Contacts of the helix formed by residues 871 - 888 (chain A) in PDB entry 5V4R
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 ARG 871 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A ALA* 4.6 19.5 + - + +
869A GLY* 4.5 10.1 - - - +
870A TYR* 1.3 72.8 - - - +
872A TYR* 1.3 65.8 + - - +
873A GLY 3.2 3.4 - - - -
874A LEU* 3.1 24.7 + - + +
875A GLU* 2.8 44.4 + - - +
878A PHE* 5.0 1.8 - - - -
904A ASP* 2.8 32.1 + - - -
907A ALA* 6.0 1.6 - - - +
909A GLN* 3.6 31.2 + - - +
911A TYR* 4.4 12.7 - - - +
869B GLY 5.0 1.3 - - - -
871B ARG* 3.7 32.6 - - - +
875B GLU* 5.1 0.6 + - - -
909B GLN* 3.2 14.3 + - - +
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Residues in contact with TYR 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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836A ASN* 3.3 47.3 - - + +
839A PHE* 4.2 3.1 - - + -
840A ARG* 3.5 24.0 - - - +
870A TYR* 3.5 2.6 - - + -
871A ARG* 1.3 76.0 - - - +
873A GLY* 1.3 58.3 + - - +
875A GLU* 3.2 18.4 + - - +
876A CYS* 2.8 46.0 + - - -
879A ARG* 3.7 18.3 + - - -
908B GLY 5.5 4.2 + - - +
909B GLN* 4.2 4.4 + - - +
910B LEU* 3.5 45.2 - - + +
911B TYR* 5.8 0.4 - - - -
914B GLU* 2.9 29.8 + - - -
941B PHE* 5.6 0.5 - - - -
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Residues in contact with GLY 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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839A PHE* 3.6 42.2 - - - -
858A PHE* 3.8 2.3 - - - -
862A ALA* 3.4 16.2 - - - +
865A ASP* 5.3 0.6 + - - -
870A TYR 4.5 3.6 + - - -
871A ARG 3.2 0.8 - - - -
872A TYR* 1.3 79.2 - - - +
874A LEU* 1.3 56.5 + - - +
876A CYS* 3.3 4.7 + - - +
877A LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 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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862A ALA* 3.7 11.5 + - + +
863A LEU* 3.9 20.4 - - + -
866A ALA* 3.9 23.6 - - + -
871A ARG* 3.1 36.5 + - + +
873A GLY* 1.3 72.8 - - - +
875A GLU* 1.3 61.5 + - - +
877A LEU* 3.2 23.6 + - + -
878A PHE* 2.9 60.1 + - + -
900A GLU* 5.2 2.7 - - + -
904A ASP* 3.9 7.2 - - + +
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Residues in contact with GLU 875 (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 ARG* 2.8 39.8 + - + +
872A TYR* 3.6 21.8 + - - +
874A LEU* 1.3 75.9 - - - +
876A CYS* 1.3 61.4 + - - +
878A PHE 3.4 0.7 + - - -
879A ARG* 3.0 42.8 + - - +
911A TYR* 3.7 35.6 - - + -
871B ARG* 4.7 6.6 + - - -
875B GLU* 3.9 14.1 - - - +
909B GLN* 4.9 3.7 - - - +
910B LEU 5.3 0.9 + - - -
911B TYR* 4.2 30.9 + - - +
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Residues in contact with CYS 876 (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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839A PHE* 3.7 29.4 - - + +
840A ARG* 3.9 5.2 - - - -
843A SER* 2.8 26.9 + - - -
858A PHE* 3.6 5.4 - - + -
872A TYR* 2.8 53.1 + - - -
873A GLY 3.4 9.2 - - - +
875A GLU* 1.3 76.3 - - - +
877A LEU* 1.3 57.0 + - - +
879A ARG* 3.4 14.6 + - - +
880A TYR* 2.9 14.9 + - - +
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Residues in contact with LEU 877 (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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855A TYR* 4.2 13.0 - - + -
858A PHE* 3.5 31.4 - - + -
859A LYS* 4.1 28.9 - - + +
862A ALA* 4.4 5.4 - - + -
863A LEU* 5.0 2.5 - - + -
873A GLY 2.9 13.8 + - - +
874A LEU* 3.2 28.9 + - + +
876A CYS* 1.3 77.3 - - - +
878A PHE* 1.3 56.8 + - - +
880A TYR* 3.1 6.5 + - + +
881A TYR* 2.9 67.4 + - + +
900A GLU* 4.7 5.4 - - + -
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Residues in contact with PHE 878 (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 ARG* 5.0 0.9 - - - -
874A LEU* 2.9 48.3 + - + +
875A GLU 3.9 3.6 - - - +
876A CYS 3.4 0.2 - - - -
877A LEU* 1.3 76.0 - - - +
879A ARG* 1.3 63.4 + - - +
881A TYR* 3.3 8.9 + + - +
882A SER* 3.0 25.8 + - - -
897A PHE* 3.8 18.8 - + - -
900A GLU* 3.5 34.3 - - + -
901A THR* 3.6 24.7 - - - -
904A ASP* 3.7 26.9 - - + -
911A TYR* 4.0 10.3 - + + -
912A GLY* 3.7 21.3 - - - -
915A LYS* 4.0 19.4 - - + +
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Residues in contact with ARG 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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843A SER* 4.0 2.4 + - - +
844A PHE* 6.2 3.3 - - - -
847A ARG* 3.9 17.9 - - - +
872A TYR* 3.7 19.0 + - - -
875A GLU* 3.0 21.4 + - - +
876A CYS* 3.5 35.7 - - - +
