Contacts of the helix formed by residues 818 - 829 (chain A) in PDB entry 4Z96
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 818 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ARG 3.8 1.3 + - - +
817A MET* 1.3 75.3 - - - +
819A TYR* 1.3 67.8 + - - +
820A PHE* 3.6 9.3 + - - +
821A GLN* 3.0 47.4 + - - +
822A VAL* 2.8 24.4 + - - +
857A TYR 5.9 0.2 - - - +
858A GLU* 5.0 6.1 - - - +
859A GLY 3.8 14.6 - - - +
860A THR* 4.6 1.8 - - + +
861A LEU 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A ASN* 1.3 74.5 - - - +
820A PHE* 1.3 64.6 + - - +
821A GLN 3.0 0.5 + - - -
822A VAL* 3.0 7.7 + - + +
823A ALA* 2.8 45.8 + - + +
834A PRO 5.0 2.6 + - - -
835A MET* 6.5 0.9 - - - -
837A LEU 3.6 20.3 + - - -
838A GLN* 4.6 0.2 - - - -
839A PHE* 3.9 26.7 + + + -
853A LEU* 3.5 39.0 + - + -
854A ARG 4.5 0.7 - - - -
855A HIS* 4.0 37.8 + - + +
857A TYR* 4.1 28.7 + - + +
859A GLY 4.3 5.1 + - - -
864A LEU* 6.4 2.2 - - - -
885A ILE* 4.1 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A ASN* 3.3 9.8 + - - +
819A TYR* 1.3 85.6 - - + +
821A GLN* 1.3 59.4 + - + +
823A ALA* 3.9 3.0 - - - +
824A LYS* 2.9 31.2 + - - +
834A PRO* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ARG 4.6 1.2 - - - +
817A MET* 3.4 28.6 - - + +
818A ASN* 3.0 45.7 + - - +
820A PHE* 1.3 78.6 - - + +
822A VAL* 1.3 64.4 + - - +
824A LYS* 3.4 5.1 + - - +
825A THR* 2.9 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A PHE* 4.1 28.9 - - + -
813A LEU* 4.0 16.3 - - + +
817A MET* 4.1 9.4 - - + -
818A ASN 2.8 19.3 + - - +
819A TYR* 3.7 7.4 - - + +
821A GLN* 1.3 75.9 - - - +
823A ALA* 1.3 63.5 + - - +
825A THR* 3.2 7.0 + - - -
826A VAL* 3.0 24.2 + - + +
839A PHE* 4.6 8.5 - - + -
861A LEU* 4.0 32.8 - - + -
864A LEU* 5.7 5.8 - - + -
876A LEU* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 823 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A TYR* 2.8 36.6 + - + +
820A PHE* 3.9 3.6 - - - +
822A VAL* 1.3 71.8 - - - +
824A LYS* 1.3 67.4 + - - +
825A THR 3.0 0.3 + - - -
826A VAL* 3.1 1.7 + - - +
827A ALA* 2.8 26.3 + - - +
834A PRO* 4.2 20.4 - - + +
837A LEU* 4.7 1.1 - - + +
839A PHE* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 824 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A PHE 2.9 23.6 + - - +
821A GLN* 3.8 6.7 - - - +
822A VAL 3.4 0.2 - - - -
823A ALA* 1.3 72.3 - - - +
825A THR* 1.3 62.6 + - - +
827A ALA* 3.7 1.2 - - - +
828A GLN* 3.3 23.6 + - - +
834A PRO* 3.9 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 825 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A VAL* 3.5 18.3 - - + +
812A THR 4.7 3.1 - - - +
813A LEU* 3.5 24.2 - - + -
817A MET* 3.6 14.9 - - - +
821A GLN 2.9 18.0 + - - -
822A VAL 3.5 4.5 - - - -
823A ALA 3.0 0.2 - - - -
824A LYS* 1.3 77.7 - - - +
826A VAL* 1.3 64.5 + - - +
827A ALA 3.4 0.3 + - - -
828A GLN* 3.9 12.5 + - - +
829A ARG* 4.2 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 826 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A PHE* 3.5 50.5 - - + -
809A PHE* 4.0 24.7 - - + -
811A VAL* 4.5 8.7 - - + -
813A LEU* 5.2 0.4 - - + -
822A VAL 3.0 17.3 + - - +
825A THR* 1.3 77.9 - - - +
827A ALA* 1.3 63.4 + - - +
829A ARG* 3.6 5.0 + - - +
830A LEU* 3.3 29.2 + - + +
837A LEU* 4.4 1.3 - - + -
839A PHE* 4.0 21.5 - - + -
878A TYR* 5.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 827 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A ALA 2.8 17.2 + - - +
824A LYS 3.7 1.6 - - - +
825A THR 3.2 0.2 - - - -
826A VAL* 1.3 76.0 - - - +
828A GLN* 1.3 58.3 + - - +
830A LEU* 2.8 21.9 + - - +
831A ASN 2.9 10.7 + - - -
832A THR 3.3 15.5 - - - +
833A ASP 3.9 1.1 - - - -
834A PRO* 3.5 40.8 - - + -
837A LEU* 3.9 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 828 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A LYS 3.3 13.9 + - - +
825A THR* 4.2 7.0 - - - +
826A VAL 3.6 0.2 - - - -
827A ALA* 1.3 77.0 - - - +
829A ARG* 1.3 55.2 + - + +
830A LEU 3.0 2.0 + - - -
831A ASN* 3.5 13.4 + - - +
832A THR 4.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 829 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A PHE* 3.9 28.5 - - + +
810A VAL* 2.4 43.9 + - - +
811A VAL* 3.7 21.5 - - - +
812A THR 4.6 2.2 - - - +
825A THR 4.4 7.6 - - - +
826A VAL 3.6 6.4 + - - +
827A ALA 3.4 1.4 - - - -
828A GLN* 1.3 72.9 - - + +
830A LEU* 1.3 69.3 + - - +
831A ASN 3.6 0.2 - - - -
----------------------------------------------------------
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