Contacts of the helix formed by residues 813 - 831 (chain A) in PDB entry 4YOZ
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 813 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A ASP 4.4 0.2 + - - -
812A VAL* 1.3 83.0 - - - +
814A ASN* 1.3 63.1 + - - +
815A GLU* 3.7 8.7 + - - +
816A LEU 3.3 11.6 + - - -
817A ARG* 3.2 18.0 + - - +
857A GLU* 2.9 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A VAL 4.2 5.7 - - - +
813A SER* 1.3 74.0 - - - +
815A GLU* 1.3 57.3 + - - +
817A ARG* 3.3 46.5 + - - +
818A ARG* 3.0 27.4 + - - +
1003A SO4 4.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A SER* 3.1 9.7 + - - +
814A ASN* 1.3 77.2 - - - +
816A LEU* 1.3 60.8 + - - +
818A ARG* 3.5 8.4 + - - +
819A LYS* 3.1 59.5 + - - +
963A LEU* 3.9 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A VAL* 3.5 26.7 - - + -
813A SER* 3.3 4.8 + - - +
815A GLU* 1.3 76.6 - - - +
817A ARG* 1.3 56.2 + - - +
819A LYS* 3.0 11.3 + - + -
820A ILE* 2.6 56.5 + - + +
848A PHE* 5.4 0.7 - - + -
851A MET* 3.5 22.0 - - + +
852A ALA* 3.7 19.3 - - + -
855A THR* 3.5 19.5 - - + +
857A GLU* 3.5 41.5 + - + +
859A ARG* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 817 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 3.8 3.8 - - + +
804A ARG* 3.7 38.5 + - - +
807A CYS* 3.5 38.5 - - + +
812A VAL* 4.7 0.8 - - - +
813A SER 3.2 13.9 + - - +
814A ASN* 3.3 38.8 + - - +
816A LEU* 1.3 76.4 - - - +
818A ARG* 1.3 55.9 + - - +
820A ILE* 3.2 5.5 + - - +
821A TRP* 2.8 31.1 + - - +
966A PHE* 3.6 37.6 - - + -
1003A SO4 2.9 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A ASN 3.0 17.8 + - - +
815A GLU* 3.7 11.7 - - - +
816A LEU 3.3 0.2 - - - -
817A ARG* 1.3 75.9 - - - +
819A LYS* 1.3 52.7 + - - +
821A TRP* 3.6 6.6 + - - +
822A THR* 2.8 36.8 + - - -
963A LEU* 3.3 47.8 + - + +
964A SER 3.5 22.7 + - - +
965A PRO* 4.4 9.3 - - - +
966A PHE* 5.2 7.9 - - + -
1003A SO4 3.1 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A GLU* 3.1 48.2 + - - +
816A LEU* 3.0 18.5 + - + +
818A ARG* 1.3 76.3 - - - +
820A ILE* 1.3 65.4 + - - +
822A THR* 3.3 2.8 + - - -
823A CYS* 3.0 18.7 + - - +
851A MET* 3.5 19.2 - - - +
855A THR* 3.8 30.2 - - + +
945A PHE* 5.4 0.3 - - - -
949A TYR* 4.4 16.1 - - + -
963A LEU* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 3.7 23.3 - - + -
807A CYS* 4.7 2.7 - - - -
812A VAL* 5.0 0.7 - - + -
816A LEU* 2.6 40.2 + - + +
817A ARG* 3.6 7.9 - - - +
819A LYS* 1.3 71.2 - - - +
821A TRP* 1.3 58.2 + - - +
823A CYS* 3.2 4.3 + - - +
824A PHE* 2.9 27.2 + - - +
844A LEU* 4.5 3.8 - - + +
847A ALA* 3.8 4.5 - - + +
848A PHE* 3.6 64.4 - - + +
851A MET* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A CYS* 3.6 24.1 - - + -
796A TYR* 3.2 44.0 - + - -
799A ALA* 3.9 12.6 - - + -
800A SER* 3.6 22.7 - - - -
803A LEU* 3.8 12.5 - - + +
817A ARG 2.8 17.3 + - - +
818A ARG* 3.7 5.4 - - - +
820A ILE* 1.3 78.8 - - - +
822A THR* 1.3 57.1 + - - +
824A PHE* 3.3 16.8 + + - +
825A GLU* 2.9 41.1 + - + +
844A LEU* 5.2 0.2 - - + -
964A SER* 4.0 16.4 - - - -
965A PRO 3.0 27.8 + - - -
966A PHE* 3.5 28.9 - + + -
967A PRO* 3.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A ARG 2.8 22.1 + - - -
819A LYS 3.5 6.3 - - - -
820A ILE 3.2 0.2 - - - -
821A TRP* 1.3 75.0 - - - +
823A CYS* 1.3 57.8 + - - +
825A GLU* 3.6 2.4 + - - +
826A PHE* 3.0 26.0 + - - +
945A PHE* 3.4 22.6 - - + -
949A TYR* 3.7 14.8 - - + +
962A PRO 3.9 10.5 - - - +
963A LEU* 3.3 12.1 - - + +
