Contacts of the helix formed by residues 784 - 803 (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 SER 784 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LEU* 2.9 14.7 - - - +
732A LEU* 4.5 0.2 - - - +
782A TYR 3.8 1.0 - - - -
783A VAL* 1.3 82.7 + - - +
785A LYS* 1.3 68.4 + - - +
786A LYS* 5.0 0.7 - - - -
787A LEU* 3.1 29.3 - - - +
788A PHE* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A GLU* 4.7 19.9 + - + +
722A PRO* 3.5 37.0 - - + -
723A ARG* 5.3 2.7 - - - +
728A LEU* 4.5 2.0 - - - +
784A SER* 1.3 72.8 - - - +
786A LYS* 1.3 67.4 + - - +
787A LEU 2.8 3.9 + - - -
789A MET* 3.0 34.1 + - - +
829A LEU* 5.2 6.5 - - - -
830A ILE 5.5 1.1 - - - -
831A ASP* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A SER* 5.0 0.4 - - - -
785A LYS* 1.3 80.3 - - - +
787A LEU* 1.3 58.1 + - - +
789A MET* 4.1 0.2 - - - -
790A ALA* 2.9 38.2 + - + +
831A ASP* 3.0 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A TYR 4.0 6.1 - - - +
782A TYR* 3.7 27.8 - - + -
783A VAL* 3.7 22.4 - - + +
784A SER* 3.1 32.6 - - - +
785A LYS 2.8 1.6 + - - -
786A LYS* 1.3 82.6 - - - +
788A PHE* 1.3 60.2 + - - +
790A ALA* 3.6 2.3 - - - +
791A ASP* 2.6 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A LEU* 3.3 60.8 - - + -
735A ILE* 4.3 11.0 - - + -
736A LEU* 3.8 17.3 - - + -
773A MET* 3.1 39.5 - - + -
777A LEU* 3.5 21.8 - - + -
782A TYR* 3.9 13.0 - - + -
784A SER 3.3 6.2 + - - +
785A LYS 4.2 0.2 - - - +
787A LEU* 1.3 80.6 - - - +
789A MET* 1.3 77.9 + - + +
791A ASP* 3.0 16.1 + - - +
792A LEU* 3.1 28.6 + - + +
820A PHE* 4.5 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A LEU* 4.6 2.5 - - + -
784A SER 4.9 0.2 - - - +
785A LYS* 3.0 33.9 + - - +
786A LYS 4.0 0.9 - - - +
788A PHE* 1.3 89.5 - - + +
790A ALA* 1.3 66.0 + - - +
792A LEU* 3.3 0.9 + - - +
793A GLN* 2.7 34.9 + - - +
820A PHE* 4.2 10.4 - - + -
824A ILE* 3.3 33.4 - - + -
829A LEU* 3.1 36.6 - - + -
830A ILE* 3.6 21.5 - - - +
831A ASP* 3.4 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A LYS* 2.9 26.5 + - + +
787A LEU* 3.6 3.6 - - - +
789A MET* 1.3 77.3 - - - +
791A ASP* 1.3 55.1 + - - +
793A GLN* 3.4 9.0 - - - +
794A ARG* 2.5 60.0 + - - +
831A ASP* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A MET* 3.4 31.4 - - - +
773A MET* 3.5 15.0 - - + +
782A TYR* 2.9 37.4 + - - -
787A LEU* 2.6 24.9 - - - +
788A PHE* 3.0 8.8 + - - +
790A ALA* 1.3 74.8 - - - +
792A LEU* 1.3 56.9 + - - +
794A ARG* 2.6 35.0 + - - +
795A VAL* 3.0 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A ILE* 4.2 5.4 - - + -
736A LEU* 4.0 13.7 - - + -
739A VAL* 4.4 13.0 - - + -
770A LEU* 5.0 5.8 - - + -
773A MET* 3.3 12.1 - - + +
788A PHE* 3.1 33.8 + - + +
789A MET 3.9 1.3 - - - +
791A ASP* 1.3 78.2 - - - +
793A GLN* 1.3 59.6 + - - +
795A VAL* 2.7 34.4 + - + +
796A PHE* 2.9 53.5 + - + -
820A PHE* 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A MET* 2.7 39.8 + - - +
790A ALA* 3.5 7.8 - - - +
792A LEU* 1.3 74.7 - - - +
794A ARG* 1.3 58.8 + - - +
796A PHE* 3.6 10.5 + - + +
797A THR* 2.8 30.2 + - + +
817A GLU* 6.1 0.7 - - + -
820A PHE* 4.3 8.7 - - + -
821A PHE* 2.7 42.6 - - + -
824A ILE* 5.3 1.5 - - - +
831A ASP* 4.4 7.7 + - - -
