Contacts of the helix formed by residues 781 - 798 (chain A) in PDB entry 5A31
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 GLU 781 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A MET 3.4 1.8 + - - -
780A GLY* 1.3 78.5 - - - +
782A GLY* 1.3 61.5 + - - +
783A ILE* 3.4 7.9 - - - +
784A CYS* 3.4 14.2 + - - +
785A SER* 3.2 21.1 + - - -
555O ASN* 5.1 8.3 + - - +
557O MET* 5.3 1.9 - - - +
593O ARG* 3.3 42.1 + - - +
750O PRO* 5.6 5.4 - - + +
753O ASN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 3.3 44.3 - - - +
779A MET* 3.6 4.2 + - - -
780A GLY 3.1 8.3 + - - -
781A GLU* 1.3 75.6 - - - +
783A ILE* 1.3 64.4 + - - +
785A SER* 3.4 2.2 + - - -
786A LEU* 3.0 21.3 + - - +
557O MET* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 4.4 2.0 - - - +
770A TYR* 3.2 50.5 - - + +
773A LEU* 3.5 23.3 - - + +
774A LYS* 3.5 14.1 - - - +
779A MET* 3.5 21.6 + - + +
780A GLY* 5.0 1.1 - - - -
781A GLU 4.1 9.2 - - - +
782A GLY* 1.3 74.4 - - - +
784A CYS* 1.3 73.3 + - + +
786A LEU* 3.2 7.7 + - + +
787A VAL* 3.1 24.8 + - - +
810A TYR* 3.2 28.0 - - + +
1807A GLU* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A GLU* 3.4 17.0 + - - +
782A GLY 3.2 0.6 - - - -
783A ILE* 1.3 84.6 - - + +
785A SER* 1.3 62.9 + - - +
787A VAL* 3.4 16.0 + - - +
788A GLU* 3.4 9.7 + - - +
810A TYR* 4.3 19.5 - - + -
813A LEU* 3.7 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 4.4 6.7 - - - -
657A TRP* 2.7 49.9 + - - -
781A GLU 3.2 10.9 + - - -
782A GLY* 3.4 8.9 + - - -
784A CYS* 1.3 76.6 - - - +
786A LEU* 1.3 64.8 + - - +
788A GLU* 3.1 22.1 + - - +
789A LEU 3.7 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 4.9 2.5 - - + -
621A CYS* 4.3 10.1 - - - -
657A TRP* 3.8 24.7 - - + -
766A LEU* 3.6 15.7 - - + +
769A VAL* 3.6 31.0 - - + -
770A TYR* 4.2 15.3 - - + +
773A LEU* 4.0 16.2 - - + -
782A GLY 3.0 12.0 + - - +
783A ILE* 3.2 10.5 + - - +
785A SER* 1.3 77.0 - - - +
787A VAL* 1.3 59.1 + - + +
789A LEU* 2.9 27.5 + - - +
790A LEU* 3.1 36.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A TYR* 3.6 40.4 - - + +
783A ILE 3.1 10.5 + - - +
784A CYS* 3.6 9.9 - - - +
785A SER 3.2 0.2 - - - -
786A LEU* 1.3 77.5 - - - +
788A GLU* 1.4 68.9 + - - +
790A LEU* 4.4 5.4 - - + +
791A VAL* 3.1 31.5 + - + +
806A TYR* 4.3 16.8 - - + -
810A TYR* 4.5 22.9 - - + -
813A LEU* 4.4 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 5.9 4.0 - - + -
784A CYS 3.4 7.9 + - - +
785A SER* 3.1 15.9 + - - +
787A VAL* 1.4 76.2 - - - +
789A LEU* 1.3 67.2 + - - +
791A VAL* 4.0 3.4 - - - +
792A GLN* 3.1 46.2 + - - +
813A LEU* 5.5 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A TRP* 3.7 31.6 - - + +
660A PHE* 4.8 0.4 - - + -
661A VAL* 4.0 25.8 - - + -
664A LEU* 4.3 25.1 - - + -
665A MET* 6.2 5.6 - - + -
