Contacts of the helix formed by residues 851 - 869 (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 ASN 851 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A PHE* 6.3 0.7 - - + -
846A LEU* 3.6 4.3 - - + +
849A HIS 3.5 4.1 + - - +
850A PHE* 1.3 81.7 + - - +
852A LYS* 1.3 65.8 + - - +
853A LYS* 3.3 11.5 + - - +
854A MET* 3.0 42.8 + - + +
855A TYR* 2.9 24.1 + - - +
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Residues in contact with LYS 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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850A PHE* 3.7 22.2 - - + -
851A ASN* 1.3 75.7 - - - +
853A LYS* 1.3 68.9 + - + +
855A TYR* 3.2 3.4 + - + +
856A GLU* 2.8 59.9 + - + +
892A ASP* 4.7 13.0 + - - +
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Residues in contact with LYS 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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851A ASN* 3.3 9.8 + - - +
852A LYS* 1.3 90.1 - - + +
854A MET* 1.3 63.1 + - - +
856A GLU* 3.3 24.7 + - + +
857A GLU* 3.0 24.3 + - - +
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Residues in contact with MET 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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808A PHE* 4.6 8.3 - - + -
813A TYR* 3.7 34.8 - - + +
841A PHE* 4.6 0.7 - - - -
842A TRP* 3.5 34.1 - - + +
845A PHE* 3.9 33.4 - - + -
846A LEU* 4.1 13.7 - - + -
851A ASN* 3.0 28.1 + - + +
853A LYS* 1.3 76.8 - - - +
855A TYR* 1.3 62.7 + - - +
857A GLU* 3.3 8.8 + - - +
858A PHE* 2.9 22.7 + - - +
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Residues in contact with TYR 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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846A LEU* 3.8 17.6 - - + +
850A PHE* 3.7 17.0 - + + -
851A ASN 2.9 17.2 + - - +
852A LYS* 3.6 3.6 - - + +
854A MET* 1.3 77.3 - - - +
856A GLU* 1.3 71.6 + - + +
858A PHE* 3.3 2.5 + + - +
859A LYS* 2.8 44.0 + - + +
877A LEU* 4.2 11.2 - - + -
880A TYR* 3.8 33.0 - + - -
881A TYR* 2.7 29.7 + + - -
893A ILE* 3.5 21.3 - - + -
896A ASP* 2.6 34.0 + - - +
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Residues in contact with GLU 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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852A LYS* 2.8 50.7 + - + +
853A LYS* 3.7 30.8 + - + +
854A MET 3.3 0.2 - - - -
855A TYR* 1.3 91.4 - - + +
857A GLU* 1.3 58.3 + - - +
859A LYS* 3.8 6.7 - - + +
860A GLN* 2.9 30.4 + - - +
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Residues in contact with GLU 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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813A TYR* 4.4 2.1 + - - -
817A ARG* 2.6 48.0 + - - -
821A LEU* 3.9 8.8 - - - +
842A TRP* 3.7 17.5 - - + -
853A LYS 3.0 16.6 + - - +
854A MET* 3.7 6.9 - - - +
855A TYR 3.2 0.2 - - - -
856A GLU* 1.3 75.0 - - - +
858A PHE* 1.3 65.7 + - - +
860A GLN* 3.3 7.9 + - - +
861A LEU* 3.0 47.0 + - + +
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Residues in contact with PHE 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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839A PHE* 3.8 26.4 - + - -
842A TRP* 3.5 36.0 - + + -
843A SER* 3.9 24.2 - - - -
846A LEU* 3.5 20.2 - - + -
854A MET 2.9 13.8 + - - +
855A TYR* 3.4 9.0 - + - +
857A GLU* 1.3 77.2 - - - +
859A LYS* 1.3 61.0 + - - +
861A LEU 4.0 0.2 - - - -
862A ALA* 3.0 21.1 + - - +
873A GLY 3.8 12.1 - - - -
876A CYS* 3.6 11.2 - - + -
877A LEU* 3.5 43.3 - - + -
880A TYR* 4.0 12.1 - + + -
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Residues in contact with LYS 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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855A TYR* 2.8 46.1 + - + +
856A GLU* 3.8 7.0 - - + +
858A PHE* 1.3 73.1 - - - +
860A GLN* 1.3 63.6 + - - +
862A ALA* 3.7 1.4 - - - +
863A LEU* 3.0 40.1 + - + +
877A LEU* 4.1 26.2 - - + -
881A TYR* 4.2 3.6 - - - +
896A ASP* 3.3 26.8 + - - +
899A GLU* 4.7 6.3 + - - -
900A GLU* 3.4 27.1 + - - -
