Contacts of the helix formed by residues 861 - 873 (chain A) in PDB entry 2VJ0
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 861 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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859A PRO* 2.8 22.8 + - + +
860A MET* 1.3 69.6 - - - +
862A THR* 1.3 65.2 + - - +
863A GLU* 3.3 17.0 + - - +
864A ILE* 3.1 39.0 + - + +
865A THR* 2.9 26.1 + - - -
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Residues in contact with THR 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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860A MET 3.6 7.1 + - - -
861A ASP* 1.3 72.0 + - - +
863A GLU* 1.3 69.3 + - - +
865A THR* 3.3 2.9 + - - -
866A LYS* 3.1 50.7 + - - +
884A PRO 6.0 2.0 - - - +
887A PHE* 4.0 22.7 - - + -
910A LEU* 5.7 3.3 - - - +
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Residues in contact with GLU 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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861A ASP* 3.3 8.0 + - - +
862A THR* 1.3 82.7 - - - +
864A ILE* 1.3 63.8 + - + +
866A LYS* 3.2 37.9 + - - +
867A ALA* 3.1 21.5 + - - +
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Residues in contact with ILE 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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858A HIS* 6.5 0.4 - - + -
859A PRO* 5.9 1.6 - - + +
861A ASP* 3.1 37.6 + - + +
863A GLU* 1.3 73.6 - - + +
865A THR* 1.3 62.3 + - - +
867A ALA* 3.1 9.6 + - + +
868A LYS* 2.8 52.2 + - + +
1939A BEN 6.1 2.7 - - - +
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Residues in contact with THR 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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859A PRO 5.1 0.7 + - - -
860A MET 4.7 0.5 - - - -
861A ASP 2.9 20.9 + - - -
862A THR* 3.6 5.6 - - - -
864A ILE* 1.3 78.4 - - - +
866A LYS* 1.3 62.0 + - - +
868A LYS* 3.1 3.9 + - - +
869A ILE* 3.0 26.1 + - + +
887A PHE* 3.7 33.4 - - + -
906A LEU* 3.7 13.9 - - + -
915A TYR* 3.7 16.7 + - - +
938A PHE* 3.7 27.7 - - + -
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Residues in contact with LYS 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 THR* 3.1 32.5 + - - +
863A GLU* 3.2 38.7 + - - +
865A THR* 1.3 75.5 - - - +
867A ALA* 1.3 62.0 + - - +
869A ILE* 3.3 3.5 + - - +
870A ILE* 3.1 31.8 + - + +
876A LEU* 3.4 33.0 - - + +
878A GLU* 4.1 20.8 + - - +
887A PHE* 3.8 15.5 - - + -
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Residues in contact with ALA 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 GLU 3.1 9.7 + - - +
864A ILE* 3.1 12.9 + - + +
866A LYS* 1.3 79.6 - - - +
868A LYS* 1.3 56.8 + - + +
870A ILE* 3.5 10.5 + - - +
871A GLY* 2.9 25.8 + - - -
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Residues in contact with LYS 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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710A CYS* 3.5 24.3 - - + -
858A HIS* 3.9 19.8 + - - +
864A ILE* 2.8 38.9 + - + +
865A THR* 3.1 6.9 + - - +
867A ALA* 1.3 70.5 - - + +
869A ILE* 1.3 61.0 + - - +
871A GLY 3.3 0.7 + - - +
872A PHE* 2.8 25.5 + - - +
937A GLN* 2.8 42.6 + - + +
938A PHE* 3.8 21.2 - - + +
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Residues in contact with ILE 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 THR* 3.0 26.9 + - + +
866A LYS 3.3 4.5 + - - +
868A LYS* 1.3 77.6 - - - +
870A ILE* 1.3 61.6 + - - +
872A PHE* 3.2 20.5 + - + +
874A SER* 3.3 32.5 + - - +
875A ALA 4.3 4.5 - - - +
876A LEU* 4.1 20.2 - - + -
887A PHE* 3.6 36.8 - - + -
889A GLY* 5.0 0.9 - - - -
904A LEU* 4.6 18.2 - - + -
906A LEU* 4.2 9.6 - - + -
934A LEU* 5.1 5.2 - - + -
938A PHE* 4.0 15.3 - - + -
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Residues in contact with ILE 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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866A LYS* 3.1 22.4 + - + +
867A ALA* 3.7 8.1 - - - +
869A ILE* 1.3 76.6 - - - +
871A GLY* 1.3 58.4 + - - +
873A GLY* 3.0 21.3 + - - -
874A SER 3.6 13.0 + - - +
875A ALA* 5.6 0.2 - - - -
876A LEU* 4.2 30.1 - - + +
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Residues in contact with GLY 871 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709A VAL 4.4 1.6 - - - +
710A CYS* 3.3 33.3 - - - +
823A ASN* 4.7 0.7 + - - -
824A LYS* 5.6 0.9 + - - -
867A ALA 2.9 16.0 + - - -
868A LYS 3.3 4.0 + - - -
870A ILE* 1.3 78.9 - - - +
872A PHE* 1.3 59.9 + - - +
873A GLY* 3.4 0.7 + - - -
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Residues in contact with PHE 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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709A VAL* 3.7 19.7 - - + -
710A CYS* 3.9 7.6 - - - -
823A ASN* 3.2 64.2 + - + +
826A PHE* 3.7 30.0 - + - -
868A LYS 2.8 12.4 + - - +
869A ILE* 3.3 12.3 - - - +
870A ILE 3.2 0.2 - - - -
871A GLY* 1.3 76.6 - - - +
873A GLY* 1.3 57.2 + - - +
874A SER* 5.0 0.4 - - - -
904A LEU* 4.9 4.7 - - + -
919A LEU* 5.9 0.9 - - + -
930A LEU* 3.7 37.5 - - + -
933A LEU* 4.0 3.6 - - + -
934A LEU* 3.8 45.8 - - + -
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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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823A ASN 4.8 0.2 - - - -
826A PHE* 3.3 24.5 - - - +
827A GLN* 3.1 8.9 + - - +
828A PRO* 3.0 31.5 - - - -
870A ILE 3.0 11.7 + - - -
871A GLY 3.2 1.9 - - - -
872A PHE* 1.3 79.6 - - - +
874A SER* 1.3 59.8 + - - +
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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