Contacts of the helix formed by residues 890 - 907 (chain B) in PDB entry 2WAC
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 LEU 890 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817B ALA* 5.8 0.2 - - + -
818B LEU* 4.3 5.2 - - + -
849B GLU* 3.9 37.9 - - + +
850B LEU* 3.9 23.1 - - + -
858B LEU* 4.1 10.1 - - + -
885B ARG* 3.5 35.0 - - + +
887B GLU* 3.2 25.1 + - + +
888B ARG 3.2 0.4 - - - -
889B LYS* 1.3 81.1 - - - +
891B LYS* 1.3 52.9 + - - +
892B GLU 3.4 2.0 - - - -
893B LEU* 3.2 20.2 + - + +
894B VAL* 2.8 44.7 + - + +
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Residues in contact with LYS 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A LEU* 5.5 9.3 - - - +
885B ARG 5.7 1.6 - - - -
887B GLU 3.3 6.7 + - - +
888B ARG* 3.9 29.3 + - + +
889B LYS 3.6 2.0 - - - -
890B LEU* 1.3 74.7 - - - +
892B GLU* 1.3 71.6 + - + +
894B VAL* 3.3 7.6 + - + +
895B ASP* 3.0 56.5 + - - +
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Residues in contact with GLU 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B LEU 3.4 0.6 - - - -
891B LYS* 1.3 83.8 - - + +
893B LEU* 1.3 57.1 + - - +
895B ASP* 3.4 8.7 + - - +
896B GLN* 2.9 49.1 + - - +
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Residues in contact with LEU 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ALA* 4.4 4.5 - - + -
818B LEU* 3.6 22.0 - - + -
849B GLU* 4.2 23.3 - - + +
860B THR* 4.0 26.7 - - + -
862B ARG* 5.9 3.6 - - - +
869B ASP* 4.5 3.8 - - - +
889B LYS 5.8 0.4 - - - +
890B LEU* 3.2 18.9 + - + +
892B GLU* 1.3 74.0 - - - +
894B VAL* 1.3 61.1 + - - +
896B GLN* 4.0 16.1 + - - +
897B TYR* 2.9 59.8 + - + +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B LEU* 3.7 30.1 - - + -
883B GLU 4.1 8.5 - - - +
884B GLN* 3.4 37.0 - - - +
885B ARG* 4.0 24.9 - - + +
890B LEU* 2.8 30.6 + - + +
891B LYS* 3.3 8.0 + - + +
893B LEU* 1.3 73.4 - - - +
895B ASP* 1.3 62.7 + - - +
897B TYR* 3.9 1.4 - - - +
898B LYS* 3.0 27.9 + - - +
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Residues in contact with ASP 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B GLN* 5.3 2.8 + - - +
891B LYS* 3.0 49.3 + - - +
892B GLU* 3.7 10.1 - - - +
894B VAL* 1.3 82.9 - - - +
896B GLN* 1.3 57.6 + - + +
898B LYS* 3.4 8.3 + - - +
899B ALA* 3.1 27.4 + - - +
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Residues in contact with GLN 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B ARG* 5.8 2.4 + - - -
872B LYS* 3.8 26.8 + - - +
892B GLU* 2.9 36.2 + - - +
893B LEU* 3.7 20.2 - - - +
895B ASP* 1.3 73.9 - - + +
897B TYR* 1.3 68.4 + - + +
899B ALA* 3.4 8.9 + - - +
900B ALA 3.2 15.9 + - - -
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Residues in contact with TYR 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ALA 3.5 21.6 + - - -
818B LEU* 3.8 21.1 - - + -
819B VAL* 4.6 2.0 - - + -
860B THR* 3.8 11.6 - - - +
869B ASP* 2.7 37.7 + - - -
871B GLY* 4.2 6.4 - - - -
872B LYS* 3.6 35.9 + - + -
875B VAL* 3.7 18.2 - - + +
882B ALA* 3.7 16.5 - - + +
883B GLU 5.7 0.2 - - - +
893B LEU* 2.9 46.5 + - + +
894B VAL 4.1 2.7 - - - +
896B GLN* 1.3 73.4 - - + +
898B LYS* 1.3 60.3 + - - +
900B ALA* 3.3 9.0 + - - +
901B GLN* 3.0 28.4 + - - +
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Residues in contact with LYS 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A GLN* 3.8 24.5 - - - +
877A GLU* 5.2 4.0 + - - -
