Contacts of the helix formed by residues 863 - 874 (chain B) in PDB entry 1L8A
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 ASP 863 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857B ALA* 4.2 1.1 - - - +
862B ILE* 1.3 74.9 - - - +
864B LYS* 1.3 81.4 + - - +
865B LYS* 3.0 41.9 + - - +
866B VAL* 2.9 39.6 + - + +
867B VAL* 3.7 5.5 + - - +
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Residues in contact with LYS 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A PRO* 3.8 22.1 + - + +
780A LEU* 3.3 32.9 + - + +
781A GLU 5.2 4.8 + - - -
857B ALA* 4.1 26.0 - - + +
862B ILE 3.7 1.4 + - - +
863B ASP* 1.3 81.6 + - - +
865B LYS* 1.3 60.5 + - - +
867B VAL* 3.2 7.6 + - - +
868B ALA 3.0 18.2 + - - -
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Residues in contact with LYS 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A LEU* 4.0 11.2 - - + +
863B ASP* 3.0 26.9 + - - +
864B LYS* 1.3 79.4 - - - +
866B VAL* 1.3 52.1 + - + +
868B ALA* 3.3 6.4 + - + +
869B ASP* 2.7 49.8 + - - +
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Residues in contact with VAL 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B TYR* 3.7 34.0 - - + -
853B LEU* 4.3 10.8 - - + -
862B ILE* 5.0 9.6 - - + -
863B ASP* 2.9 32.5 + - + +
865B LYS* 1.3 78.8 - - + +
867B VAL* 1.3 59.1 + - + +
869B ASP* 3.4 8.1 + - - +
870B ALA* 2.9 26.7 + - - +
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Residues in contact with VAL 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A MET 4.7 2.0 - - - +
779A PRO* 3.8 22.4 - - + -
850B VAL* 3.8 35.0 - - + +
853B LEU* 3.6 32.1 - - + +
854B GLY* 3.9 7.6 - - - +
857B ALA* 3.7 20.6 - - + -
862B ILE* 4.6 2.2 - - + -
863B ASP 4.0 3.4 - - - +
864B LYS* 3.2 9.1 + - - +
866B VAL* 1.3 74.3 - - - +
868B ALA* 1.3 65.6 + - - +
870B ALA* 3.1 6.8 + - - +
871B ILE* 3.0 23.4 + - + +
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Residues in contact with ALA 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A PRO* 3.8 11.4 - - + +
780A LEU* 3.7 30.1 - - + -
864B LYS 3.0 12.4 + - - +
865B LYS* 3.6 9.4 - - + +
867B VAL* 1.3 76.5 - - - +
869B ASP* 1.3 64.8 + - - +
871B ILE* 3.4 9.4 + - - +
872B ALA* 3.2 19.8 + - - +
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Residues in contact with ASP 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B LYS* 2.7 37.6 + - - +
866B VAL* 3.7 7.2 + - - +
868B ALA* 1.3 78.4 - - - +
870B ALA* 1.3 55.3 + - - +
872B ALA* 3.2 9.0 + - - +
873B LYS* 2.7 34.9 + - - +
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Residues in contact with ALA 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B TYR* 3.6 23.1 - - - +
850B VAL* 4.1 6.7 - - + -
853B LEU* 3.8 17.5 - - + -
866B VAL 2.9 13.9 + - - +
867B VAL* 3.4 9.2 - - - +
869B ASP* 1.3 72.9 - - - +
871B ILE* 1.3 68.7 + - - +
873B LYS* 3.0 5.1 + - - +
874B PHE* 2.8 41.6 + - + -
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Residues in contact with ILE 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777A LEU* 3.6 16.2 - - + +
779A PRO* 3.5 34.1 - - + -
850B VAL* 3.7 33.2 - - + -
867B VAL 3.0 16.8 + - - +
868B ALA* 3.5 9.6 - - - +
869B ASP 3.3 0.2 - - - -
870B ALA* 1.3 77.4 - - - +
872B ALA* 1.3 60.7 + - - +
874B PHE 3.8 0.2 + - - -
875B ASN* 3.4 1.0 + - - -
876B ILE* 3.0 63.3 + - + +
878B ALA* 4.6 10.5 - - + -
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Residues in contact with ALA 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868B ALA 3.2 12.4 + - - +
869B ASP* 3.4 12.3 - - - +
870B ALA 3.0 0.6 - - - -
871B ILE* 1.3 77.0 - - - +
873B LYS* 1.3 65.6 + - - +
875B ASN* 3.1 20.8 + - - +
876B ILE 5.6 0.2 - - - -
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Residues in contact with LYS 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B ASP* 3.3 26.5 + - - +
749B TYR* 2.9 35.6 + - - -
869B ASP 2.7 19.0 + - - +
870B ALA* 3.6 2.7 - - - +
872B ALA* 1.3 74.7 - - - +
874B PHE* 1.3 79.4 + - + +
875B ASN* 3.3 11.4 + - - +
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Residues in contact with PHE 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744B ILE* 4.1 22.7 - - + -
748B ASP* 5.4 0.7 - - - -
749B TYR* 4.0 2.5 - - - -
839B HIS* 3.6 14.0 - - - -
846B SER* 3.5 37.1 + - - -
849B VAL* 3.6 36.6 - - + -
850B VAL* 4.0 4.3 - - + -
870B ALA* 2.8 39.0 + - + +
873B LYS* 1.3 99.5 - - + +
875B ASN* 1.3 71.9 + - - +
876B ILE* 3.3 8.5 + - + -
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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