Contacts of the helix formed by residues 923 - 936 (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 LYS 923 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793A SER* 5.1 1.8 + - - -
794A ASP* 2.6 41.4 + - - +
898A THR* 6.3 0.2 - - + -
900A ILE* 4.5 12.1 - - + +
921A THR* 2.9 20.7 + - - -
922A SER* 1.3 83.4 + - - +
924A ASP* 1.3 74.5 + - - +
925A THR* 3.5 19.1 + - - +
926A VAL* 3.0 15.9 + - + -
927A SER* 2.9 10.9 + - - -
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Residues in contact with ASP 924 (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 GLN* 3.3 46.1 + - + +
848A GLN* 5.2 1.0 - - - +
850A VAL* 4.4 3.0 - - + +
922A SER 4.3 0.6 + - - -
923A LYS* 1.3 77.1 - - - +
925A THR* 1.3 75.7 + - - +
927A SER* 3.3 5.2 + - - -
928A GLN* 2.9 28.9 + - - +
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Residues in contact with THR 925 (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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794A ASP* 3.8 8.5 + - - -
796A THR* 4.2 15.1 + - - +
923A LYS* 3.5 23.9 + - - +
924A ASP* 1.3 92.2 + - - +
926A VAL* 1.3 60.2 + - - +
928A GLN* 3.8 6.5 - - - +
929A ARG* 2.9 30.8 + - - +
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Residues in contact with VAL 926 (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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794A ASP* 3.7 36.1 - - + +
822A LEU* 3.9 17.7 - - + -
893A ILE* 4.5 4.0 - - + -
900A ILE* 4.2 12.6 - - + -
902A CYS* 4.1 12.1 - - - -
921A THR* 3.8 9.4 - - - +
923A LYS* 3.0 24.3 + - + +
925A THR* 1.3 75.2 + - - +
927A SER* 1.3 65.8 + - - +
929A ARG* 4.0 0.2 - - - +
930A LEU* 2.9 45.5 + - + +
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Residues in contact with SER 927 (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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848A GLN 2.8 27.1 + - - -
850A VAL* 3.5 23.3 - - - +
919A LEU* 3.9 10.1 - - - +
921A THR* 2.9 32.4 + - - -
923A LYS 2.9 6.4 + - - -
924A ASP* 3.6 7.4 - - - -
926A VAL* 1.3 78.0 - - - +
928A GLN* 1.3 61.9 + - - +
931A CYS* 3.0 27.4 + - - +
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Residues in contact with GLN 928 (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 VAL* 3.4 30.6 - - + +
924A ASP 2.9 16.9 + - - +
925A THR* 3.8 7.2 - - - +
927A SER* 1.3 78.5 - - - +
929A ARG* 1.3 63.4 + - - +
931A CYS* 3.4 2.1 + - - +
932A GLU* 2.9 44.3 + - - +
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Residues in contact with ARG 929 (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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705A PHE* 4.1 11.9 - - - -
795A PHE* 4.0 17.6 + - - +
796A THR* 3.0 39.8 + - + +
797A GLU 4.6 8.3 + - - -
798A ALA* 4.6 3.4 - - - +
817A LYS* 6.1 0.4 - - - +
820A ILE 5.3 0.2 + - - -
821A THR* 4.1 15.0 - - - +
822A LEU* 4.3 17.2 - - + +
925A THR 2.9 19.5 + - - +
926A VAL 4.0 2.5 - - - +
928A GLN* 1.3 77.3 - - - +
930A LEU* 1.3 63.5 + - - +
932A GLU* 2.9 32.1 + - - +
933A LEU* 3.0 59.2 + - + +
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Residues in contact with LEU 930 (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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822A LEU* 4.3 10.5 - - + -