882B ALA* 4.6 3.9 - - - +
884B GLN* 4.8 18.9 + - + +
894B VAL 3.0 18.4 + - - +
895B ASP* 3.4 11.0 - - - +
897B TYR* 1.3 77.6 - - - +
899B ALA* 1.3 56.8 + - - +
901B GLN* 3.4 17.9 + - - +
902B GLU* 3.0 46.1 + - + +
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Residues in contact with ALA 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ASP 3.1 13.6 + - - +
896B GLN* 3.6 10.5 - - - +
897B TYR 3.3 0.2 - - - -
898B LYS* 1.3 75.0 - - - +
900B ALA* 1.3 64.3 + - - +
902B GLU* 3.5 7.5 + - - +
903B ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B LYS* 4.0 31.2 - - + +
875B VAL* 4.0 13.0 - - + -
876B ALA* 4.0 14.8 - - + +
896B GLN 3.2 11.4 + - - +
897B TYR 3.3 8.7 + - - +
899B ALA* 1.3 79.5 - - - +
901B GLN* 1.3 61.0 + - - +
903B ALA* 3.5 6.3 + - - +
904B ALA* 3.2 21.1 + - - +
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Residues in contact with GLN 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A THR* 3.8 21.2 - - - +
875B VAL* 3.6 14.7 - - + +
880B VAL 5.4 1.1 - - - +
881B LEU* 3.5 10.7 - - + +
882B ALA* 2.8 40.4 + - + +
897B TYR 3.0 15.7 + - - +
898B LYS* 3.7 18.3 - - - +
900B ALA* 1.3 74.1 - - - +
902B GLU* 1.3 60.9 + - - +
904B ALA* 3.1 7.1 + - - +
905B ARG* 2.8 28.2 + - + +
912B TRP* 3.7 24.4 + - + +
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Residues in contact with GLU 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B LYS* 3.0 37.2 + - + +
899B ALA* 3.6 9.0 - - - +
901B GLN* 1.3 77.4 + - - +
903B ALA* 1.3 58.0 + - - +
905B ARG* 2.8 47.7 + - - +
906B VAL* 3.0 39.6 + - - +
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Residues in contact with ALA 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899B ALA 3.1 14.6 + - - +
900B ALA* 3.7 7.2 - - - +
901B GLN 3.3 0.2 - - - -
902B GLU* 1.3 78.6 - - - +
904B ALA* 1.3 60.7 + - - +
906B VAL* 4.2 4.9 - - - +
907B ALA* 3.3 24.3 + - - +
909B LEU* 5.0 0.6 - - - +
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Residues in contact with ALA 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B VAL 3.5 24.9 - - - +
876B ALA 3.9 11.8 + - - +
878B GLY* 4.0 6.3 - - - +
900B ALA 3.2 8.1 + - - +
901B GLN 3.1 9.0 + - - +
903B ALA* 1.3 75.0 - - - +
905B ARG* 1.3 64.1 + - - +
907B ALA* 3.3 1.9 + - - +
908B HIS 3.1 16.5 + - - -
909B LEU* 3.2 24.0 + - + -
912B TRP* 3.8 16.6 - - + +
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Residues in contact with ARG 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A HIS* 4.8 16.4 + - - -
863A ASP* 5.2 5.8 - - - -
901B GLN* 2.8 13.6 + - + +
902B GLU* 2.8 49.1 + - - +
904B ALA* 1.3 75.9 - - - +
906B VAL* 1.3 75.8 + - - +
908B HIS* 3.1 23.4 + - - -
912B TRP* 3.5 49.2 - - + +
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Residues in contact with VAL 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902B GLU* 3.0 25.7 + - + +
903B ALA* 4.3 5.8 - - - +
905B ARG* 1.3 95.3 - - - +
907B ALA* 1.3 59.2 + - - +
908B HIS* 3.2 13.1 + - - -
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Residues in contact with ALA 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903B ALA 3.3 19.7 + - - +
904B ALA 3.9 0.2 - - - +
905B ARG 3.2 0.8 - - - -
906B VAL* 1.3 75.5 - - - +
908B HIS* 1.3 70.8 + - - +
909B LEU* 3.4 30.0 + - + +
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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