Contacts of the helix formed by residues 765 - 781 (chain A) in PDB entry 1WER
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 765 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A LEU* 4.2 34.1 - - + +
760A PHE* 2.8 26.3 + - + +
763A GLU* 3.6 18.8 - - + +
764A LYS* 1.3 84.4 - - - +
766A GLU* 1.3 64.8 + - - +
767A SER* 3.2 3.4 - - - +
768A LEU* 3.0 38.8 + - + +
769A LEU 3.1 9.9 + - - -
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Residues in contact with GLU 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A LEU* 5.0 6.5 - - + -
760A PHE* 3.4 10.9 + - - -
761A LEU* 3.3 49.1 - - + +
764A LYS* 3.2 32.9 - - - +
765A LEU* 1.3 76.7 - - - +
767A SER* 1.3 59.1 + - - +
769A LEU* 3.5 2.1 + - - +
770A LEU* 3.0 37.5 + - + +
801A TYR* 3.8 21.5 + - + -
869A THR* 3.8 24.0 - - - +
873A ILE* 5.0 0.4 - - + -
982A ASP* 3.9 8.7 - - - +
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Residues in contact with SER 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A LYS 5.3 0.6 + - - -
765A LEU* 3.2 1.7 - - - -
766A GLU* 1.3 78.2 + - - +
768A LEU* 1.3 59.2 + - - +
770A LEU 4.5 0.2 - - - +
771A CYS* 2.8 39.7 + - - +
869A THR* 3.4 27.0 - - - +
872A TYR* 4.1 12.5 - - - -
873A ILE* 4.0 14.6 - - - +
980A LEU* 3.5 24.8 - - - +
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Residues in contact with LEU 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A LEU 3.7 22.7 - - - +
733A LYS* 4.3 29.4 - - + +
735A LEU* 4.6 5.6 - - + -
760A PHE* 4.2 16.4 - - + -
765A LEU* 3.0 33.1 + - + +
767A SER* 1.3 77.5 - - - +
769A LEU* 1.3 63.2 + - - +
771A CYS* 5.0 1.1 - - - -
772A THR* 2.5 41.6 + - - +
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Residues in contact with LEU 769 (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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735A LEU* 4.2 10.0 - - + +
738A VAL* 4.2 17.0 - - + -
756A LEU* 4.1 13.2 - - + +
757A LEU* 4.5 9.4 - - + +
760A PHE* 3.6 54.7 - - + -
765A LEU 3.1 3.0 + - - +
766A GLU 3.7 6.5 - - - +
767A SER 3.2 0.2 - - - -
768A LEU* 1.3 81.1 - - - +
770A LEU* 1.3 64.9 + - + +
772A THR* 4.0 0.9 - - - -
773A LEU* 3.1 43.1 + - + +
797A LEU* 4.0 33.9 - - + -
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Residues in contact with LEU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A LEU* 4.4 13.0 - - + -
766A GLU 3.0 19.8 + - - +
769A LEU* 1.3 79.6 - - + +
771A CYS* 1.3 58.5 + - - +
773A LEU* 3.4 3.7 + - - +
774A ASN* 2.9 37.6 + - - +
794A ALA 5.2 0.4 - - - +
797A LEU* 3.5 41.5 - - + +
798A MET* 4.0 20.9 - - + +
801A TYR* 3.5 42.8 - - + -
873A ILE* 3.5 23.1 - - + -
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Residues in contact with CYS 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A SER 2.8 28.6 + - - +
768A LEU* 4.6 1.1 - - - +
770A LEU* 1.3 73.3 - - - +
772A THR* 1.3 58.1 + - - +
774A ASN* 3.7 6.5 - - - +
775A ASP* 3.0 30.1 + - - +
872A TYR* 4.3 9.0 - - - -
873A ILE* 3.9 26.5 - - - -
876A CYS* 3.8 38.5 - - + +
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Residues in contact with THR 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A LYS 4.4 7.7 + - - +
734A GLU 5.3 1.1 - - - +
735A LEU* 3.6 26.2 - - + +
739A TYR* 3.6 13.7 - - + +
768A LEU* 2.5 38.5 + - - +
771A CYS* 1.3 78.3 - - - +
773A LEU* 1.3 62.8 + - - +
775A ASP* 3.3 5.9 + - - +
776A ARG* 3.0 21.8 + - - +
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Residues in contact with LEU 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A LEU* 4.6 4.0 - - + -
738A VAL* 4.5 8.1 - - + -
739A TYR* 3.2 37.7 - - + +
742A SER* 6.0 0.4 - - - +
