Contacts of the helix formed by residues 724 - 742 (chain A) in PDB entry 1WUG
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 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A PRO 2.5 8.4 + - - +
723A ARG* 1.3 82.2 + - - +
725A PRO* 1.3 71.7 - - + +
726A ASP* 3.0 8.8 + - + +
727A GLN* 3.6 29.4 - - + +
728A LEU* 3.1 19.8 + - - +
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Residues in contact with PRO 725 (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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723A ARG 3.0 8.7 - - - +
724A ASP* 1.3 85.7 - - + +
726A ASP* 1.3 62.1 + - + +
728A LEU* 4.1 5.4 - - + -
729A TYR* 3.6 13.3 + - - +
783A VAL* 3.4 37.4 - - + +
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Residues in contact with ASP 726 (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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724A ASP* 3.0 7.8 - - + +
725A PRO* 1.3 84.6 - - + +
727A GLN* 1.3 69.9 + - + +
729A TYR* 3.4 21.1 - - - +
730A SER* 3.9 4.9 + - - -
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Residues in contact with GLN 727 (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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722A PRO* 4.3 8.7 - - + +
724A ASP* 3.2 27.5 + - + +
726A ASP* 1.3 82.3 + - + +
728A LEU* 1.3 57.3 + - - +
730A SER* 3.2 12.5 + - - -
731A THR* 2.4 38.6 + - - +
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Residues in contact with LEU 728 (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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722A PRO* 3.3 35.8 - - + +
723A ARG 5.6 0.2 - - - +
724A ASP 3.1 13.9 + - - +
725A PRO* 4.3 4.7 - - + +
727A GLN* 1.3 78.2 - - - +
729A TYR* 1.3 67.4 + - - +
731A THR* 3.6 6.1 - - - -
732A LEU* 2.7 53.7 + - + +
783A VAL* 2.9 18.2 - - + +
784A SER* 2.9 42.6 - - - +
785A LYS* 4.5 1.1 - - - +
829A LEU* 3.6 15.3 - - + -
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Residues in contact with TYR 729 (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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725A PRO 3.6 13.5 + - - +
726A ASP* 3.4 16.8 + - - +
728A LEU* 1.3 81.0 - - - +
730A SER* 1.3 65.6 + - - +
732A LEU* 3.9 2.5 - - - +
733A LYS* 3.2 30.8 + - + +
777A LEU* 3.1 40.3 + - + +
778A LYS* 3.5 21.7 + - - -
780A ARG* 3.7 31.6 - - + -
782A TYR 5.0 8.1 - - - -
783A VAL* 5.2 2.4 - - + +
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Residues in contact with SER 730 (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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726A ASP 3.9 3.3 + - - -
727A GLN* 3.2 14.5 + - - -
728A LEU 3.1 0.2 - - - -
729A TYR* 1.3 84.5 - - - +
731A THR* 1.3 73.4 + - - +
732A LEU 3.0 2.0 - - - -
733A LYS* 2.8 12.7 + - - +
734A SER* 2.7 28.9 + - - -
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Residues in contact with THR 731 (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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722A PRO* 5.5 2.4 - - + +
727A GLN* 2.4 31.5 + - - +
728A LEU* 3.6 9.8 - - - -
730A SER* 1.3 79.8 + - - +
732A LEU* 1.3 59.8 + - - +
734A SER* 3.9 5.7 + - - -
735A ILE* 3.0 29.0 + - - +
823A LYS* 4.0 2.5 + - - +
827A ALA* 3.5 35.2 - - + +
829A LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 732 (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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728A LEU* 2.7 59.9 + - + +
729A TYR 3.9 0.2 - - - +
731A THR* 1.3 72.5 - - - +
733A LYS* 1.3 66.1 + - - +
735A ILE* 3.1 7.3 + - + +
736A LEU* 3.0 23.6 + - - +
777A LEU* 3.4 17.5 - - + -
782A TYR 3.3 25.6 - - - +
784A SER 5.0 0.4 - - - +
788A PHE* 3.3 48.7 - - + -
789A MET* 4.6 3.4 - - + -
829A LEU* 4.3 15.7 - - + -
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Residues in contact with LYS 733 (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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729A TYR* 3.2 24.5 + - + +
730A SER* 2.8 15.4 + - - +
732A LEU* 1.3 80.4 - - - +
734A SER* 1.3 67.4 + - - +
