Contacts of the helix formed by residues 869 - 877 (chain A) 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 ASP 869 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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816A LEU* 5.9 0.2 - - - +
860A THR* 3.9 17.7 - - - +
861A LEU 3.5 11.3 + - - +
862A ARG* 4.6 5.4 - - + +
867A LYS 3.4 5.3 + - - +
868A VAL* 1.3 71.0 - - - +
870A PHE* 1.3 61.0 + - - +
871A GLY 3.1 10.2 + - - -
872A LYS* 3.6 17.7 - - + +
873A GLN* 3.0 28.1 + - - +
893A LEU* 4.5 5.0 - - - +
897A TYR* 2.6 38.3 + - - -
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Residues in contact with PHE 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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835A PHE* 4.4 11.0 - - + -
838A ASP* 3.7 44.0 - - + +
839A VAL* 3.6 20.6 - - + -
844A VAL* 3.8 17.5 - - + -
861A LEU* 2.9 32.2 + - + +
862A ARG 3.7 2.7 - - - -
863A ASP* 3.4 46.7 - - + -
868A VAL* 3.3 6.5 + - + -
869A ASP* 1.3 71.4 - - - +
871A GLY* 1.3 62.9 + - - +
873A GLN* 3.3 16.8 + - - +
874A LEU* 3.2 28.2 + - - +
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Residues in contact with GLY 871 (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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816A LEU* 4.0 33.7 - - - +
817A ALA 5.5 0.2 - - - -
819A VAL* 3.7 11.2 - - - +
861A LEU 4.5 0.8 + - - +
869A ASP* 3.1 6.7 + - - -
870A PHE* 1.3 77.3 - - - +
872A LYS* 1.3 60.5 + - - +
874A LEU* 3.3 16.2 + - - +
875A VAL* 3.3 16.6 + - - +
897A TYR* 4.1 6.1 - - - -
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Residues in contact with LYS 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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869A ASP* 3.2 31.8 + - + +
871A GLY* 1.3 72.6 - - - +
873A GLN* 1.3 61.0 + - - +
875A VAL* 3.0 7.8 + - - +
876A ALA* 2.8 28.0 + - + +
893A LEU* 6.2 0.2 - - + -
896A GLN* 3.8 43.5 + - + +
897A TYR* 3.6 31.1 + - + -
900A ALA* 4.2 16.4 - - + -
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Residues in contact with GLN 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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838A ASP* 4.3 16.9 - - - +
868A VAL* 3.5 28.8 - - + +
869A ASP 3.0 14.3 + - - +
870A PHE* 3.5 20.4 - - - +
872A LYS* 1.3 77.0 - - - +
874A LEU* 1.3 56.8 + - - +
876A ALA* 3.7 7.7 - - + +
877A GLU* 2.9 59.0 + - + +
884B GLN* 6.0 4.0 - - - +
898B LYS* 3.8 22.1 + - - +
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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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714A LEU* 4.8 4.5 - - + -
816A LEU* 4.0 17.7 - - + -
819A VAL* 5.0 0.2 - - + -
831A ALA* 4.5 4.9 - - - +
834A ALA* 4.2 22.4 - - + -
835A PHE* 3.9 34.1 - - + +
838A ASP* 3.9 19.5 - - - +
870A PHE 3.2 16.7 + - - +
871A GLY* 3.4 7.2 - - - +
872A LYS 3.2 0.2 - - - -
873A GLN* 1.3 75.9 - - + +
875A VAL* 1.3 59.7 + - - +
877A GLU* 3.6 7.4 + - - +
878A GLY 3.4 2.6 + - - -
879A LEU* 3.0 39.8 + - + +
880A VAL* 3.5 26.4 + - + -
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Residues in contact with VAL 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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819A VAL* 4.4 3.1 - - + -
871A GLY 3.3 14.8 + - - +
872A LYS* 3.0 8.4 + - - +
874A LEU* 1.3 76.1 - - - +
876A ALA* 1.3 56.2 + - - +
878A GLY* 2.9 21.5 + - - -
880A VAL* 3.7 26.8 - - + +
881A LEU 4.4 10.5 - - - +
882A ALA* 4.2 4.9 - - + +
897A TYR* 3.4 34.1 - - + +
900A ALA* 3.9 3.6 - - + -
901A GLN* 3.4 35.0 - - + +
904A ALA* 3.6 8.3 - - - +
912A TRP* 5.1 0.5 + - - -
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Residues in contact with ALA 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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872A LYS* 2.8 19.3 + - + +
873A GLN* 3.3 9.8 + - + +
875A VAL* 1.3 72.6 - - - +
877A GLU* 1.3 61.3 + - + +
878A GLY 3.2 0.4 - - - -
900A ALA* 3.9 22.9 - - + +
903A ALA* 5.8 2.8 - - + +
904A ALA* 3.4 14.6 + - - +
909A LEU* 3.6 11.6 - - - +
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Residues in contact with GLU 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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834A ALA* 5.3 1.2 - - - +
838A ASP* 5.3 1.6 - - - +
873A GLN* 2.9 46.8 + - + +
874A LEU* 4.0 9.9 - - - +
875A VAL 3.2 0.2 - - - -
876A ALA* 1.3 76.9 - - + +
878A GLY* 1.3 61.4 + - - +
879A LEU* 3.4 27.4 + - + +
909A LEU* 3.7 23.2 - - + +
910A ALA* 3.7 9.5 - - - +
898B LYS* 5.2 4.7 + - - -
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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