781A GLU* 3.5 24.8 + - - -
782A LEU 3.1 17.7 - - - -
783A ARG* 3.0 23.4 + - - -
817A ASP 3.9 5.9 - - - +
818A GLY* 4.1 8.3 - - - -
819A PRO* 4.4 0.5 - - - +
889A LEU* 3.7 13.4 - - - +
893A LYS* 1.3 78.1 - - - +
895A ALA* 1.3 56.4 + - - +
896A ILE* 4.4 5.9 + - - +
594B TYR* 3.6 11.8 + - - -
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Residues in contact with ALA 895 (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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780A TYR 4.0 0.3 - - - +
781A GLU* 3.5 0.5 - - - +
782A LEU* 2.9 37.2 + - + +
817A ASP 3.2 7.9 - - - +
818A GLY* 4.6 0.7 - - - -
819A PRO* 4.6 6.1 - - + +
820A MET* 3.8 32.3 - - + -
886A VAL* 4.4 20.2 - - + -
889A LEU* 3.7 5.1 - - + +
894A SER* 1.3 71.7 - - - +
896A ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 896 (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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779A ILE* 3.5 25.6 - - + -
780A TYR 3.2 15.9 - - - +
781A GLU* 4.0 10.8 - - + -
815A ASP 3.7 0.2 - - - +
816A ILE* 3.3 5.9 - - - -
817A ASP* 2.7 56.5 + - + +
820A MET* 3.5 5.8 - - - +
894A SER* 4.5 5.8 - - - +
895A ALA* 1.3 84.8 - - - +
897A LEU* 1.3 58.5 + - - +
898A TYR* 3.6 26.8 + - + +
594B TYR* 3.9 12.3 - - - +
602B PRO* 3.8 21.3 - - + -
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Residues in contact with LEU 897 (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 HIS 3.5 3.3 - - - +
779A ILE* 3.5 2.8 - - - -
780A TYR* 2.8 49.6 + - + +
795A LEU* 4.5 13.2 - - + -
797A LEU* 4.2 17.7 - - + -
814A TYR* 3.8 33.9 - - + -
815A ASP 3.3 16.8 - - - +
816A ILE* 4.6 2.7 - - + -
820A MET* 4.0 6.8 - - + +
822A CYS* 4.4 13.7 - - - -
882A ILE* 4.5 9.2 - - + -
884A CYS* 4.4 14.1 - - - -
896A ILE* 1.3 71.8 - - - +
898A TYR* 1.3 63.8 + - - +
899A VAL* 3.7 19.0 + - + -
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Residues in contact with TYR 898 (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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777A GLN* 3.7 16.8 + - + +
778A HIS 4.2 1.8 - - - -
779A ILE* 3.5 34.8 - - + +
813A HIS 4.0 0.3 - - - +
814A TYR* 3.1 3.5 - - - -
815A ASP* 2.7 60.6 + - + +
816A ILE 4.7 1.1 - - - -
817A ASP* 3.4 32.9 + - + -
896A ILE* 3.6 31.8 - - + +
897A LEU* 1.3 71.7 - - - +
899A VAL* 1.3 62.9 + - - +
900A LYS* 3.7 1.9 + - - +
602B PRO* 4.0 11.4 - - + +
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Residues in contact with VAL 899 (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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776A VAL 3.6 1.7 - - - +
777A GLN* 3.6 4.2 - - - +
778A HIS* 2.9 44.6 + - + +
780A TYR* 4.9 2.0 - - + -
797A LEU* 4.0 15.3 - - + -
799A TRP* 3.6 31.0 - - + -
811A ILE* 4.1 25.8 - - + -
814A TYR* 4.1 8.5 - - + -
882A ILE* 4.7 2.9 - - + -
897A LEU* 3.9 30.5 - - + +
898A TYR* 1.3 71.9 - - - +
900A LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 900 (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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769A GLU* 3.3 27.9 + - - -
775A VAL* 3.5 33.6 - - + +
776A VAL 4.1 1.1 - - - -
777A GLN* 3.7 22.0 - - - +
811A ILE* 3.8 2.8 - - - +
812A LEU* 3.0 31.1 + - + +
813A HIS* 2.9 28.9 + - + +
836A SER* 3.6 26.7 + - - +
838A LEU* 4.1 27.0 - - + +
898A TYR 3.7 2.2 + - - +
899A VAL* 1.3 70.6 - - - +
901A SER* 1.3 58.3 + - - +
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Residues in contact with SER 901 (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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775A VAL* 3.3 5.7 - - - +
776A VAL* 2.6 61.3 + - - +
799A TRP* 3.6 32.6 - - - -
809A LEU* 3.7 6.9 - - - +
810A TYR 3.2 21.1 - - - -
811A ILE* 4.0 4.0 - - - +
812A LEU 4.2 0.4 - - - +
899A VAL* 3.7 0.4 + - - -
900A LYS* 1.3 75.1 - - - +
902A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 902 (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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769A GLU* 3.6 25.1 - - + +
772A VAL* 4.1 21.3 - - + -
773A GLY 3.8 14.4 - - - +
774A PRO 3.5 2.7 - - - +
775A VAL* 3.7 26.0 - - + -
809A LEU* 3.5 3.8 - - - -
810A TYR* 2.6 48.5 + - + +
812A LEU* 3.3 47.3 - - + -
833A ILE* 4.1 6.7 - - + -
901A SER* 1.3 82.0 - - - +
903A LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 903 (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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753A VAL* 4.0 27.8 - - + -
755A LEU* 5.3 2.2 - - + -
772A VAL* 3.0 21.4 - - - +
773A GLY* 3.4 6.8 - - - -
774A PRO* 3.1 24.0 + - + +
776A VAL* 4.6 3.8 - - + -
808A LEU 3.7 4.0 - - - +
809A LEU* 3.9 15.7 - - + +
901A SER 4.3 0.2 - - - -
902A LEU* 1.3 70.7 - - - +
904A TRP* 1.3 60.2 + - - +
905A THR* 3.1 33.8 + - + +
908A PHE* 3.3 26.5 - - + -
920A LEU* 4.9 2.5 - - + -
949A THR* 5.8 0.4 - - + -
951A VAL* 3.6 33.7 - - + -
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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