736A LEU* 3.2 3.9 + - - +
737A GLN* 2.8 51.5 + - + +
777A LEU* 3.3 23.9 - - + +
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Residues in contact with SER 734 (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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730A SER* 2.7 19.1 + - - -
731A THR* 4.0 6.3 - - - -
733A LYS* 1.3 75.5 - - - +
735A ILE* 1.3 58.0 + - - +
737A GLN* 3.2 7.8 + - - +
738A GLN* 2.8 35.8 + - - +
823A LYS* 4.1 14.4 - - - -
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Residues in contact with ILE 735 (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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731A THR 3.0 19.3 - - - +
732A LEU* 3.1 13.0 + - + +
734A SER* 1.3 75.6 - - - +
736A LEU* 1.3 66.2 + - - +
738A GLN* 2.9 4.8 + - - +
739A VAL* 2.8 33.7 + - + +
788A PHE* 4.3 1.8 - - + -
789A MET* 4.8 0.2 - - + -
792A LEU* 4.2 4.5 - - + -
820A PHE* 3.6 33.9 - - + -
823A LYS* 3.2 35.4 - - + +
824A ILE* 3.9 10.5 - - + -
829A LEU* 3.1 32.8 - - + -
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Residues in contact with LEU 736 (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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732A LEU 3.0 12.0 + - - +
733A LYS* 3.7 5.8 - - - +
735A ILE* 1.3 80.5 - - - +
737A GLN* 1.3 64.1 + - + +
739A VAL* 4.3 3.6 - - + -
740A LYS* 3.1 29.9 + - + +
770A LEU* 3.0 40.6 - - + +
773A MET* 3.3 27.8 - - + -
774A SER* 3.8 29.4 - - - +
777A LEU* 5.4 1.3 - - + -
788A PHE* 3.8 15.9 - - + -
792A LEU* 4.0 7.6 - - + -
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Residues in contact with GLN 737 (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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733A LYS* 2.8 41.8 + - + +
734A SER* 3.3 9.4 - - - +
736A LEU* 1.3 80.3 - - - +
738A GLN* 1.3 63.8 + - + +
740A LYS* 3.5 24.7 + - - +
741A SER* 3.2 21.1 + - - -
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Residues in contact with GLN 738 (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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734A SER* 2.8 22.1 + - - +
735A ILE* 3.5 5.6 - - - +
737A GLN* 1.3 74.1 - - + +
739A VAL* 1.3 55.7 + - - +
741A SER* 3.0 8.3 + - - -
742A HIS* 2.6 35.9 + - - +
819A PHE* 3.1 40.1 - - + -
823A LYS* 4.0 15.9 - - - +
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Residues in contact with VAL 739 (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 ILE* 2.8 39.7 + - + +
736A LEU* 3.9 7.4 - - - +
738A GLN* 1.3 72.1 - - - +
740A LYS* 1.3 55.6 + - - +
742A HIS* 2.9 17.6 - - - +
745A ALA* 2.7 26.9 - - - +
770A LEU* 4.0 20.2 - - + -
792A LEU* 4.4 9.9 - - + -
796A PHE* 5.1 0.2 - - + -
816A LEU* 3.0 42.8 - - + -
819A PHE* 3.9 11.4 - - + -
820A PHE* 4.5 10.8 - - + -
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Residues in contact with LYS 740 (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 LEU* 3.1 22.9 + - + +
737A GLN* 3.5 26.0 + - - +
739A VAL* 1.3 81.4 - - - +
741A SER* 1.3 63.0 + - - +
742A HIS 3.2 6.1 + - - +
745A ALA* 3.4 14.2 - - - +
746A TRP 5.3 0.2 + - - -
749A MET* 3.2 36.2 - - + +
770A LEU* 4.4 2.4 - - + +
774A SER* 4.6 18.4 + - - -
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Residues in contact with SER 741 (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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737A GLN 3.2 9.1 + - - -
738A GLN* 3.0 11.3 + - - -
740A LYS* 1.3 77.7 - - - +
742A HIS* 1.3 71.7 + - - +
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Residues in contact with HIS 742 (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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738A GLN* 2.6 17.2 + - - +
739A VAL* 2.9 22.5 + - - +
740A LYS 3.4 7.4 - - - +
741A SER* 1.3 84.6 - - - +
743A GLN* 1.3 74.5 + - + +
744A SER* 3.4 11.1 + - - +
745A ALA* 4.1 2.6 + - - +
746A TRP 5.2 0.5 + - - -
815A ILE* 3.7 29.2 - - + -
816A LEU* 3.7 14.8 - - + +
819A PHE* 3.8 43.2 - + + +
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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