Contacts of the helix formed by residues 844 - 859 (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 844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737A HIS* 4.7 12.8 - - + -
835A GLU 4.8 1.0 - - - +
838A ARG* 3.1 26.9 + - + +
839A HIS* 2.6 36.3 + - - +
842A GLU 3.8 0.2 - - - -
843A VAL* 1.3 81.8 - - - +
845A ALA* 1.3 66.7 + - - +
846A SER* 2.7 24.9 + - - -
847A TYR* 3.0 18.5 + - - -
848A VAL* 3.1 12.7 + - - +
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Residues in contact with ALA 845 (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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737A HIS* 3.5 28.3 + - + +
740A GLU* 3.3 35.2 - - + +
741A ALA* 3.6 12.3 - - - +
744A ILE* 4.4 6.3 - - + -
844A ASP* 1.3 75.1 - - - +
846A SER* 1.3 57.6 + - - +
848A VAL* 3.2 1.8 + - - -
849A VAL* 2.9 35.8 + - - +
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Residues in contact with SER 846 (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* 5.7 1.3 - - - -
839A HIS* 3.4 21.2 - - - -
844A ASP* 2.7 21.6 + - - -
845A ALA* 1.3 79.0 - - - +
847A TYR* 1.3 58.4 + - - +
849A VAL* 3.6 4.9 + - - +
850A VAL* 3.1 32.2 + - - +
874A PHE* 3.5 41.6 - - - -
876A ILE* 3.9 2.9 - - - +
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Residues in contact with TYR 847 (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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823A LEU* 3.6 6.7 - - + +
839A HIS* 3.3 46.6 + + - -
842A GLU* 3.5 56.4 + - + +
844A ASP* 3.0 31.1 + - - +
846A SER* 1.3 76.1 + - - +
848A VAL* 1.3 62.0 + - - +
850A VAL* 3.3 4.1 + - + +
851A ALA* 2.8 30.5 + - - +
876A ILE* 3.6 37.2 - - + +
877A ASP 4.3 1.6 + - - -
880A LYS* 4.0 16.6 - - - +
776B MET* 4.7 10.0 - - + +
777B LEU* 4.5 13.7 - - + -
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Residues in contact with VAL 848 (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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728A LEU* 3.8 24.5 - - + -
737A HIS 5.0 0.2 - - - +
738A VAL* 4.3 20.6 - - + +
741A ALA* 3.6 23.3 - - + -
745A LEU* 5.6 0.2 - - + -
798A VAL* 4.1 11.1 - - + +
800A SER* 3.8 28.7 - - - -
823A LEU* 3.8 10.1 - - + -
843A VAL 4.0 3.4 - - - +
844A ASP 3.1 16.0 + - - +
845A ALA* 3.6 1.3 - - - +
847A TYR* 1.3 75.4 - - - +
849A VAL* 1.3 58.2 + - - +
851A ALA* 3.2 3.9 + - - +
852A ALA* 2.8 28.2 + - - +
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Residues in contact with VAL 849 (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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741A ALA* 3.6 31.4 - - + +
744A ILE* 3.9 16.6 - - + -
745A LEU* 4.1 13.9 - - + -
749A TYR* 4.1 7.6 - - + -
845A ALA 2.9 22.0 + - - +
846A SER* 3.7 5.6 - - - +
848A VAL* 1.3 75.4 - - - +
850A VAL* 1.3 58.5 + - - +
852A ALA* 3.1 7.1 + - - +
853A LEU* 2.9 48.4 + - + +
874A PHE* 3.6 26.0 - - + -
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Residues in contact with VAL 850 (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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821A ARG* 3.9 0.9 + - - -
846A SER 3.1 17.7 + - - +
847A TYR* 3.8 5.4 - - + +
849A VAL* 1.3 79.2 - - - +
851A ALA* 1.3 60.0 + - - +
853A LEU* 3.5 7.8 + - - +
854A GLY* 3.0 24.8 + - - -
867A VAL* 4.5 6.8 - - + +
870A ALA* 4.1 5.2 - - + -
871A ILE* 3.8 33.7 - - + +
874A PHE* 3.9 14.8 - - + -
876A ILE* 3.7 19.5 - - + -
776B MET* 4.1 25.7 - - - +
777B LEU* 4.8 5.2 - - + -
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Residues in contact with ALA 851 (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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798A VAL* 3.9 21.3 - - + -
821A ARG* 2.9 35.0 + - + +
823A LEU* 4.5 6.3 - - + -
847A TYR 2.8 18.1 + - - +
848A VAL* 3.5 5.2 - - - +
849A VAL 3.2 0.2 - - - -
850A VAL* 1.3 76.6 - - - +
852A ALA* 1.3 63.2 + - - +
854A GLY 3.3 0.9 + - - -
855A GLU* 3.2 14.4 - - - +
776B MET* 3.9 18.6 - - + -