964A SER* 3.0 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 823 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A LYS 3.0 6.4 + - - +
820A ILE 3.6 3.8 - - - +
822A THR* 1.3 73.9 - - - +
824A PHE* 1.3 66.1 + - - +
826A PHE* 3.2 4.2 + - - +
827A THR* 3.1 21.5 + - - +
847A ALA* 4.3 3.4 - - + -
850A ILE* 3.9 7.6 - - - -
851A MET* 3.5 46.7 - - + -
938A TYR* 3.3 23.3 - - - -
942A VAL* 3.6 18.6 - - - -
945A PHE* 3.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 824 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A TYR* 4.8 1.6 - + - -
799A ALA* 3.5 29.8 - - + -
820A ILE 2.9 16.7 + - - +
821A TRP* 3.6 28.3 - + - +
823A CYS* 1.3 76.3 - - - +
825A GLU* 1.3 64.5 + - - +
827A THR* 2.6 24.6 + - - -
828A LEU* 3.1 41.5 + - + +
840A LEU* 3.9 33.4 - - + -
843A LEU* 4.0 11.4 - - + -
844A LEU* 3.8 35.4 - - + -
847A ALA* 3.9 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 825 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A THR* 3.4 22.2 - - - +
588A CYS* 3.3 28.9 + - - +
589A GLU* 4.9 2.1 + - - +
796A TYR* 3.8 11.7 - - + +
821A TRP* 2.9 21.7 + - + +
822A THR 3.8 4.7 - - - +
824A PHE* 1.3 80.6 - - - +
826A PHE* 1.3 53.5 + - - +
828A LEU* 3.1 6.2 + - - +
829A VAL* 2.7 52.5 + - + +
964A SER* 3.3 33.0 + - - +
965A PRO* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 826 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A THR 3.0 14.9 + - - +
823A CYS 3.2 8.0 + - - +
825A GLU* 1.3 78.0 - - - +
827A THR* 1.3 57.7 + - - +
829A VAL* 4.7 2.7 - - - -
830A HIS* 2.7 68.8 + + + +
831A CYS* 3.4 20.5 + - - -
941A ARG 4.4 4.9 - - - -
942A VAL* 3.8 25.8 - - + -
944A SER* 6.4 0.4 - - - -
945A PHE* 3.3 55.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 827 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A CYS 3.1 11.3 + - - +
824A PHE* 2.6 28.1 + - - -
826A PHE* 1.3 76.2 - - + +
828A LEU* 1.3 57.8 + - - +
831A CYS* 2.8 43.8 + - - +
832A PRO* 3.8 0.5 - - - +
834A LEU* 4.7 3.8 - - + -
843A LEU* 3.8 24.3 + - - +
938A TYR* 3.6 28.2 + - + +
942A VAL* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 828 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A TRP* 4.5 9.8 - - + -
585A VAL* 3.5 10.0 - - - +
792A TYR* 4.6 10.8 + - + -
795A VAL* 3.9 18.6 - - + -
796A TYR* 3.6 28.0 - - + +
824A PHE* 3.1 50.1 + - + +
825A GLU 3.5 6.5 - - - +
827A THR* 1.3 79.8 + - - +
829A VAL* 1.3 57.5 + - - +
832A PRO* 3.3 27.2 - - + +
835A MET* 3.8 28.9 - - + -
840A LEU* 4.4 7.0 - - + -
843A LEU* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 829 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ASN 5.2 1.9 - - - +
585A VAL* 3.7 32.8 + - + +
586A PRO 4.1 9.0 - - - +
587A THR* 4.1 17.5 - - + -
796A TYR* 3.3 22.9 - - - +
825A GLU* 2.7 32.8 + - + +
826A PHE* 4.3 1.6 - - - +
828A LEU* 1.3 76.4 - - - +
830A HIS* 1.3 86.1 + - + +
832A PRO* 3.8 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 830 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A PHE* 2.7 52.9 + + + +
829A VAL* 1.3 95.6 + - + +
831A CYS* 1.3 62.3 + - - +
832A PRO* 3.5 6.3 - - - +
941A ARG* 4.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A PHE* 3.4 28.0 + - - -
827A THR* 2.8 22.2 + - - +
830A HIS* 1.3 85.5 - - - +
832A PRO* 1.3 65.7 - - - +
833A ASP* 3.2 3.8 - - - -
834A LEU* 3.1 33.1 + - + +
835A MET 4.4 0.2 + - - -
843A LEU* 5.2 0.3 - - - +
941A ARG* 3.4 45.1 - - - +
942A VAL* 4.9 1.6 - - - -
----------------------------------------------------------
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