823A ASN* 4.1 24.5 - - + +
826A PHE* 4.7 8.5 - - + -
872A PHE* 3.7 24.9 - - + -
893A ILE* 4.3 13.5 - - + -
902A CYS* 3.5 37.9 - - + -
919A LEU* 4.0 19.5 - - + -
921A THR* 4.6 0.7 - - + -
926A VAL* 2.9 27.9 + - + +
929A ARG* 1.3 76.3 - - - +
931A CYS* 1.3 58.2 + - - +
933A LEU* 4.6 2.7 - - + -
934A LEU* 2.9 34.1 + - - +
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Residues in contact with CYS 931 (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 VAL* 3.8 28.9 - - + -
852A ASN* 3.8 35.7 - - - -
917A LEU* 3.7 16.3 - - - +
919A LEU* 3.9 15.8 - - + +
927A SER 3.0 21.2 + - - +
928A GLN* 3.8 5.2 - - - +
930A LEU* 1.3 76.8 - - - +
932A GLU* 1.3 59.6 + - - +
935A SER* 2.8 34.1 + - - -
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Residues in contact with GLU 932 (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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796A THR* 4.6 6.9 - - - +
852A ASN* 5.6 2.2 - - - +
928A GLN* 2.9 38.5 + - - +
929A ARG* 2.9 47.7 + - - +
931A CYS* 1.3 78.2 - - - +
933A LEU* 1.3 66.7 + - + +
935A SER* 3.6 8.4 + - - -
936A GLU* 3.5 21.3 - - - +
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Residues in contact with LEU 933 (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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705A PHE* 4.2 8.3 - - + -
709A VAL* 4.0 17.0 - - + -
821A THR* 3.9 24.5 - - + -
822A LEU 4.3 4.7 - - - +
823A ASN* 3.7 22.4 - - - +
872A PHE* 4.0 12.1 - - + -
929A ARG* 3.0 63.9 + - + +
930A LEU* 3.9 7.2 - - + +
932A GLU* 1.3 79.1 - - + +
934A LEU* 1.3 63.0 + - - +
936A GLU* 3.3 13.4 + - - +
937A GLN* 3.5 18.8 + - - -
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Residues in contact with LEU 934 (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* 4.9 1.6 - - - -
868A LYS 5.1 1.1 - - - +
869A ILE* 5.1 6.3 - - + -
872A PHE* 3.8 41.1 - - + -
904A LEU* 3.9 30.3 - - + -
906A LEU* 6.3 0.4 - - + -
917A LEU* 3.8 27.1 - - + -
919A LEU* 4.7 4.0 - - + -
930A LEU 2.9 18.2 + - - +
933A LEU* 1.3 78.3 - - - +
935A SER* 1.3 63.3 + - - +
936A GLU 3.1 1.7 + - - -
937A GLN* 3.1 19.2 + - + +
938A PHE* 3.3 49.0 - - + -
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Residues in contact with SER 935 (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 ASN* 3.0 39.8 + - - +
854A PHE* 3.3 40.9 - - - -
857A LYS* 4.3 5.0 + - - -
917A LEU* 3.7 7.9 - - - +
931A CYS 2.8 24.3 + - - -
932A GLU* 3.7 8.1 - - - -
933A LEU 3.2 0.2 - - - -
934A LEU* 1.3 76.4 - - - +
936A GLU* 1.3 65.9 + - - +
937A GLN 3.2 1.2 + - - -
938A PHE 4.2 0.7 + - - -
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Residues in contact with GLU 936 (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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702A GLU* 6.2 0.2 - - - +
706A ALA* 4.4 19.4 - - + +
852A ASN* 5.3 2.6 + - - -
857A LYS* 3.2 46.6 + - - +
858A HIS* 5.0 3.5 + - - -
932A GLU 3.5 15.8 - - - +
933A LEU* 3.3 8.9 + - - +
934A LEU 3.1 1.4 + - - -
935A SER* 1.3 84.0 - - - +
937A GLN* 1.3 69.9 + - - +
938A PHE 3.5 1.1 - - - -
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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