Contacts of the strand formed by residues 896 - 905 (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 GLU 896 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A GLU 4.7 1.2 - - - +
785A HIS* 3.5 10.0 - - - -
792A GLN* 4.1 13.3 - - - +
794A HIS* 3.4 19.5 + - - -
855A CYS* 4.0 2.1 - - - -
879A ILE* 3.9 2.9 - - - +
885A TYR* 2.7 36.5 + - - -
894A LYS* 3.1 16.4 + - + +
895A LEU* 1.3 73.6 - - - +
897A PHE* 1.3 71.2 + - - +
962A ASN* 3.8 7.9 - - + -
964A TYR* 2.5 38.2 + - + +
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Residues in contact with PHE 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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782A GLU* 3.9 10.1 - - - -
785A HIS* 3.3 33.9 - + + +
792A GLN* 4.8 0.2 - - - -
895A LEU* 3.6 19.7 - - + -
896A GLU* 1.3 79.3 - - - +
898A ALA* 1.3 55.6 + - - +
899A LEU* 4.3 0.9 - - + -
952A GLY 4.1 7.4 - - - -
953A LEU* 3.6 22.2 - - + -
954A THR 3.6 29.2 - - - -
955A MET* 3.9 15.0 - - + -
961A VAL* 3.6 31.9 - - + -
962A ASN 2.8 13.2 + - - +
963A TRP* 3.4 23.4 - + + -
964A TYR* 2.6 38.9 + - - -
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Residues in contact with ALA 898 (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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785A HIS* 3.1 18.1 + - - +
786A LEU* 5.0 4.0 - - + -
789A LEU* 4.7 6.0 - - + +
792A GLN* 4.1 18.8 - - - +
877A PRO* 4.1 26.9 - - + -
897A PHE* 1.3 74.1 - - - +
899A LEU* 1.3 55.7 + - - +
943A ASN* 2.7 29.1 + - - +
964A TYR* 3.2 12.8 - - + +
966A MET* 5.5 2.0 - - - -
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Residues in contact with LEU 899 (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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785A HIS* 4.9 2.2 - - + +
789A LEU* 4.9 0.7 - - - -
897A PHE 5.2 0.4 - - - -
898A ALA* 1.3 76.9 - - - +
900A LEU* 1.3 61.4 + - - +
901A PHE* 3.8 19.0 + - + -
942A ILE* 3.9 4.0 - - + -
943A ASN* 3.3 19.5 - - - +
950A LEU* 3.9 19.7 - - + -
953A LEU* 4.5 17.0 - - + -
963A TRP* 3.6 34.5 - - + -
964A TYR 2.7 9.3 + - - -
965A LEU* 3.4 20.1 - - + -
966A MET* 2.9 26.3 + - - -
979A PHE* 5.0 1.1 - - + -
1019A LEU* 4.1 24.9 - - + -
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Residues in contact with LEU 900 (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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789A LEU* 3.5 36.0 - - + +
875A ILE* 3.9 20.9 - - + -
899A LEU* 1.3 71.4 - - - +
901A PHE* 1.3 60.5 + - - +
902A LEU* 3.7 13.4 + - + -
904A PHE* 3.5 36.6 - - + -
941A ALA 3.8 0.7 - - - +
942A ILE* 3.1 7.8 - - - -
943A ASN* 2.6 35.5 + - - +
966A MET* 3.6 22.2 - - + +
968A MET* 4.0 31.6 - - + +
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Residues in contact with PHE 901 (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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899A LEU* 3.8 24.0 - - + -
900A LEU* 1.3 74.3 - - - +
902A LEU* 1.3 60.8 + - - +
942A ILE* 3.6 47.3 - - + +
965A LEU* 4.3 6.3 - - + -
966A MET 3.0 18.9 + - - +
967A GLY* 4.2 1.9 - - - -
968A MET 3.9 11.6 + - - +
975A HIS* 3.0 38.0 - - + -
977A VAL* 3.5 47.8 - - + -
999A ILE* 4.2 5.6 - - + -
1019A LEU* 4.0 9.2 - - + -
1021A CYS* 4.3 16.6 - - + -
1031A MET* 4.3 10.1 - - - -
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Residues in contact with LEU 902 (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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870A LEU* 4.7 10.1 - - + +
871A TYR* 3.5 14.4 - - + -
875A ILE* 6.1 2.2 - - + -
900A LEU* 3.7 22.8 + - + -
901A PHE* 1.3 75.6 - - - +
903A VAL* 1.3 80.4 + - - +
904A PHE* 3.3 43.0 + - + -
941A ALA 3.1 25.2 + - - +
968A MET* 3.3 28.7 - - + +
969A GLY* 3.5 12.6 - - - +
973A ASP* 3.4 14.6 - - - +
975A HIS* 3.9 0.8 + - - -
1031A MET* 4.0 7.2 - - - +
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Residues in contact with VAL 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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871A TYR* 3.4 5.4 - - - -
902A LEU* 1.3 80.4 - - - +
904A PHE* 1.3 58.7 + - - +
905A ASP* 3.2 9.3 + - + +
938A LYS* 3.9 33.0 - - + +
939A MET 4.1 3.4 - - - -
940A HIS* 3.9 33.4 - - + +
972A ILE* 4.2 19.5 - - + +
973A ASP* 2.6 30.0 + - - +
975A HIS* 3.6 18.8 - - + -
1026A HIS* 4.1 7.6 - - - +
1031A MET* 4.2 2.2 - - + -
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Residues in contact with PHE 904 (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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726A TYR* 3.5 30.7 - + + +
762A LYS* 4.5 12.1 - - - -
788A ILE* 3.8 25.6 - - + -
870A LEU 4.0 16.6 - - - -
871A TYR* 4.0 8.7 - - - +
873A GLY* 4.9 3.8 - - - -
875A ILE* 5.0 4.0 - - + -
900A LEU* 3.5 31.2 - - + -
902A LEU* 3.3 35.4 + - + -
903A VAL* 1.3 67.2 - - - +
905A ASP* 1.3 61.0 + - - +
906A GLU* 3.1 9.1 + - - +
937A ASN 3.4 0.2 - - - +
938A LYS* 3.4 1.5 - - - -
939A MET* 3.0 41.8 + - - +
941A ALA* 3.8 17.9 - - + -
944A GLY* 4.3 9.4 - - - -
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Residues in contact with ASP 905 (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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684A ASP* 5.5 0.7 - - - +
871A TYR* 3.4 45.1 - - + +
903A VAL* 3.2 7.0 + - + +
904A PHE* 1.3 67.8 - - - +
906A GLU* 1.3 60.0 + - - +
907A ASN* 3.1 29.0 + - - +
908A GLU* 2.9 35.7 + - - +
934A ILE* 5.1 0.2 - - - +
937A ASN 3.9 1.6 - - - -
938A LYS* 3.5 32.2 - - + +
970A ASN* 5.0 7.8 + - - +
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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