769A LEU* 3.1 31.6 + - + +
770A LEU* 4.0 3.6 - - - +
772A THR* 1.3 76.4 - - - +
774A ASN* 1.3 63.5 + - - +
776A ARG* 3.3 4.5 + - + +
777A GLU* 3.0 26.9 + - - +
793A LEU* 4.1 18.4 - - + -
794A ALA* 4.0 18.6 - - + +
797A LEU* 3.3 35.2 - - + -
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Residues in contact with ASN 774 (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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770A LEU* 2.9 26.0 + - - +
771A CYS* 3.7 6.6 - - - +
773A LEU* 1.3 77.0 - - - +
775A ASP* 1.3 63.2 + - - +
777A GLU* 3.2 3.8 + - - +
778A ILE* 3.0 28.6 + - - +
788A PHE* 3.7 13.2 - - + -
794A ALA* 3.9 14.2 - - - +
798A MET* 3.6 37.1 - - - +
873A ILE* 4.0 10.9 + - - +
877A LEU* 3.6 31.7 - - + +
899A PHE* 5.0 0.6 - - - -
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Residues in contact with ASP 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A CYS 3.0 17.8 + - - +
772A THR* 3.8 6.1 - - - +
774A ASN* 1.3 77.0 - - - +
776A ARG* 1.3 56.9 + - - +
778A ILE* 3.3 6.8 + - - +
779A SER* 2.9 32.9 + - - -
880A SER* 3.0 32.6 + - - +
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Residues in contact with ARG 776 (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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736A HIS* 6.1 0.4 - - - -
739A TYR* 3.3 72.3 - - + +
772A THR 3.0 7.4 + - - +
773A LEU* 3.5 10.1 - - + +
774A ASN 3.2 0.2 - - - -
775A ASP* 1.3 74.7 + - - +
777A GLU* 1.3 67.6 + - - +
779A SER* 2.8 24.6 + - - -
780A MET* 3.1 44.3 + - + +
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Residues in contact with GLU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU 3.0 17.1 + - - +
774A ASN 3.2 7.2 + - - +
776A ARG* 1.3 79.6 - - - +
778A ILE* 1.3 62.4 + - - +
780A MET* 3.2 34.8 + - - +
781A GLU* 3.2 14.9 + - - +
787A LEU* 4.4 3.9 - - + +
788A PHE* 3.6 20.2 - - + -
792A THR* 3.7 32.2 - - - +
794A ALA* 3.6 20.4 + - + +
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Residues in contact with ILE 778 (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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774A ASN 3.0 19.9 + - - +
775A ASP* 3.6 9.0 - - - +
776A ARG 3.3 0.2 - - - -
777A GLU* 1.3 74.8 - - - +
779A SER* 1.3 63.3 + - - +
781A GLU* 3.2 13.5 + - - +
787A LEU* 4.0 13.2 - - + -
788A PHE* 3.9 14.1 - - + -
877A LEU* 4.0 23.8 - - + +
880A SER* 3.5 46.2 - - - +
881A VAL* 3.8 16.6 - - + -
884A LYS* 3.3 29.1 - - + +
885A TRP* 4.2 8.9 - - + -
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Residues in contact with SER 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A ASP* 2.9 19.1 + - - -
776A ARG* 2.8 26.6 + - - -
778A ILE* 1.3 77.6 - - - +
780A MET* 1.3 62.0 + - - +
884A LYS* 2.9 28.1 + - - +
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Residues in contact with MET 780 (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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776A ARG* 3.1 45.8 + - + +
777A GLU* 3.2 39.9 + - - +
779A SER* 1.3 83.1 + - - +
781A GLU* 1.3 61.7 + - - +
782A ASP* 3.5 11.3 + - - +
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Residues in contact with GLU 781 (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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777A GLU 3.2 10.1 + - - +
778A ILE 3.2 12.9 + - - +
780A MET* 1.3 76.3 - - - +
782A ASP* 1.3 69.6 + - - +
783A GLU* 2.9 36.3 + - - +
786A THR* 2.9 37.8 + - - +
787A LEU* 3.9 23.2 - - + +
788A PHE 4.7 1.4 + - - -
884A LYS* 3.0 29.8 + - - -
885A TRP* 3.7 9.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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