Contacts of the helix formed by residues 819 - 840 (chain S) in PDB entry 1BKD
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 PRO 819 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803S GLU* 3.7 4.5 - - + +
815S GLU* 3.8 15.9 - - - +
816S ILE 3.4 14.4 - - - +
817S ASN 3.2 9.0 - - - +
818S SER* 1.3 90.2 - - - +
820S ASN* 1.3 72.6 + - - +
822S LEU* 4.2 5.1 - - + +
823S LYS* 3.2 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 820 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795S LEU* 4.7 3.4 - - - +
798S ALA* 3.5 35.5 + - + +
799S VAL* 4.2 5.0 - - + +
800S GLN* 4.9 4.4 - - - +
803S GLU* 2.8 35.0 + - - +
819S PRO* 1.3 79.9 - - - +
821S LEU* 1.3 65.4 + - - +
823S LYS* 3.3 13.6 + - - +
824S MET* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 821 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799S VAL* 4.0 12.7 - - + +
803S GLU* 3.2 5.7 + - + +
804S LEU* 3.9 18.6 - - + -
809S TRP* 3.6 40.8 - - + -
818S SER* 3.7 13.2 - - - +
820S ASN* 1.3 78.4 - - - +
822S LEU* 1.3 59.5 + - + +
824S MET* 3.0 27.4 + - + +
825S ILE* 2.9 44.9 + - + +
930S PHE* 4.4 17.7 - - + -
934S LEU* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 822 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R GLU* 3.5 35.0 - - + -
809S TRP* 4.8 12.1 - - + +
814S LYS* 3.4 49.6 - - + +
815S GLU* 4.0 18.6 - - - +
818S SER* 3.2 17.1 + - - +
819S PRO* 4.4 4.0 - - + +
821S LEU* 1.3 73.9 - - + +
823S LYS* 1.3 61.5 + - - +
825S ILE* 4.0 8.5 - - + +
826S ARG* 2.8 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 823 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795S LEU* 4.4 17.6 - - + +
819S PRO* 3.2 29.4 + - - +
820S ASN* 3.5 13.7 + - - +
821S LEU 3.2 0.4 - - - -
822S LEU* 1.3 78.6 - - - +
824S MET* 1.3 61.5 + - - +
826S ARG* 4.1 7.5 - - - +
827S HIS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 824 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R TYR* 3.8 13.0 - - - +
792S GLU* 5.1 3.1 - - + +
795S LEU* 3.8 43.0 - - + +
796S TYR* 4.3 6.5 - - + +
799S VAL* 4.9 1.3 - - + -
820S ASN 3.1 11.9 + - - +
821S LEU* 3.0 26.6 + - + +
823S LYS* 1.3 75.8 - - - +
825S ILE* 1.3 68.2 + - + +
827S HIS* 3.1 14.2 + - - +
828S THR* 3.2 24.3 + - - -
869S ASN* 4.3 10.1 - - - +
930S PHE* 3.4 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 825 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R GLY 5.8 0.7 - - - +
63R GLU* 3.7 36.8 - - + +
64R TYR* 3.5 57.4 - - + +
809S TRP* 5.4 1.8 - - + -
821S LEU* 2.9 36.7 + - + +
822S LEU* 4.0 7.0 - - + +
824S MET* 1.3 83.6 - - + +
826S ARG* 1.3 59.0 + - - +
828S THR* 3.1 6.4 + - - -
829S THR* 2.9 26.6 + - - -
934S LEU* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 826 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R GLU* 3.2 37.2 + - - +
814S LYS* 5.5 0.6 - - - +
815S GLU* 2.8 42.6 + - - -
822S LEU* 2.8 42.8 + - - +
823S LYS* 4.1 7.4 - - - +
825S ILE* 1.3 75.7 - - - +
827S HIS* 1.3 56.4 + - - +
829S THR* 3.8 7.8 - - - +
