Contacts of the helix formed by residues 863 - 874 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857A ALA* 4.3 1.1 - - - -
862A ILE* 1.3 77.9 - - - +
864A LYS* 1.3 62.0 + - - +
865A LYS* 3.1 43.6 + - + +
866A VAL* 2.9 40.3 + - + +
867A VAL* 3.7 4.5 + - - +
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Residues in contact with LYS 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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857A ALA* 4.2 16.2 - - + +
858A LYS* 3.2 40.9 - - - +
862A ILE 3.9 0.4 + - - +
863A ASP* 1.3 73.9 + - - +
865A LYS* 1.3 64.6 + - - +
866A VAL 3.0 2.2 - - - -
867A VAL* 3.0 14.9 - - - +
868A ALA 3.0 17.7 + - - -
779B PRO* 2.7 31.1 + - + +
780B LEU* 3.3 25.4 - - + +
781B GLU 5.6 0.8 + - - -
783B PRO* 5.8 5.5 - - - +
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Residues in contact with LYS 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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863A ASP* 3.1 26.4 + - + +
864A LYS* 1.3 78.3 - - - +
866A VAL* 1.3 57.7 + - + +
868A ALA* 3.7 4.0 - - + +
869A ASP* 2.9 44.3 + - - +
780B LEU* 3.5 18.6 - - + +
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Residues in contact with VAL 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A TYR* 4.0 29.1 - - + -
853A LEU* 4.5 2.7 - - + -
862A ILE* 4.2 22.9 - - + -
863A ASP* 2.9 38.0 + - + +
865A LYS* 1.3 79.6 - - + +
867A VAL* 1.3 56.7 + - - +
869A ASP* 3.6 7.1 + - - +
870A ALA* 3.2 23.9 + - - +
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Residues in contact with VAL 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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850A VAL* 4.5 14.1 - - + +
853A LEU* 4.1 21.5 - - + +
854A GLY* 4.5 4.0 - - - +
857A ALA* 3.9 19.1 - - + -
858A LYS* 4.3 1.8 - - - +
863A ASP 3.9 1.3 - - - +
864A LYS* 3.0 27.6 - - - +
866A VAL* 1.3 71.7 - - + +
868A ALA* 1.3 57.8 + - - +
869A ASP 3.1 2.0 - - - -
870A ALA* 3.1 8.4 + - - +
871A ILE* 2.8 38.2 + - + +
776B MET 4.4 6.1 - - - +
779B PRO* 3.3 30.3 - - + -
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Residues in contact with ALA 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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864A LYS 3.0 15.1 + - - +
865A LYS* 3.4 7.6 + - + +
867A VAL* 1.3 77.9 - - - +
869A ASP* 1.3 63.9 + - - +
871A ILE* 3.6 9.8 + - - +
872A ALA* 3.3 19.8 + - - +
779B PRO* 4.2 9.2 - - + -
780B LEU* 3.7 29.6 - - + -
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Residues in contact with ASP 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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865A LYS* 2.9 33.4 + - - +
866A VAL* 3.8 7.2 - - - +
868A ALA* 1.3 79.5 - - - +
870A ALA* 1.3 54.6 + - - +
871A ILE 3.2 0.2 - - - -
872A ALA* 3.3 6.3 + - - +
873A LYS* 2.7 35.8 + - - +
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Residues in contact with ALA 870 (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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749A TYR* 3.7 13.9 - - - +
850A VAL* 4.1 6.3 - - + -
853A LEU* 3.7 24.7 - - + -
866A VAL 3.2 14.6 + - - +
867A VAL* 3.1 9.5 + - - +
869A ASP* 1.3 74.3 - - - +
871A ILE* 1.3 56.9 + - - +
873A LYS* 3.9 7.4 - - - -
874A PHE* 2.7 52.6 + - + -
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Residues in contact with ILE 871 (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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850A VAL* 3.8 22.9 - - + -
867A VAL* 2.8 21.7 + - + +
868A ALA* 3.6 9.4 - - - +
870A ALA* 1.3 79.9 - - - +
872A ALA* 1.3 60.6 + - - +
875A ASN 3.5 1.6 + - - -
876A ILE* 3.0 60.6 + - + +
878A ALA* 4.5 11.2 - - + -
776B MET 4.0 7.2 - - - +
777B LEU* 3.5 28.7 - - + +
779B PRO* 3.7 21.8 - - + -
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Residues in contact with ALA 872 (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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868A ALA 3.3 10.9 + - - +
869A ASP* 3.3 10.2 + - - +
870A ALA 3.2 0.4 - - - -
871A ILE* 1.3 76.9 - - + +
873A LYS* 1.3 69.1 + - - +
875A ASN* 3.1 19.6 + - - +
876A ILE 5.2 0.9 - - - +
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Residues in contact with LYS 873 (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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748A ASP* 3.8 26.1 + - - +
749A TYR* 3.7 20.4 + - - +
869A ASP 2.7 22.6 + - - +
870A ALA* 3.4 3.6 - - - +
872A ALA* 1.3 75.7 - - - +
874A PHE* 1.3 81.0 + - + +
875A ASN* 3.3 11.1 + - - +
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Residues in contact with PHE 874 (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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744A ILE* 4.1 26.7 - - + -
748A ASP* 5.2 0.2 - - - -
749A TYR* 4.0 5.4 - - - -
839A HIS* 3.7 9.5 - - - -
846A SER* 3.5 28.6 + - - -
849A VAL* 3.6 34.5 - - + -
850A VAL* 3.9 11.7 - - + -
870A ALA* 2.7 44.6 + - + +
872A ALA 3.2 0.2 - - - -
873A LYS* 1.3 97.4 - - + +
875A ASN* 1.3 72.7 + - - +
876A ILE* 3.3 13.7 + - + +
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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