832A LYS* 5.4 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A PHE* 3.5 54.4 - - + +
768A MET* 3.8 18.9 - - + -
790A ALA* 2.5 38.1 + - - +
791A ASP* 2.6 21.3 + - - +
793A GLN* 1.3 70.3 - - - +
795A VAL* 1.3 51.7 + - - +
797A THR* 3.0 10.0 - - + +
798A ASN* 2.7 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PHE* 3.5 44.8 - - + -
768A MET* 3.1 34.3 - - + +
769A ASP* 3.8 12.3 - - - +
770A LEU* 5.1 5.4 - - + +
773A MET* 5.6 2.5 - - + -
791A ASP 3.5 13.0 - - - +
792A LEU* 2.7 24.8 + - + +
794A ARG* 1.3 72.0 - - - +
796A PHE* 1.3 68.7 + - + +
798A ASN* 3.6 1.9 - - - +
799A CYS* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PHE* 4.0 15.3 - + - -
792A LEU* 2.9 47.9 + - + -
793A GLN* 4.0 9.4 - - + +
795A VAL* 1.3 82.6 - - + +
797A THR* 1.3 63.4 + - - +
799A CYS* 3.3 6.2 + - - +
800A LYS* 3.0 26.8 + - - +
813A ALA* 3.9 17.9 - - - +
816A LEU* 3.4 40.4 - - + -
817A GLU* 3.5 52.0 - - + +
820A PHE* 3.6 13.5 - + + -
821A PHE* 5.5 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A GLN* 2.8 26.3 + - + +
794A ARG* 3.0 19.5 - - + +
796A PHE* 1.3 77.2 - - - +
798A ASN* 1.3 69.2 + - - +
800A LYS* 3.2 16.0 + - - +
801A GLU* 2.5 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A TYR* 2.5 34.1 + - - -
764A ILE* 2.7 51.3 - - + +
766A PHE 4.1 1.4 + - - -
768A MET 3.8 18.6 + - - +
794A ARG* 2.7 30.2 + - + +
795A VAL* 3.6 4.7 - - - +
797A THR* 1.3 75.9 - - + +
799A CYS* 1.3 64.6 + - - +
801A GLU* 2.8 17.0 + - - +
802A TYR* 3.2 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PHE* 3.4 24.0 - - + -
795A VAL 3.0 19.1 + - - +
796A PHE 3.4 4.5 - - - +
798A ASN* 1.3 78.0 - - - +
800A LYS* 1.3 58.3 + - - +
801A GLU 3.1 0.2 + - - -
802A TYR* 3.7 10.3 - - - -
803A ASN* 2.9 33.6 + - - +
809A TYR* 2.8 61.5 - - + -
813A ALA* 3.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 3.0 15.0 + - - +
797A THR* 3.5 14.0 + - - +
799A CYS* 1.3 81.5 - - - +
801A GLU* 1.3 64.0 + - - +
803A ASN* 3.2 17.0 - - - +
804A PRO* 5.3 0.2 - - - +
810A TYR* 2.9 53.1 - - + +
813A ALA* 5.1 7.4 - - + -
814A ASN* 5.5 8.3 - - - +
817A GLU* 4.6 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A VAL* 3.6 24.0 - - + +
764A ILE* 3.2 20.9 - - + -
797A THR* 2.5 44.9 + - - +
798A ASN* 2.8 16.5 + - - +
800A LYS* 1.3 82.0 - - - +
802A TYR* 1.3 60.7 + - - +
803A ASN 4.5 0.7 - - - +
804A PRO* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A NP1 2.8 45.8 + - + -
752A VAL* 4.9 3.1 - - + -
757A ALA* 4.8 0.4 - - + -
758A PRO* 3.6 29.1 - - + +
759A GLY 4.5 7.9 - - - +
760A TYR* 3.9 37.2 - + + -
763A VAL* 3.6 15.5 - - + +
764A ILE* 4.4 1.1 - - + -
798A ASN 3.2 6.7 + - - +
799A CYS* 3.7 11.7 - - - -
801A GLU* 1.3 78.9 - - - +
803A ASN* 1.3 82.6 + - - +
804A PRO* 2.9 16.6 - - + +
809A TYR* 2.7 47.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A NP1 5.2 1.8 + - - -
799A CYS 2.9 18.2 + - - +
800A LYS* 3.2 19.4 - - - +
801A GLU 4.6 0.2 - - - -
802A TYR* 1.3 96.4 + - + +
804A PRO* 1.3 72.5 - - - +
805A PRO* 4.6 0.3 - - - +
807A SER* 2.8 33.4 + - - -
809A TYR* 2.8 23.6 - - + +
810A TYR* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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