830S ASN* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 827 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788S LEU* 3.9 10.9 - - + +
791S LEU* 4.1 24.4 - - + +
792S GLU* 3.0 45.2 + - + +
795S LEU* 3.6 22.0 - - + +
823S LYS 3.4 7.9 + - - +
824S MET 3.1 9.9 + - - +
826S ARG* 1.3 74.8 - - - +
828S THR* 1.3 71.4 + - - +
830S ASN* 3.1 7.6 + - - +
831S LEU* 2.9 44.1 + - + +
873S GLU* 3.9 3.4 - - - -
991S PHE 4.5 8.2 + - - -
992S GLU* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 828 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R TYR* 4.1 22.2 - - + -
67R MET* 4.4 13.5 - - + -
824S MET* 3.2 13.8 + - - -
825S ILE 3.1 10.0 + - - -
827S HIS* 1.3 79.3 - - - +
829S THR* 1.3 62.7 + - - +
831S LEU* 3.1 2.6 + - - -
832S THR* 3.0 28.4 + - - +
869S ASN* 2.8 34.2 + - - +
873S GLU* 3.4 27.9 - - + +
929S PHE* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 829 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R GLU 3.3 19.0 + - - +
64R TYR* 4.1 10.4 - - - -
65R SER* 3.5 21.6 + - - +
66R ALA* 4.1 14.6 + - + +
825S ILE 2.9 17.2 + - - -
826S ARG* 3.8 8.7 - - - +
828S THR* 1.3 75.8 - - - +
830S ASN* 1.3 64.6 + - - +
832S THR* 3.3 2.8 + - - -
833S LEU* 3.0 41.4 + - + +
997S MET* 6.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 830 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826S ARG 3.0 19.9 + - - +
827S HIS* 3.1 9.8 + - - +
829S THR* 1.3 79.3 - - - +
831S LEU* 1.3 60.9 + - + +
833S LEU* 3.6 6.2 + - - +
834S TRP* 3.0 22.0 + - - +
991S PHE 5.6 1.2 + - - -
994S LEU* 2.7 36.5 + - - +
995S ASN* 4.0 5.6 + - - +
996S PRO* 3.4 31.1 - - - +
997S MET* 5.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 831 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788S LEU* 3.4 39.5 - - + -
827S HIS* 2.9 45.2 + - + +
828S THR 3.9 2.9 - - - +
830S ASN* 1.3 78.8 - - + +
832S THR* 1.3 66.5 - - - +
833S LEU 3.1 1.6 - - - -
834S TRP* 3.1 11.7 + - + +
835S PHE* 3.0 45.5 + - + -
873S GLU* 3.9 18.2 - - + +
991S PHE* 4.5 8.3 - - + +
994S LEU* 4.2 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 832 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ALA* 3.6 21.7 - - + +
67R MET* 5.5 1.4 - - - +
828S THR* 3.0 20.6 + - - +
829S THR* 3.7 4.7 - - - -
831S LEU* 1.3 76.7 - - - +
833S LEU* 1.3 63.8 + - - +
835S PHE* 3.3 5.6 + - - +
836S GLU* 3.2 35.3 + - - +
873S GLU* 3.0 28.1 + - - +
876S SER* 4.0 10.4 - - - -
877S ALA* 3.5 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 833 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R SER* 5.7 0.2 - - - +
66R ALA* 4.0 19.5 - - + -
829S THR* 3.0 33.7 + - + +
830S ASN* 3.8 7.4 - - - +
832S THR* 1.3 75.7 - - - +
834S TRP* 1.3 59.6 + - - +
836S GLU* 3.3 23.6 + - - +
837S LYS* 2.9 29.3 + - - +
996S PRO* 4.3 8.0 - - + +
997S MET* 3.9 34.1 - - + -
1002S GLU* 6.3 2.2 - - + -
1005S PHE* 4.3 20.4 - - + -
1006S THR* 5.7 4.9 - - - +
1009S LEU* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 834 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775S ASP* 4.4 4.6 + - - -
776S LEU* 3.7 37.5 - - + -
