Contacts of the helix formed by residues 784 - 802 (chain A) in PDB entry 5QSY
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 ASN 784 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A MET 4.9 3.6 + - - -
731A GLU* 3.3 50.9 - - + +
782A ASN* 2.9 24.6 + - - +
783A VAL* 1.3 93.4 - - - +
785A THR* 1.3 65.1 + - - +
786A PRO* 3.2 1.6 - - + -
787A VAL* 3.1 16.6 + - + +
788A LYS* 3.4 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A VAL 4.1 9.0 - - - +
784A ASN* 1.3 73.7 - - - +
786A PRO* 1.3 73.1 - - - +
788A LYS* 3.6 9.9 - - - +
789A GLU* 3.0 39.9 + - - +
836A HIS* 4.2 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A GLU* 3.4 36.8 - - - +
732A GLN* 5.0 2.9 - - - +
735A VAL* 3.9 14.1 - - + +
784A ASN* 3.3 4.9 - - - -
785A THR* 1.3 94.8 - - - +
787A VAL* 1.3 54.3 + - - +
789A GLU* 3.6 13.5 + - - +
790A GLN* 3.1 26.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
731A GLU* 3.9 23.6 - - + +
734A VAL* 3.7 38.1 - - + -
735A VAL* 4.1 7.9 - - + -
738A LEU* 4.3 2.7 - - + -
779A CYS* 3.6 17.5 - - + +
782A ASN* 3.5 38.8 - - + +
784A ASN 3.1 8.6 + - - +
786A PRO* 1.3 73.4 - - - +
788A LYS* 1.3 61.2 + - - +
790A GLN* 3.2 3.1 + - - +
791A ALA* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A CYS 4.2 6.1 - - - +
780A LEU* 3.2 29.9 + - - +
781A SER* 4.1 4.8 + - - +
782A ASN 2.8 31.6 + - - +
783A VAL* 4.1 14.2 + - - +
784A ASN 3.4 3.8 + - - +
785A THR* 3.3 13.4 + - - +
787A VAL* 1.3 76.1 - - - +
789A GLU* 1.3 54.6 + - - +
791A ALA* 3.8 2.8 - - - +
792A PHE* 2.7 37.4 + - - +
832A PHE* 3.7 16.3 - - + -
836A HIS* 3.6 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A THR* 3.0 29.2 + - - +
786A PRO* 3.6 15.4 - - - +
788A LYS* 1.3 81.8 - - - +
790A GLN* 1.3 55.8 + - - +
792A PHE* 3.4 1.4 + - - +
793A MET* 2.8 33.1 + - - +
832A PHE* 3.7 25.1 - - + -
836A HIS* 5.2 7.8 - - + +
864A LYS* 2.8 43.5 + - + +
865A ARG* 5.3 0.7 - - - +
868A LEU* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A VAL* 3.6 30.0 - - + +
738A LEU* 3.9 27.6 - - + -
739A GLN* 3.2 27.9 + - - +
786A PRO 3.1 18.4 + - - +
787A VAL* 3.2 5.8 + - - +
789A GLU* 1.3 73.1 - - - +
791A ALA* 1.3 59.2 + - - +
793A MET* 3.2 9.0 + - - +
794A LEU* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A LEU* 4.2 8.2 - - + +
776A CYS* 3.4 33.9 - - - +
779A CYS* 3.8 15.0 - - + -
780A LEU* 4.2 8.5 - - + +
787A VAL 2.8 16.1 + - - +
788A LYS 3.8 3.1 - - - +
790A GLN* 1.3 75.8 - - - +
792A PHE* 1.3 57.4 + - - +
794A LEU* 3.2 4.9 + - - +
795A LEU* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A LEU* 4.0 8.2 - - + +
788A LYS 2.7 22.9 + - - +
789A GLU 3.7 3.8 - - - +
791A ALA* 1.3 74.7 - - - +
793A MET* 1.3 64.2 + - - +
795A LEU* 3.3 3.5 + - - +
796A CYS* 3.0 50.8 + - + -
829A LEU* 3.4 47.3 - - + -
832A PHE* 3.3 48.9 - + + -
833A VAL* 4.0 6.3 - - + -
837A VAL* 5.5 0.4 - - + -
868A LEU* 3.4 32.1 - - + -
871A ALA* 5.6 0.2 - - + -
872A PHE* 3.8 19.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A GLU 2.8 17.1 + - - +
790A GLN* 3.2 13.4 + - - +
792A PHE* 1.3 73.4 - - - +
794A LEU* 1.3 61.2 + - + +
796A CYS* 3.2 2.2 + - - -
797A ASP* 2.8 56.1 + - - +
867A ASN* 4.4 8.5 - - - +
868A LEU* 3.4 34.1 - - + -