668A MET* 5.9 1.8 - - + -
766A LEU* 4.3 22.7 - - + -
785A SER 3.7 1.4 + - - +
786A LEU 2.9 11.9 + - - +
788A GLU* 1.3 85.5 - - + +
790A LEU* 1.3 66.0 + - + +
792A GLN* 3.5 3.8 + - - +
793A LEU* 3.0 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A PHE* 4.1 20.4 - - + -
766A LEU* 3.4 27.8 - - + -
767A HIS* 3.8 21.3 - - - +
770A TYR* 4.0 8.5 - - + -
786A LEU* 3.1 29.0 + - + +
787A VAL* 3.3 8.0 + - + +
789A LEU* 1.3 85.0 - - + +
791A VAL* 1.3 53.4 + - - +
793A LEU* 3.4 3.9 + - + +
794A ALA* 2.6 39.9 + - - +
806A TYR* 3.2 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A VAL* 3.1 19.6 + - + +
788A GLU* 4.0 2.9 - - - +
790A LEU* 1.3 76.8 - - - +
792A GLN* 1.3 55.0 + - - +
794A ALA* 3.9 4.7 - - - +
795A ARG* 2.8 55.3 + - + +
803A VAL* 5.0 11.2 - - + +
806A TYR* 3.9 29.4 - - + -
813A LEU* 4.0 23.6 - - + +
814A ALA* 4.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A MET* 5.8 17.2 - - + +
788A GLU* 3.1 44.8 + - - +
789A LEU* 4.0 4.0 - - - +
791A VAL* 1.3 79.0 - - - +
793A LEU* 1.3 62.4 + - - +
795A ARG* 3.8 7.1 + - - +
796A ASP* 3.4 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LEU* 6.1 0.4 - - + -
665A MET* 5.5 7.6 - - - -
668A MET* 3.6 31.4 - - + -
759A ILE* 4.4 4.5 - - + -
762A ILE* 4.9 8.1 - - + -
763A PHE* 3.2 44.0 - - + -
766A LEU* 5.9 1.1 - - + -
789A LEU* 3.0 37.5 + - + +
790A LEU* 3.6 5.8 - - + +
792A GLN* 1.3 77.5 - - - +
794A ALA* 1.3 58.1 + - - +
796A ASP* 3.3 5.7 + - - +
797A LEU* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A PHE* 3.7 22.2 - - + -
790A LEU 2.6 23.5 + - - +
791A VAL* 3.9 3.1 - - - +
793A LEU* 1.3 77.9 - - - +
795A ARG* 1.3 65.3 + - - +
797A LEU* 3.4 5.0 + - - -
798A LYS 3.0 17.7 + - - -
799A LEU* 3.6 12.6 + - + -
802A TYR* 4.7 7.9 - - + -
803A VAL* 4.1 18.1 - - + +
806A TYR* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A VAL* 2.8 38.0 + - + +
792A GLN* 4.0 8.3 - - - +
794A ALA* 1.3 71.7 - - - +
796A ASP* 1.3 62.3 + - - +
798A LYS* 3.1 22.0 + - - +
803A VAL* 4.1 21.4 - - + +
814A ALA* 4.1 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A GLN 3.4 12.7 + - - +
793A LEU* 3.3 5.7 + - - +
795A ARG* 1.3 80.5 - - - +
797A LEU* 1.3 62.5 + - - +
798A LYS* 3.4 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A ILE* 4.0 22.0 - - + -
760A PRO* 4.6 18.2 - - + -
763A PHE* 3.7 26.2 - - + -
793A LEU* 2.9 42.2 + - + +
794A ALA* 3.4 5.4 + - - +
796A ASP* 1.3 69.8 - - - +
798A LYS* 1.3 70.1 + - - +
799A LEU* 3.4 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A ALA 3.0 6.6 + - - -
795A ARG* 3.1 13.8 + - - +
796A ASP 4.3 4.7 - - - +
797A LEU* 1.3 81.6 - - - +
799A LEU* 1.3 65.9 + - - +
800A GLY* 3.7 1.3 - - - -
----------------------------------------------------------
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