Contacts of the helix formed by residues 878 - 893 (chain A) in PDB entry 5A7R
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 878 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A TYR* 3.6 28.3 + - + +
835A GLN* 2.8 29.0 + - - +
836A PHE* 4.8 4.6 - - + -
872A CYS* 3.5 3.9 - - - -
877A GLY* 1.3 71.1 - - - -
879A ALA* 1.3 60.8 + - - +
880A ARG* 3.2 18.5 + - - +
881A LEU* 3.0 32.6 + - + +
882A LYS* 3.0 25.0 + - - +
951A LYS* 5.6 1.9 - - - -
952A LEU* 5.6 2.6 - - - +
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Residues in contact with ALA 879 (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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869A ASN* 4.0 11.0 - - - +
872A CYS* 3.5 19.6 - - + -
877A GLY 3.8 1.8 + - - -
878A ASP* 1.3 74.4 + - - +
880A ARG* 1.3 59.2 + - - +
882A LYS* 4.4 0.9 - - - +
883A ALA* 2.9 32.2 + - - +
899A TYR* 4.2 3.5 + - - +
907A LEU* 3.8 30.7 - - + +
1976A GOL 4.2 17.8 + - - +
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Residues in contact with ARG 880 (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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878A ASP* 3.2 14.3 + - - +
879A ALA* 1.3 79.4 - - - +
881A LEU* 1.3 62.3 + - - +
883A ALA* 4.7 0.2 - - - -
884A LEU* 3.3 10.9 + - - +
904A ASP* 5.0 4.9 + - - -
906A GLU* 4.1 12.5 - - - +
907A LEU* 3.7 46.8 - - + +
910A ASP* 3.0 31.8 + - + -
952A LEU* 5.6 2.5 - - + -
953A TYR* 2.7 63.1 + - + -
1976A GOL 6.0 1.8 - - - -
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Residues in contact with LEU 881 (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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835A GLN* 3.8 47.3 - - + +
836A PHE* 3.8 16.6 - - + -
841A MET* 4.2 10.8 - - + -
878A ASP* 3.0 19.0 + - + +
880A ARG* 1.3 75.4 - - - +
882A LYS* 1.3 68.9 + - + +
884A LEU* 3.2 4.7 + - + +
885A ILE* 3.0 43.6 + - + +
932A LEU* 4.2 15.5 - - + -
952A LEU* 3.8 27.2 - - + +
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Residues in contact with LYS 882 (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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826A ALA* 4.0 10.0 - - - +
827A LEU 4.9 0.2 + - - -
829A PHE* 3.9 18.6 - - - -
835A GLN* 5.0 3.0 + - - +
844A GLU* 3.0 31.7 + - + +
869A ASN 5.8 0.2 - - - -
870A TRP* 3.5 57.9 + - + +
871A GLY* 4.6 5.9 + - - -
872A CYS* 3.8 13.5 - - - -
877A GLY* 4.9 3.0 - - - -
878A ASP 3.0 16.2 + - - +
879A ALA 4.1 1.3 - - - +
881A LEU* 1.3 80.3 - - + +
883A ALA* 1.3 63.7 + - - +
885A ILE* 3.6 15.8 - - + +
886A GLN* 2.9 32.7 + - - +
899A TYR* 5.8 1.1 - - - +
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Residues in contact with ALA 883 (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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879A ALA 2.9 20.2 + - - +
880A ARG 4.0 3.6 - - - +
882A LYS* 1.3 77.2 - - - +
884A LEU* 1.3 58.1 + - - +
886A GLN* 3.2 4.4 + - - +
887A ILE* 2.9 34.8 + - + +
899A TYR* 3.7 23.0 + - + -
911A ILE* 3.6 38.1 - - + -
953A TYR* 4.2 1.3 - - - +
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Residues in contact with LEU 884 (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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880A ARG 3.3 6.6 + - - +
881A LEU* 3.2 9.9 + - - +
883A ALA* 1.3 77.7 - - - +
885A ILE* 1.3 58.6 + - + +
887A ILE* 3.2 23.0 + - + +
888A LEU* 2.9 38.7 + - + +
914A MET* 4.7 8.1 - - + -
915A HIS* 6.4 0.4 - - - -
918A LEU* 4.0 22.7 - - + -
928A VAL* 4.1 21.1 - - + -
932A LEU* 4.3 16.4 - - + -
952A LEU* 4.6 2.2 - - + -
953A TYR* 4.2 21.7 + - + +
956A ILE* 3.7 29.8 - - + -
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Residues in contact with ILE 885 (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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841A MET* 4.3 17.0 - - + +
844A GLU* 3.9 28.3 - - + +
845A LEU* 3.5 45.6 - - + +
848A ALA* 5.0 1.3 - - + -
870A TRP* 4.7 8.3 - - + -
881A LEU* 3.0 45.1 + - + +
882A LYS* 3.6 14.6 - - + +
883A ALA 3.3 0.2 - - - -
884A LEU* 1.3 75.6 - - - +
886A GLN* 1.3 63.8 + - - +
888A LEU* 3.3 2.5 + - - -
889A ALA* 3.0 20.3 + - - +
932A LEU* 4.7 9.6 - - + -