871A ALA* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A LEU* 3.7 44.4 - - + +
739A GLN* 4.2 4.5 - - - +
742A HIS* 3.4 41.3 - - + +
772A PHE* 4.2 8.1 - - + -
776A CYS* 4.0 12.3 - - - -
790A GLN* 2.9 40.4 + - - +
791A ALA 3.7 3.1 - - - +
793A MET* 1.3 77.1 - - + +
795A LEU* 1.3 59.4 + - - +
797A ASP* 3.3 4.6 + - + +
798A LEU* 2.8 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 3.9 31.0 - - + +
776A CYS* 3.6 40.6 - - + +
777A GLN* 3.8 6.3 - - - +
780A LEU* 4.2 15.7 - - + -
791A ALA 2.8 31.8 + - - +
792A PHE 3.6 4.3 - - - +
794A LEU* 1.3 72.8 - - - +
796A CYS* 1.3 56.3 + - - +
798A LEU* 4.8 1.8 - - - -
799A LEU* 2.8 40.8 + - + +
825A LEU* 4.1 26.2 - - + -
829A LEU* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A PHE* 3.0 58.0 + - - +
793A MET* 3.8 3.1 - - - +
795A LEU* 1.3 76.6 - - - +
797A ASP* 1.3 61.6 + - - +
800A MET* 3.6 18.9 + - - +
829A LEU* 4.5 3.6 - - - -
871A ALA* 3.7 32.5 - - + +
872A PHE* 4.1 8.1 - - - -
874A LYS* 5.6 1.4 + - - -
875A LEU* 3.9 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A HIS* 3.7 27.6 + - + -
746A LEU* 5.5 1.2 - - - +
793A MET* 2.8 40.0 + - - +
794A LEU* 3.5 7.0 - - - +
796A CYS* 1.3 73.6 - - - +
798A LEU* 1.3 59.7 + - - +
800A MET* 3.0 7.9 + - - +
801A ILE* 2.9 42.8 + - - +
871A ALA* 5.5 0.9 - - - +
874A LYS* 5.6 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A HIS* 3.5 28.3 - - + +
745A ILE* 4.3 15.9 - - + -
746A LEU* 5.1 4.0 - - + -
769A VAL* 5.4 3.1 - - + -
772A PHE* 3.6 35.4 - - + -
773A LEU* 3.7 29.2 - - + -
776A CYS* 4.7 2.7 - - - -
794A LEU 2.8 26.4 + - - +
797A ASP* 1.3 69.9 - - - +
799A LEU* 1.3 62.1 + - - +
801A ILE* 4.3 4.7 - - + +
802A PHE* 2.8 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 4.4 23.6 - - + -
795A LEU* 2.8 25.5 + - + +
798A LEU* 1.3 76.5 - - - +
800A MET* 1.3 58.4 + - - +
802A PHE* 4.4 1.9 - - - -
803A SER* 3.4 20.6 + - - +
819A PHE* 5.1 11.0 - - + +
821A PRO* 3.8 42.4 - - + -
825A LEU* 4.4 10.3 - - + -
829A LEU* 3.6 31.0 - - + -
875A LEU* 3.8 20.9 - - + -
880A ILE* 3.5 13.2 - - + +
881A VAL* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A CYS 3.6 12.9 + - - +
797A ASP* 3.0 10.5 + - - +
799A LEU* 1.3 77.3 - - - +
801A ILE* 1.3 61.8 + - + +
803A SER* 2.7 26.4 + - - -
805A GLN* 3.2 25.1 + - - +
874A LYS* 3.5 66.9 - - + +
875A LEU* 3.7 14.1 - - + +
878A TYR* 4.1 17.0 - - + -
880A ILE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A HIS* 5.1 1.6 - - + -
746A LEU* 3.7 26.7 - - + -
749A LEU* 3.5 31.9 - - + -
797A ASP* 2.9 36.2 + - + +
798A LEU* 3.1 6.5 + - + +
800A MET* 1.3 79.7 - - + +
802A PHE* 1.3 68.9 + - + +
803A SER 3.3 1.8 + - - -
805A GLN* 3.2 22.6 + - - +
806A LEU* 3.7 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A ILE* 4.0 19.5 - - + -
746A LEU* 5.6 0.4 - - + -
749A LEU* 3.7 34.8 - - + -
765A LEU* 4.4 7.2 - - + -
769A VAL* 3.6 40.4 - - + -
773A LEU* 5.9 1.1 - - + -
798A LEU* 2.8 36.4 + - + +
799A LEU* 4.4 1.8 - - - -
801A ILE* 1.3 83.6 - - + +
803A SER* 1.3 61.3 + - - +
806A LEU* 4.0 12.1 - - + -
817A LEU* 3.3 30.7 - - + +
818A VAL* 3.4 3.3 - - - -
819A PHE* 2.8 47.0 + + + +
----------------------------------------------------------
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