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Residues in contact with GLN 860 (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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856A GLU 2.9 19.5 + - - +
857A GLU* 3.3 8.3 + - - +
859A LYS* 1.3 79.2 - - - +
861A LEU* 1.3 69.7 + - - +
863A LEU* 3.4 5.8 + - - +
864A GLU* 2.9 60.7 + - + +
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Residues in contact with LEU 861 (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 LEU* 3.6 30.3 - - + -
824A ARG* 3.4 30.3 - - - +
835A MET* 3.8 6.5 - - + -
839A PHE* 3.9 16.4 - - + -
842A TRP* 3.7 23.6 - - + -
857A GLU* 3.0 27.5 + - + +
860A GLN* 1.3 89.9 - - - +
862A ALA* 1.3 60.8 + - - +
864A GLU* 3.3 6.1 + - - +
865A ASP* 2.9 35.0 + - - +
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Residues in contact with ALA 862 (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 11.6 - - + -
858A PHE* 3.0 21.9 + - + +
859A LYS 3.7 3.8 - - - +
861A LEU* 1.3 78.8 - - - +
863A LEU* 1.3 57.7 + - - +
865A ASP* 3.5 2.3 + - - +
866A ALA* 3.0 28.4 + - - +
873A GLY* 3.4 31.9 - - - +
874A LEU* 3.7 10.7 + - - +
877A LEU* 4.4 12.6 - - + -
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Residues in contact with LEU 863 (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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859A LYS* 3.0 35.2 + - + +
860A GLN* 3.9 4.9 - - - +
862A ALA* 1.3 73.2 - - - +
864A GLU* 1.3 66.4 + - - +
866A ALA* 3.3 4.9 + - + +
867A LYS* 3.0 23.4 + - - +
874A LEU* 3.9 28.5 - - + -
877A LEU* 5.0 1.6 - - + -
900A GLU* 3.5 38.1 - - + +
903A LYS* 3.8 15.0 - - - +
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Residues in contact with GLU 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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824A ARG* 3.2 25.9 + - - +
829A ILE* 4.6 7.3 - - + +
860A GLN* 2.9 52.6 + - + +
861A LEU* 3.7 7.6 - - - +
863A LEU* 1.3 76.5 - - + +
865A ASP* 1.3 62.3 + - - +
867A LYS* 3.3 8.5 + - - +
868A GLU* 3.3 25.4 + - - +
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Residues in contact with ASP 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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824A ARG* 2.7 40.8 + - - -
829A ILE* 3.2 22.9 - - + +
830A GLY* 4.4 8.7 + - - -
835A MET* 5.1 1.2 - - - +
836A ASN* 5.5 0.7 - - - +
839A PHE* 3.2 26.4 - - + -
861A LEU 2.9 16.1 + - - +
862A ALA* 3.7 5.4 - - - +
864A GLU* 1.3 76.0 - - - +
866A ALA* 1.3 63.2 + - - +
868A GLU* 3.0 13.7 + - - +
869A GLY 3.1 0.2 + - - -
870A TYR* 3.0 32.2 + - + +
873A GLY 5.3 2.4 + - - +
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Residues in contact with ALA 866 (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 3.0 17.4 + - - +
863A LEU* 3.8 7.0 - - + +
864A GLU 3.3 0.2 - - - -
865A ASP* 1.3 75.8 - - - +
867A LYS* 1.3 63.8 + - - +
869A GLY* 3.1 13.2 + - - -
870A TYR 3.3 12.3 + - - +
871A ARG* 4.6 15.2 + - + +
874A LEU* 3.9 32.1 - - + -
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Residues in contact with LYS 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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863A LEU 3.0 13.2 + - - +
864A GLU* 3.6 11.2 - - - +
865A ASP 3.2 0.4 - - - -
866A ALA* 1.3 78.2 - - - +
868A GLU* 1.3 62.0 + - + +
869A GLY* 3.4 0.7 + - - -
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Residues in contact with GLU 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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829A ILE* 3.5 41.4 - - + +
864A GLU 3.3 14.6 + - - +
865A ASP 3.0 8.5 + - - +
867A LYS* 1.3 79.4 - - + +
869A GLY* 1.3 58.6 + - - +
870A TYR* 3.7 17.1 - - + -
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Residues in contact with GLY 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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866A ALA 3.1 14.2 + - - -
867A LYS 3.2 1.2 - - - -
868A GLU* 1.3 79.4 - - - +
870A TYR* 1.3 59.0 + - - +
871A ARG* 3.9 7.1 + - - +
909B GLN* 2.8 29.8 + - - -
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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