784S ILE* 5.4 0.9 - - + -
830S ASN 3.0 17.4 + - - +
831S LEU* 3.1 11.8 + - + +
833S LEU* 1.3 75.9 - - - +
835S PHE* 1.3 98.5 + + - +
837S LYS* 3.4 9.2 + - + +
838S CYS* 2.9 53.4 + - - -
990S PHE* 4.1 19.6 - + - -
991S PHE* 3.7 25.6 - + - -
994S LEU* 3.4 37.6 - - + +
996S PRO* 3.5 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 835 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776S LEU* 4.4 8.3 - - + -
784S ILE* 5.7 0.2 - - + -
788S LEU* 4.6 9.0 - - + -
831S LEU* 3.0 44.2 + - + -
832S THR* 3.5 9.6 - - - +
834S TRP* 1.3 101.5 - + - +
836S GLU* 1.3 65.4 + - - +
838S CYS* 3.2 3.9 + - - +
839S ILE* 3.0 31.0 + - + +
855S ILE* 3.7 35.4 - - + +
858S ILE* 4.6 12.8 - - + -
862S PHE* 5.1 0.9 - + - -
873S GLU* 4.5 6.3 - - - -
874S VAL* 3.7 41.1 - - + -
877S ALA* 3.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 836 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ALA* 4.7 3.3 - - - +
832S THR* 3.2 31.3 + - - +
833S LEU* 3.3 20.7 + - - +
835S PHE* 1.3 78.3 - - - +
837S LYS* 1.3 58.3 + - - +
839S ILE* 3.2 2.3 + - - +
840S VAL* 2.8 35.2 + - - +
877S ALA* 3.8 10.7 - - + +
880S SER* 3.1 38.6 + - - +
882S PRO* 4.4 8.0 - - + +
883S VAL* 4.1 14.6 - - + -
1009S LEU* 3.2 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 837 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833S LEU 2.9 16.9 + - - +
834S TRP* 3.7 12.1 - - + +
836S GLU* 1.3 76.2 - - - +
838S CYS* 1.3 57.8 + - - +
840S VAL 4.7 0.2 - - - +
841S GLU* 2.9 76.7 + - + +
995S ASN 5.4 0.4 - - - -
996S PRO* 3.6 38.5 + - + +
1005S PHE* 3.8 14.6 - - + -
1008S TYR* 5.1 0.8 - - - -
1009S LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 838 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775S ASP* 5.1 4.0 - - - -
776S LEU* 4.1 28.7 - - + -
834S TRP* 2.9 62.8 + - - +
835S PHE* 3.2 6.0 + - - +
837S LYS* 1.3 79.0 - - - +
839S ILE* 1.3 57.9 + - - +
841S GLU* 4.1 1.5 - - - -
842S THR* 2.5 32.1 + - - -
851S VAL* 4.0 5.3 - - + +
1031S TYR* 4.3 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 839 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835S PHE* 3.0 21.3 + - + +
836S GLU 3.5 5.4 - - - +
838S CYS* 1.3 75.5 - - - +
840S VAL* 1.3 60.7 + - - +
842S THR* 2.9 30.0 + - - +
848S ARG* 3.6 9.5 - - + +
851S VAL* 4.0 8.5 - - + -
852S VAL* 4.0 29.4 - - + -
855S ILE* 3.8 23.6 - - + -
877S ALA* 5.6 2.2 - - + +
878S MET* 4.0 12.1 - - + -
883S VAL* 3.7 32.5 - - + -
886S LEU* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 840 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836S GLU 2.8 22.5 + - - +
837S LYS 4.6 0.2 - - - +
839S ILE* 1.3 74.3 - - - +
841S GLU* 1.3 59.3 + - + +
842S THR 3.2 1.0 + - - -
843S GLU* 4.6 0.2 - - - +
882S PRO* 3.9 37.2 - - + +
883S VAL* 4.4 6.7 - - + -
886S LEU* 4.5 7.6 - - + -
1009S LEU* 3.4 21.8 - - + +
1012S LYS* 3.1 41.3 - - + +
1013S SER* 4.0 8.7 - - - +
1016S ILE* 3.4 22.4 - - - +
----------------------------------------------------------
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