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Residues in contact with ALA 852 (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 VAL* 4.5 14.3 - - + +
728A LEU* 4.6 2.7 - - + -
745A LEU* 3.7 30.3 - - + -
798A VAL* 3.7 16.3 - - + +
848A VAL 2.8 17.3 + - - +
849A VAL 3.5 4.0 - - - +
851A ALA* 1.3 76.5 - - - +
853A LEU* 1.3 62.9 + - - +
855A GLU* 3.2 17.0 + - - +
856A LEU* 3.3 17.0 + - - +
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Residues in contact with LEU 853 (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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745A LEU* 3.7 21.3 - - + -
749A TYR* 3.8 40.4 - - + -
751A VAL* 4.7 7.6 - - + -
849A VAL* 2.9 24.7 + - + +
850A VAL* 3.9 4.3 - - - +
852A ALA* 1.3 75.8 - - - +
854A GLY* 1.3 58.0 + - - +
856A LEU* 3.3 3.3 + - + -
857A ALA* 2.9 27.8 + - - +
862A ILE* 3.1 29.0 - - + +
866A VAL* 4.4 6.7 - - + +
867A VAL* 4.1 10.1 - - + -
870A ALA* 3.7 29.8 - - + -
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Residues in contact with GLY 854 (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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821A ARG* 3.3 22.4 - - - -
850A VAL 3.0 12.9 + - - -
851A ALA 3.3 0.2 + - - -
852A ALA 3.1 0.6 - - - -
853A LEU* 1.3 77.8 - - - +
855A GLU* 1.3 57.7 + - - +
857A ALA* 4.5 0.2 - - - -
858A LYS* 2.9 49.4 + - - +
867A VAL* 4.6 6.5 - - - -
776B MET 5.8 0.9 - - - -
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Residues in contact with GLU 855 (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 VAL* 4.8 1.7 - - - +
796A PRO* 3.5 28.7 - - + +
797A ALA 2.9 24.2 + - - +
798A VAL* 3.2 23.6 - - - +
819A ASP* 2.9 34.5 - - + +
821A ARG* 3.3 22.6 + - - +
851A ALA 3.2 12.7 - - - +
852A ALA* 3.2 6.7 + - - +
854A GLY* 1.3 74.7 - - - +
856A LEU* 1.3 66.4 + - - +
858A LYS* 3.3 7.0 + - - +
859A ARG* 3.1 28.4 + - - +
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Residues in contact with LEU 856 (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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723A LYS 4.8 0.7 - - - +
724A GLY* 4.3 9.0 - - - -
725A LYS 4.1 4.5 - - - +
726A VAL* 3.9 17.5 - - + -
751A VAL* 3.4 42.8 - - + -
796A PRO* 4.1 16.2 - - + -
852A ALA 3.3 12.0 + - - +
853A LEU* 3.3 9.6 + - + +
855A GLU* 1.3 79.1 - - - +
857A ALA* 1.3 58.4 + - - +
859A ARG* 3.4 2.8 + - - +
860A GLY 3.3 2.4 + - - -
861A GLU* 2.8 59.9 + - + +
862A ILE* 3.3 21.0 + - + -
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Residues in contact with ALA 857 (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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853A LEU 2.9 17.6 + - - +
854A GLY 3.8 4.9 - - - +
855A GLU 3.2 0.2 - - - -
856A LEU* 1.3 74.8 - - - +
858A LYS* 1.3 66.9 + - + +
859A ARG 3.0 1.6 - - - -
860A GLY* 2.8 20.1 + - - -
862A ILE* 3.3 26.3 - - + +
863A ASP 4.2 3.6 - - - +
864A LYS* 4.2 15.3 - - + +
867A VAL* 3.9 19.5 - - + -
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Residues in contact with LYS 858 (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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819A ASP* 5.8 2.2 - - - +
821A ARG* 3.7 18.5 - - - +
854A GLY* 2.9 36.1 + - - +
855A GLU* 3.3 8.5 + - - +
857A ALA* 1.3 84.5 - - - +
859A ARG* 1.3 59.7 + - + +
860A GLY 3.2 1.1 + - - -
864A LYS* 3.2 36.0 - - - +
867A VAL* 4.3 0.4 - - - +
775B ASN 5.5 1.8 - - - -
776B MET* 5.4 3.8 - - - +
779B PRO* 3.6 24.0 - - - +
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Residues in contact with ARG 859 (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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725A LYS 5.4 0.2 + - - -
794A ASP* 4.4 3.6 + - - -
795A ALA* 4.8 1.4 - - - +
796A PRO* 3.1 45.2 - - - +
818A ASP* 3.2 26.1 + - - +
819A ASP* 5.6 1.6 - - - -
855A GLU* 3.1 19.5 + - - +
856A LEU* 3.6 5.2 - - - +
857A ALA 3.0 0.6 - - - -
858A LYS* 1.3 77.3 - - + +
860A GLY* 1.3 58.5 + - - +
861A GLU* 2.6 60.3 + - - +
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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