Contacts of the helix formed by residues 824 - 840 (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 824 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A PRO* 3.5 2.1 - - - +
823A THR* 1.3 81.2 + - - +
825A ASN* 1.3 61.2 + - - +
826A GLU* 2.9 34.1 + - - +
827A ASP* 3.3 29.3 + - - +
828A LYS* 3.1 31.3 + - - +
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Residues in contact with ASN 825 (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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823A THR 3.7 2.3 + - - +
824A ASP* 1.3 75.7 - - - +
826A GLU* 1.3 66.9 + - + +
828A LYS* 3.2 24.0 + - - +
829A GLU* 3.2 28.9 + - - +
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Residues in contact with GLU 826 (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 ASP* 2.9 13.0 + - - +
825A ASN* 1.3 77.3 - - + +
827A ASP* 1.3 65.9 + - - +
829A GLU* 3.5 23.4 + - - +
830A GLU* 3.3 21.8 + - - +
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Residues in contact with ASP 827 (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 PRO* 3.5 22.6 - - + +
824A ASP* 3.3 29.2 + - + +
825A ASN 3.3 0.2 - - - -
826A GLU* 1.3 77.1 - - - +
828A LYS* 1.3 64.2 + - - +
830A GLU* 3.5 7.0 + - - +
831A ALA* 3.1 23.7 + - - +
879A LEU* 4.3 2.1 - - - +
910A ALA 5.8 1.0 - - - -
911A ILE* 3.4 30.3 - - + +
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Residues in contact with LYS 828 (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* 4.1 31.5 - - + +
822A PRO* 2.8 36.2 + - + +
823A THR* 3.1 20.6 + - - +
824A ASP 3.1 15.1 + - - +
825A ASN* 3.2 25.2 + - - +
827A ASP* 1.3 76.1 - - - +
829A GLU* 1.3 62.9 + - + +
831A ALA* 3.3 5.5 + - - +
832A LEU* 3.1 30.3 + - + +
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Residues in contact with GLU 829 (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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825A ASN* 3.2 13.0 + - - +
826A GLU* 3.6 31.2 + - - +
827A ASP 3.4 0.4 - - - -
828A LYS* 1.3 76.8 - - + +
830A GLU* 1.3 57.6 + - - +
832A LEU* 3.2 11.2 + - + +
833A ARG* 2.9 29.1 + - - +
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Residues in contact with GLU 830 (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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826A GLU 3.3 14.2 + - - +
827A ASP* 3.8 7.2 - - - +
828A LYS 3.3 0.2 - - - -
829A GLU* 1.3 79.2 - - - +
831A ALA* 1.3 58.8 + - - +
833A ARG* 2.8 45.6 + - - -
834A ALA* 2.8 33.3 + - - +
879A LEU* 4.0 22.9 - - + +
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Residues in contact with ALA 831 (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* 4.6 2.9 - - + +
821A LEU* 3.9 12.8 - - + -
822A PRO* 4.4 0.7 - - + -
827A ASP 3.1 14.2 + - - +
828A LYS 3.4 9.2 - - - +
830A GLU* 1.3 76.9 - - - +
832A LEU* 1.3 58.1 + - - +
834A ALA* 3.5 5.8 + - - +
835A PHE* 3.1 29.1 + - - +
874A LEU* 4.5 3.7 - - - +
879A LEU* 3.7 26.8 - - - +
880A VAL* 3.7 18.6 - - + -
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Residues in contact with LEU 832 (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 ILE* 4.7 7.3 - - + +
711A THR 3.3 25.6 - - - +
712A GLU* 3.8 31.2 - - + +
714A LEU* 3.7 28.7 - - + -
821A LEU* 4.5 7.2 - - + -
828A LYS* 3.1 22.3 + - + +
829A GLU* 3.7 9.4 - - + +
831A ALA* 1.3 73.4 - - - +
833A ARG* 1.3 64.7 + - - +