878A PHE* 1.3 74.5 - - - +
880A TYR* 1.3 63.6 + - - +
882A SER 3.3 0.2 + - - -
883A TYR* 2.9 40.0 + - + +
911A TYR* 2.6 45.1 + - - +
915A LYS* 3.5 14.8 - - - -
1001A MGT 3.7 28.9 + - - -
911B TYR* 4.9 8.7 - - - -
914B GLU* 4.2 12.9 + - - -
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Residues in contact with TYR 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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842A TRP 4.7 0.2 - - - -
843A SER* 3.6 22.6 + - - +
846A LEU* 3.5 39.9 + - + -
847A ARG* 3.9 11.2 - - + +
850A PHE* 3.3 29.1 - - - -
855A TYR* 3.8 25.8 - + - -
858A PHE* 4.0 13.9 - + + -
876A CYS 2.9 14.8 + - - +
877A LEU* 3.1 17.9 + - + +
879A ARG* 1.3 76.1 - - - +
881A TYR* 1.3 66.9 + + - +
884A GLY* 2.6 41.6 + - - -
885A LEU* 3.9 1.0 + - + -
890A ARG* 5.0 3.8 + - - -
893A ILE* 3.9 21.9 - - + +
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Residues in contact with TYR 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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855A TYR* 2.7 35.8 + + - -
859A LYS* 4.2 2.9 - - - +
877A LEU* 2.9 55.4 + - + +
878A PHE* 3.6 9.4 - + - +
879A ARG 3.3 0.2 - - - -
880A TYR* 1.3 77.6 - + - +
882A SER* 1.3 58.2 + - - +
885A LEU* 2.9 38.4 + - + +
893A ILE* 3.7 32.1 - - + -
896A ASP* 3.5 7.3 - - - +
897A PHE* 3.4 54.0 - + + -
900A GLU* 3.9 17.4 - - + +
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Residues in contact with SER 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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878A PHE 3.0 16.3 + - - -
879A ARG 4.1 0.9 - - - -
881A TYR* 1.3 78.1 - - - +
883A TYR* 1.3 68.9 + - - +
886A GLU* 3.4 21.8 + - - +
897A PHE* 4.2 8.5 - - - -
915A LYS* 2.8 41.6 + - - +
918A ALA* 4.0 7.1 - - - +
919A PHE* 3.4 20.5 + - - +
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Residues in contact with TYR 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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847A ARG* 3.4 35.3 - - - +
879A ARG* 2.9 33.5 + - + +
882A SER* 1.3 79.5 - - - +
884A GLY* 1.3 65.4 + - - +
886A GLU* 3.4 19.3 + - - +
887A LYS* 3.2 21.7 + - - +
915A LYS* 4.7 8.7 - - + -
1001A MGT 2.3 50.4 + - - -
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Residues in contact with GLY 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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847A ARG* 3.9 28.1 - - - +
880A TYR* 2.6 31.0 + - - -
883A TYR* 1.3 73.3 - - - +
885A LEU* 1.3 59.7 + - - +
887A LYS* 3.1 5.2 + - - +
888A LYS* 3.0 27.5 + - - +
890A ARG* 5.7 1.2 + - - -
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Residues in contact with LEU 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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880A TYR* 3.9 1.5 + - + -
881A TYR* 2.9 17.4 + - - +
884A GLY* 1.3 72.8 - - - +
886A GLU* 1.3 65.8 + - - +
888A LYS 3.4 18.6 - - - +
889A PHE* 3.5 12.1 + - + +
890A ARG* 3.4 39.7 - - + +
893A ILE* 3.9 23.6 - - + +
894A PHE* 3.8 24.2 - - + +
897A PHE* 3.5 34.8 - - + -
919A PHE* 3.5 21.0 - - + -
923A SER* 4.7 1.9 + - - -
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Residues in contact with GLU 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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882A SER 3.4 19.8 + - - +
883A TYR* 3.5 21.6 - - - +
884A GLY 3.2 0.8 - - - -
885A LEU* 1.3 81.6 - - - +
887A LYS* 1.3 61.0 + - - +
888A LYS* 3.6 0.3 + - - -
889A PHE 5.3 0.2 + - - -
919A PHE* 3.7 11.6 - - + -
922A TYR* 3.7 51.7 - - + +
923A SER* 4.5 9.1 + - - -
924A LYS 5.6 0.9 + - - -
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Residues in contact with LYS 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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847A ARG* 4.6 15.5 - - + +
848A ASP* 5.5 4.5 - - - +
883A TYR 3.2 9.5 + - - +
884A GLY* 3.1 11.0 + - - +
886A GLU* 1.3 82.3 - - - +
888A LYS* 1.3 61.5 + - + +
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Residues in contact with LYS 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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847A ARG 5.4 4.3 - - - +
884A GLY 3.0 15.9 + - - +
885A LEU* 3.4 10.4 - - - +
886A GLU 3.5 0.4 - - - -
887A LYS* 1.3 80.7 - - + +
889A PHE* 1.3 73.6 + - - +
890A ARG* 3.6 46.9 + - - +
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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