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Residues in contact with GLN 886 (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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736A VAL* 4.8 2.3 - - - +
824A ILE* 5.3 0.5 - - - +
848A ALA* 4.8 1.6 - - + -
852A PHE* 3.8 22.7 - - + -
867A THR* 2.6 35.4 + - + +
868A GLY 3.0 25.9 + - - -
870A TRP* 3.8 37.6 - - + +
882A LYS* 2.9 24.2 + - - +
883A ALA* 3.7 3.8 - - - +
885A ILE* 1.3 76.4 - - - +
887A ILE* 1.3 59.7 + - + +
889A ALA* 4.5 4.5 - - - -
890A ALA* 2.9 30.7 + - - +
897A VAL* 4.6 4.0 - - + +
899A TYR* 4.0 11.7 - - + -
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Residues in contact with ILE 887 (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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715A LEU* 4.1 23.3 - - + -
716A THR* 5.0 2.9 + - - +
718A LEU* 4.6 6.7 - - + -
883A ALA* 2.9 23.3 + - + +
884A LEU* 3.5 19.3 - - + +
886A GLN* 1.3 77.7 - - + +
888A LEU* 1.3 56.9 + - - +
890A ALA* 3.9 1.7 - - - +
891A ALA* 3.0 27.4 + - - +
897A VAL* 4.5 24.6 - - + +
899A TYR* 6.0 2.5 - - + -
911A ILE* 4.1 25.8 - - + +
915A HIS* 4.1 36.8 - - + +
953A TYR* 6.1 0.2 - - - +
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Residues in contact with LEU 888 (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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708A TRP* 4.0 4.3 - - + -
715A LEU* 3.8 22.0 - - + -
845A LEU* 3.7 24.2 - - + -
884A LEU* 2.9 27.4 + - + +
887A ILE* 1.3 72.8 - - - +
889A ALA* 1.3 65.4 + - - +
891A ALA* 3.3 6.0 + - - +
892A ALA* 3.0 23.6 + - - +
925A VAL* 4.0 23.1 - - + +
928A VAL* 3.8 40.6 - - + -
929A TYR* 4.2 15.5 - - + +
932A LEU* 4.3 15.3 - - + -
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Residues in contact with ALA 889 (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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708A TRP* 4.1 11.0 - - + -
845A LEU* 3.8 9.8 - - + +
848A ALA* 3.7 29.6 - - + -
849A TYR* 3.7 18.3 - - + +
852A PHE* 4.0 4.7 - - + -
885A ILE 3.0 15.9 + - - +
886A GLN 3.4 2.9 + - - +
888A LEU* 1.3 76.3 - - - +
890A ALA* 1.3 57.5 + - - +
892A ALA* 3.3 3.3 + - - +
893A ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 890 (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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716A THR* 4.6 0.2 - - - +
852A PHE* 3.7 18.1 - - + -
865A VAL* 4.9 2.7 - - + -
886A GLN 2.9 18.1 + - - +
887A ILE 3.9 2.0 - - - +
889A ALA* 1.3 73.8 - - - +
891A ALA* 1.3 60.9 + - - +
893A ALA* 3.2 3.9 + - - +
894A GLU 2.8 23.9 + - - -
895A ARG* 2.9 27.5 + - + +
897A VAL* 3.5 27.8 - - + -
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Residues in contact with ALA 891 (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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713A LYS* 3.9 9.0 - - - +
714A PRO 3.6 20.9 - - - +
715A LEU* 4.0 14.4 - - + -
716A THR* 3.9 16.4 + - - +
887A ILE 3.0 18.4 + - - +
888A LEU 3.3 6.0 + - - +
890A ALA* 1.3 77.5 - - - +
892A ALA* 1.3 58.0 + - - +
894A GLU* 3.0 23.9 + - - +
925A VAL* 3.7 15.7 - - + -
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Residues in contact with ALA 892 (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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706A PRO* 4.7 5.2 - - + -
708A TRP* 3.8 21.5 - - + -
711A CYS* 4.8 9.9 - - - -
713A LYS* 3.3 32.9 + - + -
849A TYR* 3.8 22.5 + - + -
853A LEU* 5.1 1.6 - - - +
888A LEU 3.0 16.0 + - - +
889A ALA 3.7 4.7 - - - +
891A ALA* 1.3 74.8 - - - +
893A ALA* 1.3 59.9 + - - +
925A VAL* 4.5 1.9 - - + +
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Residues in contact with ALA 893 (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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849A TYR* 4.0 5.4 - - + -
852A PHE* 3.9 34.3 - - + +
853A LEU* 4.1 23.1 - - + +
862A LEU* 3.8 11.1 - - - +
889A ALA 3.0 16.5 + - - +
890A ALA 3.2 4.0 + - - +
892A ALA* 1.3 74.3 - - - +
894A GLU* 1.3 70.3 + - - +
895A ARG* 3.5 9.4 + - + +
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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