835A PHE* 4.1 1.0 - - - +
836A SER* 3.1 26.0 + - - -
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Residues in contact with ARG 833 (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 GLU 2.9 17.9 + - - +
830A GLU* 2.8 42.7 + - - +
832A LEU* 1.3 76.1 - - - +
834A ALA* 1.3 72.6 + - - +
836A SER* 3.5 5.3 + - - -
837A GLU* 2.5 55.6 + - - +
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Residues in contact with ALA 834 (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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830A GLU* 2.8 22.2 + - - +
831A ALA 3.8 3.6 - - - +
833A ARG* 1.3 92.3 - - - +
835A PHE* 1.3 58.6 + - - +
837A GLU* 3.5 4.5 + - - +
838A ASP* 3.1 31.8 + - - +
874A LEU* 4.2 5.2 - - + -
877A GLU* 5.3 1.3 - - - +
879A LEU* 3.7 27.1 - - + -
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Residues in contact with PHE 835 (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 ILE* 4.0 25.6 - - + -
714A LEU* 3.5 26.7 - - + -
716A PHE* 4.3 13.2 - + + -
816A LEU* 3.8 29.2 - - + -
831A ALA 3.1 18.3 + - - +
832A LEU 4.1 2.2 - - - +
834A ALA* 1.3 74.2 - - - +
836A SER* 1.3 60.1 + - - +
838A ASP* 3.3 9.6 + - + +
839A VAL* 3.1 61.4 + - + +
861A LEU* 3.7 17.9 - - + -
870A PHE* 4.4 10.3 - - + -
874A LEU* 3.9 25.5 - - + +
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Residues in contact with SER 836 (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 ILE* 3.5 20.5 - - - +
832A LEU 3.1 18.9 + - - -
833A ARG* 3.8 5.6 - - - -
835A PHE* 1.3 75.1 - - - +
837A GLU* 1.3 60.9 + - - +
840A LEU* 3.0 51.5 + - - +
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Residues in contact with GLU 837 (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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833A ARG* 2.5 54.8 + - - +
834A ALA* 3.7 5.6 - - - +
836A SER* 1.3 76.8 - - - +
838A ASP* 1.3 65.0 + - - +
842A HIS* 3.6 15.6 - - - -
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Residues in contact with ASP 838 (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* 3.1 17.4 + - - +
835A PHE* 3.4 12.3 - - + +
836A SER 3.2 0.2 - - - -
837A GLU* 1.3 80.2 - - - +
839A VAL* 1.3 62.6 + - + +
842A HIS* 2.9 19.2 + - - +
844A VAL* 5.2 0.2 - - - +
870A PHE* 3.7 44.6 - - + +
873A GLN* 4.3 11.3 - - - +
874A LEU* 3.9 18.2 - - - +
877A GLU* 5.3 2.1 - - - +
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Residues in contact with VAL 839 (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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707A VAL* 3.7 34.9 - - + +
710A ILE* 4.0 5.4 - - + -
835A PHE* 3.1 49.2 + - + +
838A ASP* 1.3 83.6 - - + +
840A LEU* 1.3 70.4 + - - +
841A ASN 3.2 0.9 + - - -
842A HIS* 2.9 25.0 + - - +
844A VAL* 4.3 5.4 - - + -
861A LEU* 4.2 6.5 - - + -
870A PHE* 3.6 35.7 - - + -
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Residues in contact with LEU 840 (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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707A VAL* 3.8 6.1 - - - +
708A THR* 3.7 31.9 - - - +
709A GLU* 3.9 7.6 - - - +
710A ILE* 3.9 20.6 - - + +
836A SER* 3.0 36.7 + - - +
838A ASP 4.0 0.2 - - - -
839A VAL* 1.3 79.5 - - - +
841A ASN* 1.3 84.6 + - - +
842A HIS* 3.3 13.9 + - - -
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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